1
|
Lin X, Gupta D, Vaitsiankova A, Bhandari SK, Leung KSK, Menolfi D, Lee BJ, Russell HR, Gershik S, Gu W, McKinnon PJ, Dantzer F, Rothenberg E, Tomkinson AE, Zha S. Inactive Parp2 causes Tp53-dependent lethal anemia by blocking replication-associated nick ligation in erythroblasts. bioRxiv 2024:2024.03.12.584665. [PMID: 38559022 PMCID: PMC10980059 DOI: 10.1101/2024.03.12.584665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
PARP1&2 enzymatic inhibitors (PARPi) are promising cancer treatments. But recently, their use has been hindered by unexplained severe anemia and treatment-related leukemia. In addition to enzymatic inhibition, PARPi also trap PARP1&2 at DNA lesions. Here, we report that unlike Parp2 -/- mice, which develop normally, mice expressing catalytically-inactive Parp2 (E534A, Parp2 EA/EA ) succumb to Tp53- and Chk2 -dependent erythropoietic failure in utero , mirroring Lig1 -/- mice. While DNA damage mainly activates PARP1, we demonstrate that DNA replication activates PARP2 robustly. PARP2 is selectively recruited and activated by 5'-phosphorylated nicks (5'p-nicks) between Okazaki fragments, typically resolved by Lig1. Inactive PARP2, but not its active form or absence, impedes Lig1- and Lig3-mediated ligation, causing dose-dependent replication fork collapse, particularly harmful to erythroblasts with ultra-fast forks. This PARylation-dependent structural function of PARP2 at 5'p-nicks explains the detrimental effects of PARP2 inhibition on erythropoiesis, revealing the mechanism behind the PARPi-induced anemia and leukemia, especially those with TP53/CHK2 loss. Significance This work shows that the hematological toxicities associated with PARP inhibitors stem not from impaired PARP1 or PARP2 enzymatic activity but rather from the presence of inactive PARP2 protein. Mechanistically, these toxicities reflect a unique role of PARP2 at 5'-phosphorylated DNA nicks during DNA replication in erythroblasts.
Collapse
|
2
|
Yang C, He Y, Wang Y, McKinnon PJ, Shahani V, Miller DD, Pfeffer LM. Next-generation bromodomain inhibitors of the SWI/SNF complex enhance DNA damage and cell death in glioblastoma. J Cell Mol Med 2023; 27:2770-2781. [PMID: 37593885 PMCID: PMC10494295 DOI: 10.1111/jcmm.17907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
Glioblastoma (GBM) is an aggressive brain cancer with a poor prognosis. While surgical resection is the primary treatment, adjuvant temozolomide (TMZ) chemotherapy and radiotherapy only provide slight improvement in disease course and outcome. Unfortunately, most treated patients experience recurrence of highly aggressive, therapy-resistant tumours and eventually succumb to the disease. To increase chemosensitivity and overcome therapy resistance, we have modified the chemical structure of the PFI-3 bromodomain inhibitor of the BRG1 and BRM catalytic subunits of the SWI/SNF chromatin remodelling complex. Our modifications resulted in compounds that sensitized GBM to the DNA alkylating agent TMZ and the radiomimetic bleomycin. We screened these chemical analogues using a cell death ELISA with GBM cell lines and a cellular thermal shift assay using epitope tagged BRG1 or BRM bromodomains expressed in GBM cells. An active analogue, IV-129, was then identified and further modified, resulting in new generation of bromodomain inhibitors with distinct properties. IV-255 and IV-275 had higher bioactivity than IV-129, with IV-255 selectively binding to the bromodomain of BRG1 and not BRM, while IV-275 bound well to both BRG1 and BRM bromodomains. In contrast, IV-191 did not bind to either bromodomain or alter GBM chemosensitivity. Importantly, both IV-255 and IV-275 markedly increased the extent of DNA damage induced by TMZ and bleomycin as determined by nuclear γH2AX staining. Our results demonstrate that these next-generation inhibitors selectively bind to the bromodomains of catalytic subunits of the SWI/SNF complex and sensitize GBM to the anticancer effects of TMZ and bleomycin. This approach holds promise for improving the treatment of GBM.
Collapse
Affiliation(s)
- Chuanhe Yang
- Department of Pathology and Laboratory MedicineCollege of Medicine, University of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Yali He
- Department of Pharmaceutical SciencesCollege of Pharmacy, University of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Yinan Wang
- Department of Pathology and Laboratory MedicineCollege of Medicine, University of Tennessee Health Science CenterMemphisTennesseeUSA
| | | | - Vijay Shahani
- Recursion Pharmaceuticals IncTorontoOntarioM5V 2A2Canada
| | - Duane D. Miller
- Department of Pharmaceutical SciencesCollege of Pharmacy, University of Tennessee Health Science CenterMemphisTennesseeUSA
- The Center for Cancer ResearchUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Lawrence M. Pfeffer
- Department of Pathology and Laboratory MedicineCollege of Medicine, University of Tennessee Health Science CenterMemphisTennesseeUSA
- The Center for Cancer ResearchUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
| |
Collapse
|
3
|
Reuss DE, Downing SM, Camacho CV, Wang YD, Piro RM, Herold-Mende C, Wang ZQ, Hofmann TG, Sahm F, von Deimling A, McKinnon PJ, Frappart PO. Simultaneous Nbs1 and p53 inactivation in neural progenitors triggers high-grade gliomas. Neuropathol Appl Neurobiol 2023; 49:e12915. [PMID: 37296499 DOI: 10.1111/nan.12915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 04/25/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023]
Abstract
AIMS Nijmegen breakage syndrome (NBS) is a rare autosomal recessive disorder caused by hypomorphic mutations of NBS1. NBS1 is a member of the MRE11-RAD50-NBS1 (MRN) complex that binds to DNA double-strand breaks and activates the DNA damage response (DDR). Nbs1 inactivation in neural progenitor cells leads to microcephaly and premature death. Interestingly, p53 homozygous deletion rescues the NBS1-deficient phenotype allowing long-term survival. The objective of this work was to determine whether simultaneous inactivation of Nbs1 and p53 in neural progenitors triggered brain tumorigenesis and if so in which category this tumour could be classified. METHODS We generated a mouse model with simultaneous genetic inactivation of Nbs1 and p53 in embryonic neural stem cells and analysed the arising tumours with in-depth molecular analyses including immunohistochemistry, array comparative genomic hybridisation (aCGH), whole exome-sequencing and RNA-sequencing. RESULTS NBS1/P53-deficient mice develop high-grade gliomas (HGG) arising in the olfactory bulbs and in the cortex along the rostral migratory stream. In-depth molecular analyses using immunohistochemistry, aCGH, whole exome-sequencing and RNA-sequencing revealed striking similarities to paediatric human HGG with shared features with radiation-induced gliomas (RIGs). CONCLUSIONS Our findings show that concomitant inactivation of Nbs1 and p53 in mice promotes HGG with RIG features. This model could be useful for preclinical studies to improve the prognosis of these deadly tumours, but it also highlights the singularity of NBS1 among the other DNA damage response proteins in the aetiology of brain tumours.
Collapse
Affiliation(s)
- David E Reuss
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Susanna M Downing
- Center for Pediatric Neurological Disease Research, St. Jude Translational Neuroscience, Departments of Genetics and Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Cristel V Camacho
- Center for Pediatric Neurological Disease Research, St. Jude Translational Neuroscience, Departments of Genetics and Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yong-Dong Wang
- Center for Pediatric Neurological Disease Research, St. Jude Translational Neuroscience, Departments of Genetics and Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rosario M Piro
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milan, Italy
| | - Christel Herold-Mende
- Department of Neurosurgery, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Zhao-Qi Wang
- Leibniz Institute on Ageing-Fritz Lipmann Institute, Jena, Germany
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Thomas G Hofmann
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Peter J McKinnon
- Center for Pediatric Neurological Disease Research, St. Jude Translational Neuroscience, Departments of Genetics and Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Pierre-Olivier Frappart
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| |
Collapse
|
4
|
Aditi, McKinnon PJ. Genome integrity and inflammation in the nervous system. DNA Repair (Amst) 2022; 119:103406. [PMID: 36148701 PMCID: PMC9844216 DOI: 10.1016/j.dnarep.2022.103406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 01/19/2023]
Abstract
Preservation of genomic integrity is crucial for nervous system development and function. DNA repair deficiency results in several human diseases that are characterized by both neurodegeneration and neuroinflammation. Recent research has highlighted a role for compromised genomic integrity as a key factor driving neuropathology and triggering innate immune signaling to cause inflammation. Here we review the mechanisms by which DNA damage engages innate immune signaling and how this may promote neurological disease. We also consider the contributions of different neural cell types towards DNA damage-driven neuroinflammation. A deeper knowledge of genome maintenance mechanisms that prevent aberrant immune activation in neural cells will guide future therapies to ameliorate neurological disease.
Collapse
Affiliation(s)
- Aditi
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Dept. Cell & Mol. Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter J McKinnon
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Dept. Cell & Mol. Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| |
Collapse
|
5
|
Zuckermann M, He C, Andrews J, Sloan-Henry R, Bianski B, Xie J, Wang Y, Twarog N, Onar-Thomas A, Ernst K, Yang L, Li Y, Dalton J, Li X, Chepyala D, Zhu X, Zhang J, Xu K, Hover L, McKinnon PJ, Pfister SM, Rankovic Z, Freeman BB, Shelat AA, Chiang J, Jones DTW, Tinkle CL, Baker SJ. MODL-06. Targeting c-MET in combination with radiation is effective in MET-fusion driven high-grade glioma. Neuro Oncol 2022. [PMCID: PMC9165032 DOI: 10.1093/neuonc/noac079.629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Oncogenic fusion events involving c-MET have been observed in up to 12% of pediatric high-grade glioma (pHGG). MET inhibitors have displayed potent initial responses in MET rearranged tumors but acquired resistance to single agent modalities invariably occurs. To identify new treatment options against these tumors, we established two novel orthotopic mouse models including an immunocompetent, murine allograft and an intracranial patient-derived xenograft (PDX), both harboring distinct MET fusions. We analyzed the pharmacokinetic and pharmacodynamic profiles of two MET inhibitors, crizotinib and capmatinib, and examined their efficacy against tumor cell cultures derived from the aforementioned models. Capmatinib outperformed crizotinib in terms of specificity, potency and brain availability, resulting in a highly differential cellular response compared to crizotinib treatment. We evaluated the efficacy of both compounds in combination with radiotherapy (RT) and found that radiation further potentiated the inhibitory effect of capmatinib on tumor cell growth. We then utilized both models to assess the combinatorial effect of capmatinib and radiation on intracranial tumors in vivo and found that the combination therapy significantly increased overall survival in both cohorts. In the PDX model, the combination, relative to either intervention alone, induced a remarkable decrease of tumor burden, which persisted throughout the observation period in all treated animals. RNA-sequencing of capmatinib-treated tumors and tumor cell cultures revealed impaired expression of DNA repair genes. Further, we showed that capmatinib enhanced radiation-induced DNA damage, as demonstrated by increased γ-H2AX foci in treated cells, providing mechanistic insight for the cooperative effects of the combined treatment. Our results validate capmatinib as an effective inhibitor of MET in pHGG and demonstrate the outstanding efficacy of capmatinib and radiation against MET-driven pHGG in two complementary preclinical models, informing future clinical trials.
Collapse
Affiliation(s)
- Marc Zuckermann
- Hopp Children’s Cancer Center Heidelberg (KiTZ) , Heidelberg , Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Chen He
- Developmental Neurobiology, St. Jude Children’s Research Hospital , Memphis , USA
| | - Jared Andrews
- Developmental Neurobiology, St. Jude Children’s Research Hospital , Memphis , USA
| | - Roketa Sloan-Henry
- Center for Pediatric Neurological Disease Research, St. Jude Children’s Research Hospital , Memphis , USA
| | - Brandon Bianski
- Radiation Oncology, St. Jude Children’s Research Hospital , Memphis , USA
| | - Jia Xie
- Radiation Oncology, St. Jude Children’s Research Hospital , Memphis , USA
| | - Yingzhe Wang
- Preclinical Pharmacokinetics Shared Resource, St. Jude Children’s Research Hospital , Memphis , USA
| | - Nathaniel Twarog
- Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital , Memphis , USA
| | - Arzu Onar-Thomas
- Biostatistics, St. Jude Children’s Research Hospital , Memphis , USA
| | - Kati Ernst
- Hopp Children’s Cancer Center Heidelberg (KiTZ) , Heidelberg , Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Lei Yang
- Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital , Memphis , USA
| | - Yong Li
- Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital , Memphis , USA
| | - James Dalton
- Pathology, St. Jude Children’s Research Hospital , Memphis , USA
| | - Xiaoyu Li
- Pathology, St. Jude Children’s Research Hospital , Memphis , USA
| | - Divyabharathi Chepyala
- Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital , Memphis , USA
| | - Xiaoyan Zhu
- Developmental Neurobiology, St. Jude Children’s Research Hospital , Memphis , USA
| | - Junyuan Zhang
- Developmental Neurobiology, St. Jude Children’s Research Hospital , Memphis , USA
| | - Ke Xu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital , Memphis , USA
- Computational Biology, St. Jude Children’s Research Hospital , Memphis , USA
| | - Laura Hover
- Developmental Neurobiology, St. Jude Children’s Research Hospital , Memphis , USA
| | - Peter J McKinnon
- Center for Pediatric Neurological Disease Research, St. Jude Children’s Research Hospital , Memphis , USA
| | - Stefan M Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ) , Heidelberg , Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Zoran Rankovic
- Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital , Memphis , USA
| | - Burgess B Freeman
- Preclinical Pharmacokinetics Shared Resource, St. Jude Children’s Research Hospital , Memphis , USA
| | - Anang A Shelat
- Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital , Memphis , USA
| | - Jason Chiang
- Pathology, St. Jude Children’s Research Hospital , Memphis , USA
| | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ) , Heidelberg , Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | | | - Suzanne J Baker
- Developmental Neurobiology, St. Jude Children’s Research Hospital , Memphis , USA
| |
Collapse
|
6
|
Kwak YD, Shaw TI, Downing SM, Tewari A, Jin H, Li Y, Dumitrache LC, Katyal S, Khodakhah K, Russell HR, McKinnon PJ. Chromatin architecture at susceptible gene loci in cerebellar Purkinje cells characterizes DNA damage-induced neurodegeneration. Sci Adv 2021; 7:eabg6363. [PMID: 34910524 DOI: 10.1126/sciadv.abg6363] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The pathogenesis of inherited genome instability neurodegenerative syndromes remains largely unknown. Here, we report new disease-relevant murine models of genome instability–driven neurodegeneration involving disabled ATM and APTX that develop debilitating ataxia. We show that neurodegeneration and ataxia result from transcriptional interference in the cerebellum via aberrant messenger RNA splicing. Unexpectedly, these splicing defects were restricted to only Purkinje cells, disrupting the expression of critical homeostatic regulators including ITPR1, GRID2, and CA8. Abundant genotoxic R loops were also found at these Purkinje cell gene loci, further exacerbating DNA damage and transcriptional disruption. Using ATAC-seq to profile global chromatin accessibility in the cerebellum, we found a notably unique chromatin conformation specifically in Purkinje chromatin at the affected gene loci, thereby promoting susceptibility to DNA damage. These data reveal the pathogenic basis of DNA damage in the nervous system and suggest chromatin conformation as a feature in directing genome instability–associated neuropathology.
Collapse
Affiliation(s)
- Young Don Kwak
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
| | | | - Susanna M Downing
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
| | - Ambika Tewari
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yang Li
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
| | - Lavinia C Dumitrache
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
| | - Sachin Katyal
- CancerCare Manitoba Research Institute, CancerCare Manitoba and Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E OV9, Canada
| | - Kamran Khodakhah
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Helen R Russell
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
| | - Peter J McKinnon
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN 38105, USA
| |
Collapse
|
7
|
Perez H, Abdallah MF, Chavira JI, Norris AS, Egeland MT, Vo KL, Buechsenschuetz CL, Sanghez V, Kim JL, Pind M, Nakamura K, Hicks GG, Gatti RA, Madrenas J, Iacovino M, McKinnon PJ, Mathews PJ. A novel, ataxic mouse model of ataxia telangiectasia caused by a clinically relevant nonsense mutation. eLife 2021; 10:64695. [PMID: 34723800 PMCID: PMC8601662 DOI: 10.7554/elife.64695] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 10/29/2021] [Indexed: 12/14/2022] Open
Abstract
Ataxia Telangiectasia (A-T) and Ataxia with Ocular Apraxia Type 1 (AOA1) are devastating neurological disorders caused by null mutations in the genome stability genes, A-T mutated (ATM) and Aprataxin (APTX), respectively. Our mechanistic understanding and therapeutic repertoire for treating these disorders are severely lacking, in large part due to the failure of prior animal models with similar null mutations to recapitulate the characteristic loss of motor coordination (i.e., ataxia) and associated cerebellar defects. By increasing genotoxic stress through the insertion of null mutations in both the Atm (nonsense) and Aptx (knockout) genes in the same animal, we have generated a novel mouse model that for the first time develops a progressively severe ataxic phenotype associated with atrophy of the cerebellar molecular layer. We find biophysical properties of cerebellar Purkinje neurons (PNs) are significantly perturbed (e.g., reduced membrane capacitance, lower action potential [AP] thresholds, etc.), while properties of synaptic inputs remain largely unchanged. These perturbations significantly alter PN neural activity, including a progressive reduction in spontaneous AP firing frequency that correlates with both cerebellar atrophy and ataxia over the animal’s first year of life. Double mutant mice also exhibit a high predisposition to developing cancer (thymomas) and immune abnormalities (impaired early thymocyte development and T-cell maturation), symptoms characteristic of A-T. Finally, by inserting a clinically relevant nonsense-type null mutation in Atm, we demonstrate that Small Molecule Read-Through (SMRT) compounds can restore ATM production, indicating their potential as a future A-T therapeutic.
Collapse
Affiliation(s)
- Harvey Perez
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - May F Abdallah
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - Jose I Chavira
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - Angelina S Norris
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - Martin T Egeland
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - Karen L Vo
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - Callan L Buechsenschuetz
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - Valentina Sanghez
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - Jeannie L Kim
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States
| | - Molly Pind
- Department of Biochemistry and Medical Genetics,Max Rady College of Medicine, University of Manitoba, Manitoba, Canada
| | - Kotoka Nakamura
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, Los Angeles, United States
| | - Geoffrey G Hicks
- Department of Biochemistry and Medical Genetics,Max Rady College of Medicine, University of Manitoba, Manitoba, Canada
| | - Richard A Gatti
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, Los Angeles, United States
| | - Joaquin Madrenas
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States.,Department of Medicine, Harbor-UCLA Medical Center, Torrance, United States
| | - Michelina Iacovino
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States.,Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, United States
| | - Peter J McKinnon
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, St. Jude Children's Research Hospital, Memphis, United States
| | - Paul J Mathews
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, United States.,Department of Neurology, Harbor-UCLA Medical Center, Torrance, United States
| |
Collapse
|
8
|
Downing SM, Schreiner PA, Kwak YD, Li Y, Shaw TI, Russell HR, McKinnon PJ. Genome instability independent of type I interferon signaling drives neuropathology caused by impaired ribonucleotide excision repair. Neuron 2021; 109:3962-3979.e6. [PMID: 34655526 DOI: 10.1016/j.neuron.2021.09.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/25/2022]
Abstract
Aicardi-Goutières syndrome (AGS) is a monogenic type I interferonopathy characterized by neurodevelopmental defects and upregulation of type I interferon signaling and neuroinflammation. Mutations in genes that function in nucleic acid metabolism, including RNASEH2, are linked to AGS. Ribonuclease H2 (RNASEH2) is a genome surveillance factor critical for DNA integrity by removing ribonucleotides incorporated into replicating DNA. Here we show that RNASEH2 is necessary for neurogenesis and to avoid activation of interferon-responsive genes and neuroinflammation. Cerebellar defects after RNASEH2B inactivation are rescued by p53 but not cGAS deletion, suggesting that DNA damage signaling, not neuroinflammation, accounts for neuropathology. Coincident inactivation of Atm and Rnaseh2 further affected cerebellar development causing ataxia, which was dependent upon aberrant activation of non-homologous end-joining (NHEJ). The loss of ATM also markedly exacerbates cGAS-dependent type I interferon signaling. Thus, DNA damage-dependent signaling rather than type I interferon signaling underlies neurodegeneration in this class of neurodevelopmental/neuroinflammatory disease.
Collapse
Affiliation(s)
- Susanna M Downing
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Patrick A Schreiner
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Young Don Kwak
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yang Li
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Helen R Russell
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter J McKinnon
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA; St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
| |
Collapse
|
9
|
Komulainen E, Badman J, Rey S, Rulten S, Ju L, Fennell K, Kalasova I, Ilievova K, McKinnon PJ, Hanzlikova H, Staras K, Caldecott KW. Parp1 hyperactivity couples DNA breaks to aberrant neuronal calcium signalling and lethal seizures. EMBO Rep 2021; 22:e51851. [PMID: 33932076 PMCID: PMC8097344 DOI: 10.15252/embr.202051851] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 12/21/2022] Open
Abstract
Defects in DNA single-strand break repair (SSBR) are linked with neurological dysfunction but the underlying mechanisms remain poorly understood. Here, we show that hyperactivity of the DNA strand break sensor protein Parp1 in mice in which the central SSBR protein Xrcc1 is conditionally deleted (Xrcc1Nes-Cre ) results in lethal seizures and shortened lifespan. Using electrophysiological recording and synaptic imaging approaches, we demonstrate that aberrant Parp1 activation triggers seizure-like activity in Xrcc1-defective hippocampus ex vivo and deregulated presynaptic calcium signalling in isolated hippocampal neurons in vitro. Moreover, we show that these defects are prevented by Parp1 inhibition or deletion and, in the case of Parp1 deletion, that the lifespan of Xrcc1Nes-Cre mice is greatly extended. This is the first demonstration that lethal seizures can be triggered by aberrant Parp1 activity at unrepaired SSBs, highlighting PARP inhibition as a possible therapeutic approach in hereditary neurological disease.
Collapse
Affiliation(s)
- Emilia Komulainen
- Genome Damage and Stability CentreSchool of Life SciencesUniversity of SussexBrightonUK
| | - Jack Badman
- Genome Damage and Stability CentreSchool of Life SciencesUniversity of SussexBrightonUK
- Sussex NeuroscienceSchool of Life SciencesUniversity of SussexBrightonUK
| | - Stephanie Rey
- Sussex NeuroscienceSchool of Life SciencesUniversity of SussexBrightonUK
| | - Stuart Rulten
- Genome Damage and Stability CentreSchool of Life SciencesUniversity of SussexBrightonUK
| | - Limei Ju
- Genome Damage and Stability CentreSchool of Life SciencesUniversity of SussexBrightonUK
| | - Kate Fennell
- Sussex NeuroscienceSchool of Life SciencesUniversity of SussexBrightonUK
| | - Ilona Kalasova
- Department of Genome DynamicsInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Kristyna Ilievova
- Department of Genome DynamicsInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Peter J McKinnon
- Department of GeneticsSt Jude Children’s Research HospitalMemphisTNUSA
| | - Hana Hanzlikova
- Genome Damage and Stability CentreSchool of Life SciencesUniversity of SussexBrightonUK
- Department of Genome DynamicsInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Kevin Staras
- Sussex NeuroscienceSchool of Life SciencesUniversity of SussexBrightonUK
| | - Keith W Caldecott
- Genome Damage and Stability CentreSchool of Life SciencesUniversity of SussexBrightonUK
- Department of Genome DynamicsInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| |
Collapse
|
10
|
McNeill DR, Whitaker AM, Stark WJ, Illuzzi JL, McKinnon PJ, Freudenthal BD, Wilson DM. Functions of the major abasic endonuclease (APE1) in cell viability and genotoxin resistance. Mutagenesis 2021; 35:27-38. [PMID: 31816044 DOI: 10.1093/mutage/gez046] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/12/2019] [Indexed: 12/24/2022] Open
Abstract
DNA is susceptible to a range of chemical modifications, with one of the most frequent lesions being apurinic/apyrimidinic (AP) sites. AP sites arise due to damage-induced (e.g. alkylation) or spontaneous hydrolysis of the N-glycosidic bond that links the base to the sugar moiety of the phosphodiester backbone, or through the enzymatic activity of DNA glycosylases, which release inappropriate bases as part of the base excision repair (BER) response. Unrepaired AP sites, which lack instructional information, have the potential to cause mutagenesis or to arrest progressing DNA or RNA polymerases, potentially causing outcomes such as cellular transformation, senescence or death. The predominant enzyme in humans responsible for repairing AP lesions is AP endonuclease 1 (APE1). Besides being a powerful AP endonuclease, APE1 possesses additional DNA repair activities, such as 3'-5' exonuclease, 3'-phophodiesterase and nucleotide incision repair. In addition, APE1 has been shown to stimulate the DNA-binding activity of a number of transcription factors through its 'REF1' function, thereby regulating gene expression. In this article, we review the structural and biochemical features of this multifunctional protein, while reporting on new structures of the APE1 variants Cys65Ala and Lys98Ala. Using a functional complementation approach, we also describe the importance of the repair and REF1 activities in promoting cell survival, including the proposed passing-the-baton coordination in BER. Finally, results are presented indicating a critical role for APE1 nuclease activities in resistance to the genotoxins methyl methanesulphonate and bleomycin, supporting biologically important functions as an AP endonuclease and 3'-phosphodiesterase, respectively.
Collapse
Affiliation(s)
- Daniel R McNeill
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Amy M Whitaker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Wesley J Stark
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | | | - Peter J McKinnon
- Department of Genetics and Tumor Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - David M Wilson
- Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| |
Collapse
|
11
|
Sinha A, Saleh A, Endersby R, Yuan SH, Chokshi CR, Brown KR, Kuzio B, Kauppinen T, Singh SK, Baker SJ, McKinnon PJ, Katyal S. RAD51-Mediated DNA Homologous Recombination Is Independent of PTEN Mutational Status. Cancers (Basel) 2020; 12:cancers12113178. [PMID: 33138032 PMCID: PMC7693555 DOI: 10.3390/cancers12113178] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 10/20/2020] [Indexed: 12/22/2022] Open
Abstract
Simple Summary PTEN is an important tumor suppressor that is frequently mutated in malignancy. PTEN mutational loss has been associated with reduced RAD51 expression and homologous recombination deficiency (HRD), however; recent studies have failed to recapitulate these findings. Here, we show that RAD51 expression, foci formation and homologous recombination repair activity are unaltered in normal and tumorigenic PTEN-deficient cells and patient samples. Furthermore, we show that PTEN-deficient tumor cell lines do not synergize with the clinical PARP inhibitor olaparib, underscoring a need to discontinue its use in treating patients with PTEN-deficient tumors that do not otherwise exhibit HRD. Abstract PTEN mutation occurs in a variety of aggressive cancers and is associated with poor patient outcomes. Recent studies have linked mutational loss of PTEN to reduced RAD51 expression and function, a key factor involved in the homologous recombination (HR) pathway. However, these studies remain controversial, as they fail to establish a definitive causal link to RAD51 expression that is PTEN-dependent, while other studies have not been able to recapitulate the relationship between the PTEN expression and the RAD51/HR function. Resolution of this apparent conundrum is essential due to the clinically-significant implication that PTEN-deficient tumors may be sensitive to poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) commonly used in the clinical management of BRCA-mutated and other HR-deficient (HRD) tumors. Methods: Primary Pten-deficient (and corresponding wild-type) mouse embryonic fibroblasts (MEFs) and astrocytes and PTEN-null human tumor cell lines and primary cells were assessed for RAD51 expression (via the Western blot analysis) and DNA damage repair analyses (via alkali comet and γH2AX foci assays). RAD51 foci analysis was used to measure HR-dependent DNA repair. Xrcc2-deficient MEFs served as an HR-deficient control, while the stable knockdown of RAD51 (shRAD51) served to control for the relative RAD51/HR-mediated repair and the phospho-53BP1 foci analysis served to confirm and measure non-homologous end joining (NHEJ) activity in PTEN-deficient and shRAD51-expressing (HRD) lines. Cell proliferation studies were used to measure any potential added sensitivity of PTEN-null cells to the clinically-relevant PARPi, olaparib. RAD51 levels and DNA damage response signaling were assessed in PTEN-mutant brain tumor initiating cells (BTICs) derived from primary and recurrent glioblastoma multiforme (GBM) patients, while expression of RAD51 and its paralogs were examined as a function of the PTEN status in the RNA expression datasets isolated from primary GBM tumor specimens and BTICs. Results: Pten knockout primary murine cells display unaltered RAD51 expression, endogenous and DNA strand break-induced RAD51 foci and robust DNA repair activity. Defective HR was only observed in the cells lacking Xrcc2. Likewise, human glioblastoma multiforme (GBM) cell lines with known PTEN deficiency (U87, PTEN-mutated; U251 and U373, PTEN-null) show apparent expression of RAD51 and display efficient DNA repair activity. Only GBM cells stably expressing shRNAs against RAD51 (shRAD51) display dysfunctional DNA repair activity and reduced proliferative capacity, which is exacerbated by PARPi treatment. Furthermore, GBM patient-derived BTICs displayed robust RAD51 expression and intact DNA damage response signaling in spite of PTEN-inactivating mutations. RNA expression analysis of primary GBM tissue specimens and BTICs demonstrate stable levels of RAD51 and its paralogs (RAD51B, RAD51C, RAD51D, XRCC2, XRCC3, and DMC1), regardless of the PTEN mutational status. Conclusions: Our findings demonstrate definitively that PTEN loss does not alter the RAD51 expression, its paralogs, or the HR activity. Furthermore, deficiency in PTEN alone is not sufficient to impart enhanced sensitivity to PARPi associated with HRD. This study is the first to unequivocally demonstrate that PTEN deficiency is not linked to the RAD51 expression or the HR activity amongst primary neural and non-neural Pten-null cells, PTEN-deficient tumor cell lines, and primary PTEN-mutant GBM patient-derived tissue specimens and BTICs.
Collapse
Affiliation(s)
- Asha Sinha
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Ali Saleh
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Raelene Endersby
- Telethon Kids Institute, Perth Children’s Hospital, 15 Hospital Avenue, Perth, WA 6009, Australia;
- Centre for Child Health Research, University of Western Australia, 15 Hospital Avenue, Perth, WA 6009, Australia
| | - Shek H. Yuan
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Chirayu R. Chokshi
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8S 4L8, Canada; (C.R.C.); (S.K.S.)
| | - Kevin R. Brown
- Donnelly Centre, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada;
| | - Bozena Kuzio
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Tiina Kauppinen
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Health Sciences Centre, 710 William Avenue, Winnipeg, MB R3E 0Z3, Canada
| | - Sheila K. Singh
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8S 4L8, Canada; (C.R.C.); (S.K.S.)
- Department of Surgery, Faculty of Health Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Suzanne J. Baker
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA;
| | - Peter J. McKinnon
- Department of Genetics, St Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA;
| | - Sachin Katyal
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
- Correspondence: ; Tel.: +1-204-787-2765; Fax: +1-204-787-2190
| |
Collapse
|
12
|
Callen E, Zong D, Wu W, Wong N, Stanlie A, Ishikawa M, Pavani R, Dumitrache LC, Byrum AK, Mendez-Dorantes C, Martinez P, Canela A, Maman Y, Day A, Kruhlak MJ, Blasco MA, Stark JM, Mosammaparast N, McKinnon PJ, Nussenzweig A. 53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination. Mol Cell 2019; 77:26-38.e7. [PMID: 31653568 DOI: 10.1016/j.molcel.2019.09.024] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/17/2019] [Accepted: 09/20/2019] [Indexed: 01/28/2023]
Abstract
53BP1 activity drives genome instability and lethality in BRCA1-deficient mice by inhibiting homologous recombination (HR). The anti-recombinogenic functions of 53BP1 require phosphorylation-dependent interactions with PTIP and RIF1/shieldin effector complexes. While RIF1/shieldin blocks 5'-3' nucleolytic processing of DNA ends, it remains unclear how PTIP antagonizes HR. Here, we show that mutation of the PTIP interaction site in 53BP1 (S25A) allows sufficient DNA2-dependent end resection to rescue the lethality of BRCA1Δ11 mice, despite increasing RIF1 "end-blocking" at DNA damage sites. However, double-mutant cells fail to complete HR, as excessive shieldin activity also inhibits RNF168-mediated loading of PALB2/RAD51. As a result, BRCA1Δ1153BP1S25A mice exhibit hallmark features of HR insufficiency, including premature aging and hypersensitivity to PARPi. Disruption of shieldin or forced targeting of PALB2 to ssDNA in BRCA1D1153BP1S25A cells restores RNF168 recruitment, RAD51 nucleofilament formation, and PARPi resistance. Our study therefore reveals a critical function of shieldin post-resection that limits the loading of RAD51.
Collapse
Affiliation(s)
- Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Dali Zong
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Wei Wu
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Nancy Wong
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Andre Stanlie
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Momoko Ishikawa
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Lavinia C Dumitrache
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Andrea K Byrum
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Carlos Mendez-Dorantes
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Paula Martinez
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Center, Madrid 28029, Spain
| | - Andres Canela
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yaakov Maman
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Amanda Day
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Michael J Kruhlak
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Maria A Blasco
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Center, Madrid 28029, Spain
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Peter J McKinnon
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
13
|
Pribyl LJ, Downing SM, Camacho CV, Larson JD, Baker SJ, McKinnon PJ. Abstract LB-289: Genomic instability and the development of high-grade gliomas. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-lb-289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Genome stability is crucial for normal mammalian development. Broadly, genome maintenance is carried out by two distinct mechanisms; functional integration of DNA replication and DNA damage response signaling. Neural cells are particularly sensitive to DNA strand breaks and defective DNA damage responses can result in detrimental effects to the nervous system, including neurodegenerative disease and cancer. It remains unclear which DNA repair pathways are critical for preventing DNA damage accumulation in stem and progenitor cells. The same mechanisms that protect progenitor genomes also suppress DNA mutations that can result in cancer. A primary objective of the current study is delineation of key factors for genome stability that prevent tumorigenesis during cortical neurogenesis. We have compared the differential effects of inactivation of homologous recombination (HR) and non-homologous end-joining (NHEJ) towards tumorigenesis by directing their deletion specifically to early cortical progenitors in mouse models. We recently found that coincident loss of either of these repair pathways result in high-grade glioma formation. Furthermore, modelling histone H3 mutations found in human high-grade glioma, specifically the H3.3 K27M mutation, we found that gliomagenesis was accelerated after defective HR (Brca2 loss) or NHEJ (Lig4 loss), although the resultant cancers showed distinct differences in penetrance and diffusion throughout the cortex. Interestingly, gliomas resulting from NHEJ inhibition were more penetrant and diffuse than brain tumors subsequent from HR loss. Gene expression analysis through RNA sequencing is currently being used to identify causative events that drive these individual tumor identities. Embryonic analysis has further shown that inhibition of these repair pathways in combination with the H3.3 K27M mutation results in distinct spatiotemporal DNA damage early in cortical development. Our recent discoveries support cortical progenitor susceptibility to genomic damage is not only influenced by a critical early period of development but also the suppression of specific tumorigenic mutations involving DNA damage repair pathways and histone modifications during neurogenesis.
Citation Format: Lee J. Pribyl, Susanna M. Downing, Cristel V. Camacho, Jon D. Larson, Suzanne J. Baker, Peter J. McKinnon. Genomic instability and the development of high-grade gliomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-289.
Collapse
Affiliation(s)
- Lee J. Pribyl
- 1UTHSC & St. Jude Children's Research Hospital, Memphis, TN
| | | | | | | | | | | |
Collapse
|
14
|
Larson JD, Kasper LH, Paugh BS, Jin H, Wu G, Kwon CH, Fan Y, Shaw TI, Silveira AB, Qu C, Xu R, Zhu X, Zhang J, Russell HR, Peters JL, Finkelstein D, Xu B, Lin T, Tinkle CL, Patay Z, Onar-Thomas A, Pounds SB, McKinnon PJ, Ellison DW, Zhang J, Baker SJ. Histone H3.3 K27M Accelerates Spontaneous Brainstem Glioma and Drives Restricted Changes in Bivalent Gene Expression. Cancer Cell 2019; 35:140-155.e7. [PMID: 30595505 PMCID: PMC6570409 DOI: 10.1016/j.ccell.2018.11.015] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/13/2018] [Accepted: 11/23/2018] [Indexed: 12/31/2022]
Abstract
Diffuse intrinsic pontine gliomas (DIPGs) are incurable childhood brainstem tumors with frequent histone H3 K27M mutations and recurrent alterations in PDGFRA and TP53. We generated genetically engineered inducible mice and showed that H3.3 K27M enhanced neural stem cell self-renewal while preserving regional identity. Neonatal induction of H3.3 K27M cooperated with activating platelet-derived growth factor receptor α (PDGFRα) mutant and Trp53 loss to accelerate development of diffuse brainstem gliomas that recapitulated human DIPG gene expression signatures and showed global changes in H3K27 posttranslational modifications, but relatively restricted gene expression changes. Genes upregulated in H3.3 K27M tumors were enriched for those associated with neural development where H3K27me3 loss released the poised state of apparently bivalent promoters, whereas downregulated genes were enriched for those encoding homeodomain transcription factors.
Collapse
Affiliation(s)
- Jon D Larson
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lawryn H Kasper
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Barbara S Paugh
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hongjian Jin
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chang-Hyuk Kwon
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Timothy I Shaw
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - André B Silveira
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Raymond Xu
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaoyan Zhu
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junyuan Zhang
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Helen R Russell
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jennifer L Peters
- Cellular Imaging Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Tong Lin
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christopher L Tinkle
- Department of Radiation Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Zoltan Patay
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Arzu Onar-Thomas
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stanley B Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter J McKinnon
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| |
Collapse
|
15
|
Ratnaparkhe M, Wong JKL, Wei PC, Hlevnjak M, Kolb T, Simovic M, Haag D, Paul Y, Devens F, Northcott P, Jones DTW, Kool M, Jauch A, Pastorczak A, Mlynarski W, Korshunov A, Kumar R, Downing SM, Pfister SM, Zapatka M, McKinnon PJ, Alt FW, Lichter P, Ernst A. Defective DNA damage repair leads to frequent catastrophic genomic events in murine and human tumors. Nat Commun 2018; 9:4760. [PMID: 30420702 PMCID: PMC6232171 DOI: 10.1038/s41467-018-06925-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 10/08/2018] [Indexed: 12/22/2022] Open
Abstract
Chromothripsis and chromoanasynthesis are catastrophic events leading to clustered genomic rearrangements. Whole-genome sequencing revealed frequent complex genomic rearrangements (n = 16/26) in brain tumors developing in mice deficient for factors involved in homologous-recombination-repair or non-homologous-end-joining. Catastrophic events were tightly linked to Myc/Mycn amplification, with increased DNA damage and inefficient apoptotic response already observable at early postnatal stages. Inhibition of repair processes and comparison of the mouse tumors with human medulloblastomas (n = 68) and glioblastomas (n = 32) identified chromothripsis as associated with MYC/MYCN gains and with DNA repair deficiencies, pointing towards therapeutic opportunities to target DNA repair defects in tumors with complex genomic rearrangements. Chromothripsis and chromoanasynthesis lead to locally clustered rearrangements affecting one or a few chromosomes, but their impact on cancer development and progression is unclear. Here the authors analyse the role of DNA repair factors in brain tumors by whole-genome sequencing of tumors from mouse models of medulloblastoma or high grade gliomas.
Collapse
Affiliation(s)
- Manasi Ratnaparkhe
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ); Faculty of Biosciences, Heidelberg University Germany, Heidelberg, 69120, Germany
| | - John K L Wong
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Pei-Chi Wei
- Boston Children's Hospital, Howard Hughes Medical Institute and Department of Genetics, Harvard Medical School, Boston, 02115, MA, USA
| | - Mario Hlevnjak
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Thorsten Kolb
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Milena Simovic
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ); Faculty of Biosciences, Heidelberg University Germany, Heidelberg, 69120, Germany
| | - Daniel Haag
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, 69120, Germany
| | - Yashna Paul
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Frauke Devens
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Paul Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.,Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105-3678, United States
| | - David T W Jones
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, 69120, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, 69120, Germany
| | - Anna Jauch
- Institute of Human Genetics, University of Heidelberg, Heidelberg, 69120, Germany
| | - Agata Pastorczak
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, 91-738, Poland
| | - Wojciech Mlynarski
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, 91-738, Poland
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Department of Neuropathology, Heidelberg University Hospital and German Cancer Consortium (DKTK), Heidelberg, 69120, Germany
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology; German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center, Heidelberg, 69120, Germany
| | - Susanna M Downing
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, 38105-3678, TN, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, 69120, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Peter J McKinnon
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, 38105-3678, TN, USA
| | - Frederick W Alt
- Boston Children's Hospital, Howard Hughes Medical Institute and Department of Genetics, Harvard Medical School, Boston, 02115, MA, USA
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Aurélie Ernst
- Division of Molecular Genetics, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.
| |
Collapse
|
16
|
Ratnaparkhe M, Wong J, Wei PC, Hlevnjak M, Northcott P, Jones DT, Kool M, Jauch A, Pastorczak A, Korshunov A, Kumar R, Downing SM, Pfister SM, Zapatka M, McKinnon PJ, Alt FW, Lichter P, Ernst A. Abstract 1352: Inactivation of factors of DNA double-strand break repair by homologous recombination or non-homologous end-joining leads to frequent catastrophic genomic events in murine and human tumors. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-1352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Chromothripsis and chromoanasynthesis are two forms of genomic instability leading to complex genomic rearrangements that affect one or very few chromosomes. These one-off catastrophic events play a role in numerous tumor entities as well as in some congenital diseases. The availability of murine models recapitulating both phenomena would substantially facilitate the investigation of the mechanistic aspects underlying catastrophic genomic events.
Homologous recombination repair (HR) and canonical Non-Homologous-End-Joining (cNHEJ) represent the two major processes for DNA double-strand break repair in mammalian cells. Conditional inactivation of key factors of either of these two pathways, such as Brca2 for HR and Xrcc4 or Lig4 for cNHEJ in nestin-expressing or Emx1-expressing murine neural progenitor cells leads to medulloblastomas and gliomas in a p53-deficient background. We showed by whole-genome sequencing that these tumors frequently display chromothripsis or chromoanasynthesis (33 to 73% of the analyzed tumors, n= 27) and that catastrophic rearrangements drive tumor development.
FISH analysis identified a link between chromoanasynthesis and increased numerical and structural aberrations and with the presence of marker chromosomes. In addition, amplifications of c-Myc and n-Myc likely facilitate catastrophic events. Detailed analysis of the microhomologies at the breakpoint junctions on the chromosomes affected by complex genomic rearrangements identified cNHEJ and alternative end-joining as likely repair processes involved in chromothripsis and chromoanasynthesis.
Treatment of cells derived from the mouse tumors with inhibitors of HR and/or alternative end-joining (e.g. RAD51 and PARP inhibitors, respectively) in combination with DNA damage revealed the dependence of these tumor cells on specific repair processes and showed that these DNA repair deficiencies can be utilized for synthetic lethality approaches.
Comparison of the mouse tumors with whole-genome sequencing data from human medulloblastomas (n=68) and gliomas (n=32) identified an association between chromothripsis and deficiencies in repair processes, by analyzing copy-number level aberrations affecting repair factors and mutational signatures of DNA double-strand break repair defects. This link between DNA repair deficiency and chromothripsis was further confirmed in additional tumor entities such as breast cancer (n=356) and melanoma (n=69).
In analogy to the clinical use of PARP inhibitors in the context of BRCA-deficient breast cancer, our findings point towards therapeutic opportunities to target DNA repair defects in tumors with complex genomic rearrangements.
Citation Format: Manasi Ratnaparkhe, John Wong, Pei-Chi Wei, Mario Hlevnjak, Paul Northcott, David T. Jones, Marcel Kool, Anna Jauch, Agata Pastorczak, Andrey Korshunov, Rajiv Kumar, Susanna M. Downing, Stefan M. Pfister, Marc Zapatka, Peter J. McKinnon, Frederick W. Alt, Peter Lichter, Aurelie Ernst. Inactivation of factors of DNA double-strand break repair by homologous recombination or non-homologous end-joining leads to frequent catastrophic genomic events in murine and human tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1352.
Collapse
Affiliation(s)
| | - John Wong
- 1German Cancer Research Center, Heidelberg, Germany
| | - Pei-Chi Wei
- 2Boston Children's Hospital and Harvard Medical School, Boston, MA
| | | | | | | | - Marcel Kool
- 1German Cancer Research Center, Heidelberg, Germany
| | - Anna Jauch
- 4Heidelberg University, Heidelberg, Germany
| | | | | | - Rajiv Kumar
- 1German Cancer Research Center, Heidelberg, Germany
| | | | | | - Marc Zapatka
- 1German Cancer Research Center, Heidelberg, Germany
| | | | - Frederick W. Alt
- 2Boston Children's Hospital and Harvard Medical School, Boston, MA
| | | | | |
Collapse
|
17
|
Abstract
Multiple DNA repair pathways maintain genome stability and ensure that DNA remains essentially unchanged over the life of a cell. Various human diseases occur if DNA repair is compromised, and most of these impact the nervous system, in some cases exclusively. However, it is often unclear what specific endogenous damage underpins disease pathology. Generally, the types of causative DNA damage are associated with replication, transcription, or oxidative metabolism; other direct sources of endogenous lesions may arise from aberrant topoisomerase activity or ribonucleotide incorporation into DNA. This review focuses on the etiology of DNA damage in the nervous system and the genome stability pathways that prevent human neurologic disease.
Collapse
Affiliation(s)
- Peter J McKinnon
- Department of Genetics, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| |
Collapse
|
18
|
Larson JD, Kasper LH, Wu G, Fan Y, Finkelstein D, Jin H, Paugh BS, Silveira AB, Xu B, Zhu X, Zhang J, Russell HR, McKinnon PJ, Ellison DW, Zhang J, Baker SJ. Abstract 3006: Oncogenic activity of H3.3 K27M in a spontaneous DIPG mouse model. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pediatric diffuse high-grade gliomas (HGG) cause a devastatingly poor outcome. Diffuse intrinsic pontine gliomas (DIPG) are brainstem HGGs found almost exclusively in children and represent approximately 50 percent of all pediatric HGGs. Recurrent, clonal somatic mutations in histone H3 are a molecular hallmark that distinguish the genetic mechanisms underlying pediatric and adult HGG, and indicate a strong link between epigenetic dysfunction and pediatric brain tumorigenesis. H3 K27M mutations found in nearly 80 percent of DIPGs and over half of non-brainstem HGGs occurring in thalamus or other midline structures, induce a dominant loss of genome-wide H3K27me3. In contrast, mutually exclusive H3.3 G34R/V mutations occur in approximately 14 percent of cortical HGG tumors in older children through young adulthood suggesting a distinct developmental origin compared to K27M mutant tumors. DNA methylation and gene expression patterns distinguish G34R/V and K27M tumors, but the oncogenic mechanisms and reasons for brain region selectivity of histone mutations remain uncertain. To study these mutations in the developing mammalian brain and investigate how they contribute to oncogenesis, we generated conditionally activated, epitope-tagged knock-in mice to express K27M, G34R or non-mutated H3.3 proteins from the endogenous H3f3a locus. Untransformed embryonic neural precursor or astrocyte cells expressing H3.3 K27M demonstrated H3K27me3 loss and a growth advantage in vitro with brain region-specific, stage-dependent expression and epigenetic signatures. DIPGs frequently harbor genetic alterations in TP53 and PDGFRα in addition to H3.3 K27M, and mice with induced brain-specific Trp53 deletion plus mutated PDGFRαV544ins expression developed spontaneous HGG in vivo. Induction of H3.3 K27M significantly accelerated PDGFRαV544ins;Trp53 knockout HGG formation involving the brainstem. Importantly, the non-mutated H3.3 epitope-tagged protein did not affect tumor burden or latency. The H3.3 K27M tumors recapitulate characteristics observed in human DIPG including histopathological features, strong nuclear K27M expression and robust loss of H3K27me3 throughout the tumors. We relate the genetic, epigenetic and transcriptional landscapes of these models to primary pediatric DIPG to help identify their developmental origins and oncogenic mechanisms downstream of histone H3.3 K27M.
Citation Format: Jon D. Larson, Lawryn H. Kasper, Gang Wu, Yiping Fan, David Finkelstein, Hongjian Jin, Barbara S. Paugh, Andre B. Silveira, Beisi Xu, Xiaoyan Zhu, Junyuan Zhang, Helen R. Russell, Peter J. McKinnon, David W. Ellison, Jinghui Zhang, Suzanne J. Baker. Oncogenic activity of H3.3 K27M in a spontaneous DIPG mouse model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3006. doi:10.1158/1538-7445.AM2017-3006
Collapse
Affiliation(s)
| | | | - Gang Wu
- St. Jude Children's Research Hospital, Memphis, TN
| | - Yiping Fan
- St. Jude Children's Research Hospital, Memphis, TN
| | | | - Hongjian Jin
- St. Jude Children's Research Hospital, Memphis, TN
| | | | | | - Beisi Xu
- St. Jude Children's Research Hospital, Memphis, TN
| | - Xiaoyan Zhu
- St. Jude Children's Research Hospital, Memphis, TN
| | | | | | | | | | | | | |
Collapse
|
19
|
Chiang SC, Meagher M, Kassouf N, Hafezparast M, McKinnon PJ, Haywood R, El-Khamisy SF. Mitochondrial protein-linked DNA breaks perturb mitochondrial gene transcription and trigger free radical-induced DNA damage. Sci Adv 2017; 3:e1602506. [PMID: 28508041 PMCID: PMC5409496 DOI: 10.1126/sciadv.1602506] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 03/02/2017] [Indexed: 05/06/2023]
Abstract
Breakage of one strand of DNA is the most common form of DNA damage. Most damaged DNA termini require end-processing in preparation for ligation. The importance of this step is highlighted by the association of defects in the 3'-end processing enzyme tyrosyl DNA phosphodiesterase 1 (TDP1) and neurodegeneration and by the cytotoxic induction of protein-linked DNA breaks (PDBs) and oxidized nucleic acid intermediates during chemotherapy and radiotherapy. Although much is known about the repair of PDBs in the nucleus, little is known about this process in the mitochondria. We reveal that TDP1 resolves mitochondrial PDBs (mtPDBs), thereby promoting mitochondrial gene transcription. Overexpression of a toxic form of mitochondrial topoisomerase I (TOP1mt*), which generates excessive mtPDBs, results in a TDP1-dependent compensatory up-regulation of mitochondrial gene transcription. In the absence of TDP1, the imbalance in transcription of mitochondrial- and nuclear-encoded electron transport chain (ETC) subunits results in misassembly of ETC complex III. Bioenergetics profiling further reveals that TDP1 promotes oxidative phosphorylation under both basal and high energy demands. It is known that mitochondrial dysfunction results in free radical leakage and nuclear DNA damage; however, the detection of intermediates of radical damage to DNA is yet to be shown. Consequently, we report an increased accumulation of carbon-centered radicals in cells lacking TDP1, using electron spin resonance spectroscopy. Overexpression of the antioxidant enzyme superoxide dismutase 1 (SOD1) reduces carbon-centered adducts and protects TDP1-deficient cells from oxidative stress. Conversely, overexpression of the amyotrophic lateral sclerosis-associated mutant SOD1G93A leads to marked sensitivity. Whereas Tdp1 knockout mice develop normally, overexpression of SOD1G93A suggests early embryonic lethality. Together, our data show that TDP1 resolves mtPDBs, thereby regulating mitochondrial gene transcription and oxygen consumption by oxidative phosphorylation, thus conferring cellular protection against reactive oxygen species-induced damage.
Collapse
Affiliation(s)
- Shih-Chieh Chiang
- Krebs Institute and Sheffield Institute for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN Sheffield, U.K
| | - Martin Meagher
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K
| | - Nick Kassouf
- RAFT Institute, Mount Vernon Hospital, Northwood, Middlesex HA6 2RN, U.K
| | - Majid Hafezparast
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, U.K
| | - Peter J. McKinnon
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN 38105–3678, USA
| | - Rachel Haywood
- RAFT Institute, Mount Vernon Hospital, Northwood, Middlesex HA6 2RN, U.K
| | - Sherif F. El-Khamisy
- Krebs Institute and Sheffield Institute for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN Sheffield, U.K
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12588, Egypt
- Corresponding author.
| |
Collapse
|
20
|
Illuzzi JL, McNeill DR, Bastian P, Brenerman B, Wersto R, Russell HR, Bunz F, McKinnon PJ, Becker KG, Wilson DM. Tumor-associated APE1 variant exhibits reduced complementation efficiency but does not promote cancer cell phenotypes. Environ Mol Mutagen 2017; 58:84-98. [PMID: 28181292 PMCID: PMC5321783 DOI: 10.1002/em.22074] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/10/2017] [Indexed: 06/06/2023]
Abstract
Base excision repair (BER) is the major pathway for coping with most forms of endogenous DNA damage, and defects in the process have been associated with carcinogenesis. Apurinic/apyrimidinic endonuclease 1 (APE1) is a central participant in BER, functioning as a critical endonuclease in the processing of noncoding abasic sites in DNA. Evidence has suggested that APE1 missense mutants, as well as altered expression or localization of the protein, can contribute to disease manifestation. We report herein that the tumor-associated APE1 variant, R237C, shows reduced complementation efficiency of the methyl methanesulfonate hypersensitivity and impaired cell growth exhibited by APE1-deficient mouse embryonic fibroblasts. Overexpression of wild-type APE1 or the R237C variant in the nontransformed C127I mouse cell line had no effect on proliferation, cell cycle status, steady-state DNA damage levels, mitochondrial function, or cellular transformation. A human cell line heterozygous for an APE1 knockout allele had lower levels of endogenous APE1, increased cellular sensitivity to DNA-damaging agents, impaired proliferation with time, and a distinct global gene expression pattern consistent with a stress phenotype. Our results indicate that: (i) the tumor-associated R237C variant is a possible susceptibility factor, but not likely a driver of cancer cell phenotypes, (ii) overexpression of APE1 does not readily promote cellular transformation, and (iii) haploinsufficiency at the APE1 locus can have profound cellular consequences, consistent with BER playing a critical role in proliferating cells. Environ. Mol. Mutagen. 58:84-98, 2017. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Jennifer L. Illuzzi
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224
| | - Daniel R. McNeill
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224
| | - Paul Bastian
- Laboratory of Genetics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224
| | - Boris Brenerman
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224
| | - Robert Wersto
- Flow Cytometry Unit, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224
| | - Helen R. Russell
- Genetics Department, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Fred Bunz
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231
| | - Peter J. McKinnon
- Genetics Department, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Kevin G. Becker
- Laboratory of Genetics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224
| | - David M. Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224
| |
Collapse
|
21
|
Hoch N, Hanzlikova H, Rulten SL, Tétreault M, Koumulainen E, Ju L, Hornyak P, Zeng Z, Gittens W, Rey S, Staras K, Mancini GM, McKinnon PJ, Wang ZQ, Wagner J, Yoon G, Caldecott KW. XRCC1 mutation is associated with PARP1 hyperactivation and cerebellar ataxia. Nature 2017; 541:87-91. [PMID: 28002403 PMCID: PMC5218588 DOI: 10.1038/nature20790] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 11/15/2016] [Indexed: 01/14/2023]
Abstract
XRCC1 is a molecular scaffold protein that assembles multi-protein complexes involved in DNA single-strand break repair. Here we show that biallelic mutations in the human XRCC1 gene are associated with ocular motor apraxia, axonal neuropathy, and progressive cerebellar ataxia. Cells from a patient with mutations in XRCC1 exhibited not only reduced rates of single-strand break repair but also elevated levels of protein ADP-ribosylation. This latter phenotype is recapitulated in a related syndrome caused by mutations in the XRCC1 partner protein PNKP and implicates hyperactivation of poly(ADP-ribose) polymerase/s as a cause of cerebellar ataxia. Indeed, remarkably, genetic deletion of Parp1 rescued normal cerebellar ADP-ribose levels and reduced the loss of cerebellar neurons and ataxia in Xrcc1-defective mice, identifying a molecular mechanism by which endogenous single-strand breaks trigger neuropathology. Collectively, these data establish the importance of XRCC1 protein complexes for normal neurological function and identify PARP1 as a therapeutic target in DNA strand break repair-defective disease.
Collapse
Affiliation(s)
- Nicolas Hoch
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
- CAPES Foundation, Ministry of Education of Brazil, Brasilia/DF 70040-020, Brazil
| | - Hana Hanzlikova
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Stuart L. Rulten
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Martine Tétreault
- Department of Human Genetics, McGill University and Genome Québec Innovation Centre, Montréal, Québec, H3A 0G4, Canada
| | - Emilia Koumulainen
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Limei Ju
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Peter Hornyak
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Zhihong Zeng
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - William Gittens
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Stephanie Rey
- Neuroscience, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Kevin Staras
- Neuroscience, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Grazia M.S. Mancini
- Department of Clinical Genetics, Erasmus MC, P.O. Box 2040, 3000 CA, Rotterdam, the Netherlands
| | | | - Zhao-Qi Wang
- Leibniz Institute for Age Research, Fritz Lipmann Institute, 1107745 Jena, Germany
| | - Justin Wagner
- The Children's Hospital of Eastern Ontario Research Institute, Ottawa, K1L 8H1, Canada
| | | | - Grace Yoon
- Division of Clinical and Metabolic Genetics, and Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, M5G 1X8, Canada
| | - Keith W. Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| |
Collapse
|
22
|
Ho Y, Li X, Jamison S, Harding HP, McKinnon PJ, Ron D, Lin W. PERK Activation Promotes Medulloblastoma Tumorigenesis by Attenuating Premalignant Granule Cell Precursor Apoptosis. Am J Pathol 2016; 186:1939-1951. [PMID: 27181404 PMCID: PMC4929388 DOI: 10.1016/j.ajpath.2016.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/18/2016] [Accepted: 03/04/2016] [Indexed: 12/26/2022]
Abstract
Evidence suggests that activation of pancreatic endoplasmic reticulum kinase (PERK) signaling in response to endoplasmic reticulum stress negatively or positively influences cell transformation by regulating apoptosis. Patched1 heterozygous deficient (Ptch1(+/-)) mice reproduce human Gorlin's syndrome and are regarded as the best animal model to study tumorigenesis of the sonic hedgehog subgroup of medulloblastomas. It is believed that medulloblastomas in Ptch1(+/-) mice results from the transformation of granule cell precursors (GCPs) in the developing cerebellum. Here, we determined the role of PERK signaling on medulloblastoma tumorigenesis by assessing its effects on premalignant GCPs and tumor cells. We found that PERK signaling was activated in both premalignant GCPs in young Ptch1(+/-) mice and medulloblastoma cells in adult mice. We demonstrated that PERK haploinsufficiency reduced the incidence of medulloblastomas in Ptch1(+/-) mice. Interestingly, PERK haploinsufficiency enhanced apoptosis of premalignant GCPs in young Ptch1(+/-) mice but had no significant effect on medulloblastoma cells in adult mice. Moreover, we showed that the PERK pathway was activated in medulloblastomas in humans. These results suggest that PERK signaling promotes medulloblastoma tumorigenesis by attenuating apoptosis of premalignant GCPs during the course of malignant transformation.
Collapse
Affiliation(s)
- Yeung Ho
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota; Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Xiting Li
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota; Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota; Department of Periodontics, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Stephanie Jamison
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota; Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Heather P Harding
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Peter J McKinnon
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - David Ron
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Wensheng Lin
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota; Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota.
| |
Collapse
|
23
|
Dumitrache LC, McKinnon PJ. Polynucleotide kinase-phosphatase (PNKP) mutations and neurologic disease. Mech Ageing Dev 2016; 161:121-129. [PMID: 27125728 DOI: 10.1016/j.mad.2016.04.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/12/2016] [Accepted: 04/24/2016] [Indexed: 12/30/2022]
Abstract
A variety of human neurologic diseases are caused by inherited defects in DNA repair. In many cases, these syndromes almost exclusively impact the nervous system, underscoring the critical requirement for genome stability in this tissue. A striking example of this is defective enzymatic activity of polynucleotide kinase-phosphatase (PNKP), leading to microcephaly or neurodegeneration. Notably, the broad neural impact of mutations in PNKP can result in markedly different disease entities, even when the inherited mutation is the same. For example microcephaly with seizures (MCSZ) results from various hypomorphic PNKP mutations, as does ataxia with oculomotor apraxia 4 (AOA4). Thus, other contributing factors influence the neural phenotype when PNKP is disabled. Here we consider the role for PNKP in maintaining brain function and how perturbation in its activity can account for the varied pathology of neurodegeneration or microcephaly present in MCSZ and AOA4 respectively.
Collapse
Affiliation(s)
- Lavinia C Dumitrache
- Dept. of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter J McKinnon
- Dept. of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| |
Collapse
|
24
|
Al-Khalaf MH, Blake LE, Larsen BD, Bell RA, Brunette S, Parks RJ, Rudnicki MA, McKinnon PJ, Jeffrey Dilworth F, Megeney LA. Temporal activation of XRCC1-mediated DNA repair is essential for muscle differentiation. Cell Discov 2016; 2:15041. [PMID: 27462438 PMCID: PMC4860966 DOI: 10.1038/celldisc.2015.41] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/28/2015] [Indexed: 01/04/2023] Open
Abstract
Transient DNA strand break formation has been identified as an effective means to enhance gene expression in living cells. In the muscle lineage, cell differentiation is contingent upon the induction of caspase-mediated DNA strand breaks, which act to establish the terminal gene expression program. This coordinated DNA nicking is rapidly resolved, suggesting that myoblasts may deploy DNA repair machinery to stabilize the genome and entrench the differentiated phenotype. Here, we identify the base excision repair pathway component XRCC1 as an indispensable mediator of muscle differentiation. Caspase-triggered XRCC1 repair foci form rapidly within differentiating myonuclei, and then dissipate as the maturation program proceeds. Skeletal myoblast deletion of Xrcc1 does not have an impact on cell growth, yet leads to perinatal lethality, with sustained DNA damage and impaired myofiber development. Together, these results demonstrate that XRCC1 manages a temporally responsive DNA repair process to advance the muscle differentiation program.
Collapse
Affiliation(s)
- Mohammad H Al-Khalaf
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Leanne E Blake
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, The Ottawa Hospital , Ottawa, ON, Canada
| | - Brian D Larsen
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Ryan A Bell
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, The Ottawa Hospital , Ottawa, ON, Canada
| | - Steve Brunette
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, The Ottawa Hospital , Ottawa, ON, Canada
| | - Robin J Parks
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Michael A Rudnicki
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Peter J McKinnon
- Department of Genetics, St Jude Children's Research Hospital , Memphis, TN, USA
| | - F Jeffrey Dilworth
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Lynn A Megeney
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| |
Collapse
|
25
|
Larson JD, Silveira AB, Kasper LH, Russell HR, Qu C, McKinnon PJ, Baker SJ. Abstract IA14: The unique genomic landscape of pediatric high-grade glioma. Cancer Res 2015. [DOI: 10.1158/1538-7445.brain15-ia14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Diffuse high-grade gliomas (HGGs) of childhood are a devastating spectrum of disease with no effective cures. The two-year survival for pediatric HGG ranges from 30 percent, for tumors arising in the cerebral cortex, to less than 10 percent for diffuse intrinsic pontine gliomas (DIPGs), which arise in the brainstem. Frequent recurrent somatic mutations in histone H3 distinguish the genetic drivers among pediatric and adult HGG. Mutually exclusive somatic heterozygous H3F3A or HIST1H3B mutations encoding a K27M variant of histone H3.3 or H3.1, respectively, are found in nearly 80 percent of DIPGs and 22 percent of non-brainstem HGG, where they occur predominantly in thalamic and other midline tumors. Strikingly, heterozygous H3F3A mutations encoding histone H3.3 G34R or G34V occur in approximately 14 percent of non-brainstem HGG, and are associated predominantly with cortical tumors arising in older children through young adulthood, suggesting a distinct developmental origin compared to the majority of tumors harboring K27M mutations. Recurrent mutations of the BMP receptor ACVR1/ALK2 have not been reported outside the brainstem, and are further restricted to the youngest DIPG patients, highlighting critical connections between development and gliomagenesis. Experiments to model the connections between oncogenic activity and developmental context will be discussed.
Citation Format: Jon D. Larson, Andre B. Silveira, Lawryn H. Kasper, Helen R. Russell, Chunxu Qu, Peter J. McKinnon, Suzanne J. Baker. The unique genomic landscape of pediatric high-grade glioma. [abstract]. In: Proceedings of the AACR Special Conference: Advances in Brain Cancer Research; May 27-30, 2015; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2015;75(23 Suppl):Abstract nr IA14.
Collapse
Affiliation(s)
| | | | | | | | - Chunxu Qu
- St. Jude Children's Research Hospital, Memphis, TN
| | | | | |
Collapse
|
26
|
Shimada M, Dumitrache LC, Russell HR, McKinnon PJ. Polynucleotide kinase-phosphatase enables neurogenesis via multiple DNA repair pathways to maintain genome stability. EMBO J 2015; 34:2465-80. [PMID: 26290337 DOI: 10.15252/embj.201591363] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 07/09/2015] [Indexed: 11/09/2022] Open
Abstract
Polynucleotide kinase-phosphatase (PNKP) is a DNA repair factor possessing both 5'-kinase and 3'-phosphatase activities to modify ends of a DNA break prior to ligation. Recently, decreased PNKP levels were identified as the cause of severe neuropathology present in the human microcephaly with seizures (MCSZ) syndrome. Utilizing novel murine Pnkp alleles that attenuate expression and a T424GfsX48 frame-shift allele identified in MCSZ individuals, we determined how PNKP inactivation impacts neurogenesis. Mice with PNKP inactivation in neural progenitors manifest neurodevelopmental abnormalities and postnatal death. This severe phenotype involved defective base excision repair and non-homologous end-joining, pathways required for repair of both DNA single- and double-strand breaks. Although mice homozygous for the T424GfsX48 allele were lethal embryonically, attenuated PNKP levels (akin to MCSZ) showed general neurodevelopmental defects, including microcephaly, indicating a critical developmental PNKP threshold. Directed postnatal neural inactivation of PNKP affected specific subpopulations including oligodendrocytes, indicating a broad requirement for genome maintenance, both during and after neurogenesis. These data illuminate the basis for selective neural vulnerability in DNA repair deficiency disease.
Collapse
Affiliation(s)
- Mikio Shimada
- Department of Genetics, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Helen R Russell
- Department of Genetics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter J McKinnon
- Department of Genetics, St Jude Children's Research Hospital, Memphis, TN, USA
| |
Collapse
|
27
|
Zindy F, Lee Y, Kawauchi D, Ayrault O, Merzoug LB, Li Y, McKinnon PJ, Roussel MF. Dicer Is Required for Normal Cerebellar Development and to Restrain Medulloblastoma Formation. PLoS One 2015; 10:e0129642. [PMID: 26091048 PMCID: PMC4474721 DOI: 10.1371/journal.pone.0129642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/11/2015] [Indexed: 11/18/2022] Open
Abstract
Dicer, a ribonuclease III enzyme, is required for the maturation of microRNAs. To assess its role in cerebellar and medulloblastoma development, we genetically deleted Dicer in Nestin-positive neural progenitors and in mice lacking one copy for the Sonic Hedgehog receptor, Patched 1. We found that conditional loss of Dicer in mouse neural progenitors induced massive Trp53-independent apoptosis in all proliferative zones of the brain and decreased proliferation of cerebellar granule progenitors at embryonic day 15.5 leading to abnormal cerebellar development and perinatal lethality. Loss of one copy of Dicer significantly accelerated the formation of mouse medulloblastoma of the Sonic Hedgehog subgroup in Patched1-heterozygous mice. We conclude that Dicer is required for proper cerebellar development, and to restrain medulloblastoma formation.
Collapse
Affiliation(s)
- Frederique Zindy
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Youngsoo Lee
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Daisuke Kawauchi
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Olivier Ayrault
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Leila Ben Merzoug
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Yang Li
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Peter J. McKinnon
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Martine F. Roussel
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
- * E-mail:
| |
Collapse
|
28
|
Heo J, Li J, Summerlin M, Hays A, Katyal S, McKinnon PJ, Nitiss KC, Nitiss JL, Hanakahi LA. TDP1 promotes assembly of non-homologous end joining protein complexes on DNA. DNA Repair (Amst) 2015; 30:28-37. [PMID: 25841101 DOI: 10.1016/j.dnarep.2015.03.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 02/25/2015] [Accepted: 03/09/2015] [Indexed: 11/16/2022]
Abstract
The repair of DNA double-strand breaks (DSB) is central to the maintenance of genomic integrity. In tumor cells, the ability to repair DSBs predicts response to radiation and many cytotoxic anti-cancer drugs. DSB repair pathways include homologous recombination and non-homologous end joining (NHEJ). NHEJ is a template-independent mechanism, yet many NHEJ repair products carry limited genetic changes, which suggests that NHEJ includes mechanisms to minimize error. Proteins required for mammalian NHEJ include Ku70/80, the DNA-dependent protein kinase (DNA-PKcs), XLF/Cernunnos and the XRCC4:DNA ligase IV complex. NHEJ also utilizes accessory proteins that include DNA polymerases, nucleases, and other end-processing factors. In yeast, mutations of tyrosyl-DNA phosphodiesterase (TDP1) reduced NHEJ fidelity. TDP1 plays an important role in repair of topoisomerase-mediated DNA damage and 3'-blocking DNA lesions, and mutation of the human TDP1 gene results in an inherited human neuropathy termed SCAN1. We found that human TDP1 stimulated DNA binding by XLF and physically interacted with XLF to form TDP1:XLF:DNA complexes. TDP1:XLF interactions preferentially stimulated TDP1 activity on dsDNA as compared to ssDNA. TDP1 also promoted DNA binding by Ku70/80 and stimulated DNA-PK activity. Because Ku70/80 and XLF are the first factors recruited to the DSB at the onset of NHEJ, our data suggest a role for TDP1 during the early stages of mammalian NHEJ.
Collapse
Affiliation(s)
- Jinho Heo
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - Jing Li
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - Matthew Summerlin
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - Annette Hays
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - Sachin Katyal
- University of Manitoba, Department of Pharmacology and Therapeutics, Manitoba Institute of Cell Biology, 675 McDermot Avenue, Winnipeg, Manitoba, Canada R3E 0V9
| | - Peter J McKinnon
- Department of Genetics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Karin C Nitiss
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - John L Nitiss
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - Leslyn A Hanakahi
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA; Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA.
| |
Collapse
|
29
|
Zindy F, Kawauchi D, Lee Y, Ayrault O, Ben Merzoug L, McKinnon PJ, Ventura A, Roussel MF. Role of the miR-17∼92 cluster family in cerebellar and medulloblastoma development. Biol Open 2014; 3:597-605. [PMID: 24928431 PMCID: PMC4154296 DOI: 10.1242/bio.20146734] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The miR-17∼92 cluster family is composed of three members encoding microRNAs that share seed sequences. To assess their role in cerebellar and medulloblastoma (MB) development, we deleted the miR-17∼92 cluster family in Nestin-positive neural progenitors and in mice heterozygous for the Sonic Hedgehog (SHH) receptor Patched 1 (Ptch1(+/-)). We show that mice in which we conditionally deleted the miR-17∼92 cluster (miR-17∼92(floxed/floxed); Nestin-Cre(+)) alone or together with the complete loss of the miR-106b∼25 cluster (miR-106b∼25(-/-)) were born alive but with small brains and reduced cerebellar foliation. Remarkably, deletion of the miR-17∼92 cluster abolished the development of SHH-MB in Ptch1(+/-) mice. Using an orthotopic transplant approach, we showed that granule neuron precursors (GNPs) purified from the cerebella of postnatal day 7 (P7) Ptch1(+/-); miR-106b∼25(-/-) mice and overexpressing Mycn induced MBs in the cortices of naïve recipient mice. In contrast, GNPs purified from the cerebella of P7 Ptch1(+/-); miR-17∼92(floxed/floxed); Nestin-Cre(+) animals and overexpressing Mycn failed to induce tumors in recipient animals. Taken together, our findings demonstrate that the miR-17∼92 cluster is dispensable for cerebellar development, but required for SHH-MB development.
Collapse
Affiliation(s)
- Frederique Zindy
- Department of Tumor Cell Biology, Danny Thomas Research Center, St Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Daisuke Kawauchi
- Department of Tumor Cell Biology, Danny Thomas Research Center, St Jude Children's Research Hospital, Memphis, TN 38105-3678, USA Present address: Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Youngsoo Lee
- Department of Genetics, Danny Thomas Research Center, St Jude Children's Research Hospital, Memphis, TN 38105-3678, USA Present address: Genomic Instability Research Center, Ajou University, School of Medicine, Suwon 443-749, South Korea
| | - Olivier Ayrault
- Department of Tumor Cell Biology, Danny Thomas Research Center, St Jude Children's Research Hospital, Memphis, TN 38105-3678, USA Present address: Institut Curie/CNRS UMR 3306/INSERM U1005 - Building 110 - Centre Universitaire, 91405 Orsay, Cedex, France
| | - Leila Ben Merzoug
- Department of Tumor Cell Biology, Danny Thomas Research Center, St Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Peter J McKinnon
- Department of Genetics, Danny Thomas Research Center, St Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Martine F Roussel
- Department of Tumor Cell Biology, Danny Thomas Research Center, St Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| |
Collapse
|
30
|
Katyal S, Lee Y, Nitiss KC, Downing SM, Li Y, Shimada M, Zhao J, Russell HR, Petrini JHJ, Nitiss JL, McKinnon PJ. Aberrant topoisomerase-1 DNA lesions are pathogenic in neurodegenerative genome instability syndromes. Nat Neurosci 2014; 17:813-21. [PMID: 24793032 PMCID: PMC4074009 DOI: 10.1038/nn.3715] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/09/2014] [Indexed: 01/10/2023]
Abstract
DNA damage is considered to be a prime factor in several spinocerebellar neurodegenerative diseases; however, the DNA lesions underpinning disease etiology are unknown. We observed the endogenous accumulation of pathogenic topoisomerase-1 (Top1)-DNA cleavage complexes (Top1ccs) in murine models of ataxia telangiectasia and spinocerebellar ataxia with axonal neuropathy 1. We found that the defective DNA damage response factors in these two diseases cooperatively modulated Top1cc turnover in a non-epistatic and ATM kinase-independent manner. Furthermore, coincident neural inactivation of ATM and DNA single-strand break repair factors, including tyrosyl-DNA phosphodiesterase-1 or XRCC1, resulted in increased Top1cc formation and excessive DNA damage and neurodevelopmental defects. Notably, direct Top1 poisoning to elevate Top1cc levels phenocopied the neuropathology of the mouse models described above. Our results identify a critical endogenous pathogenic lesion associated with neurodegenerative syndromes arising from DNA repair deficiency, indicating that genome integrity is important for preventing disease in the nervous system.
Collapse
Affiliation(s)
- Sachin Katyal
- Dept. of Genetics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, USA
- University of Manitoba, Dept of Pharmacology and Therapeutics, Manitoba Institute of Cell Biology, Winnipeg, Canada
| | - Youngsoo Lee
- Dept. of Genetics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, USA
- GIRC, Ajou University School of Medicine, Suwon, Korea
| | - Karin C. Nitiss
- Dept. of Biopharmaceutical Sciences, University of Illinois-Chicago, 1601 Parkview Avenue, Rockford, Illinois, 61107, USA
| | - Susanna M. Downing
- Dept. of Genetics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, USA
| | - Yang Li
- Dept. of Genetics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, USA
| | - Mikio Shimada
- Dept. of Genetics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, USA
| | - Jingfeng Zhao
- Dept. of Genetics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, USA
| | - Helen R. Russell
- Dept. of Genetics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, USA
| | - John H. J. Petrini
- Molecular Biology Program Memorial Sloan-Kettering Cancer Center and Cornell University Graduate School of Medical Sciences
| | - John L. Nitiss
- Dept. of Biopharmaceutical Sciences, University of Illinois-Chicago, 1601 Parkview Avenue, Rockford, Illinois, 61107, USA
| | - Peter J. McKinnon
- Dept. of Genetics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105, USA
| |
Collapse
|
31
|
Yeo AJ, Becherel OJ, Luff JE, Cullen JK, Wongsurawat T, Jenjaroenpoon P, Kuznetsov VA, McKinnon PJ, Lavin MF. R-loops in proliferating cells but not in the brain: implications for AOA2 and other autosomal recessive ataxias. PLoS One 2014; 9:e90219. [PMID: 24637776 PMCID: PMC3956458 DOI: 10.1371/journal.pone.0090219] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 01/27/2014] [Indexed: 11/18/2022] Open
Abstract
Disruption of the Setx gene, defective in ataxia oculomotor apraxia type 2 (AOA2) leads to the accumulation of DNA/RNA hybrids (R-loops), failure of meiotic recombination and infertility in mice. We report here the presence of R-loops in the testes from other autosomal recessive ataxia mouse models, which correlate with fertility in these disorders. R-loops were coincident in cells showing high basal levels of DNA double strand breaks and in those cells undergoing apoptosis. Depletion of Setx led to high basal levels of R-loops and these were enhanced further by DNA damage both in vitro and in vivo in tissues with proliferating cells. There was no evidence for accumulation of R-loops in the brains of mice where Setx, Atm, Tdp1 or Aptx genes were disrupted. These data provide further evidence for genome destabilization as a consequence of disrupted transcription in the presence of DNA double strand breaks arising during DNA replication or recombination. They also suggest that R-loop accumulation does not contribute to the neurodegenerative phenotype in these autosomal recessive ataxias.
Collapse
Affiliation(s)
- Abrey J. Yeo
- QIMR Berghofer Medical Research Institute, Radiation Biology and Oncology Laboratory, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Olivier J. Becherel
- QIMR Berghofer Medical Research Institute, Radiation Biology and Oncology Laboratory, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biology, University of Queensland, St. Lucia, Queensland, Australia
| | - John E. Luff
- QIMR Berghofer Medical Research Institute, Radiation Biology and Oncology Laboratory, Brisbane, Queensland, Australia
| | - Jason K. Cullen
- QIMR Berghofer Medical Research Institute, Radiation Biology and Oncology Laboratory, Brisbane, Queensland, Australia
| | - Thidathip Wongsurawat
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Singapore, Singapore
- School of Computer Engineering, Nanyang Technological University, Singapore, Singapore
| | - Piroon Jenjaroenpoon
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Singapore, Singapore
| | - Vladimir A. Kuznetsov
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Singapore, Singapore
- School of Computer Engineering, Nanyang Technological University, Singapore, Singapore
| | - Peter J. McKinnon
- Department of Genetics and Tumour Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Martin F. Lavin
- QIMR Berghofer Medical Research Institute, Radiation Biology and Oncology Laboratory, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, Herston, Queensland, Australia
| |
Collapse
|
32
|
Barzilai A, McKinnon PJ. Genome maintenance in the nervous system; insight into the role of the DNA damage response in brain development and disease. DNA Repair (Amst) 2013; 12:541-2. [PMID: 23870284 DOI: 10.1016/j.dnarep.2013.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
33
|
Abstract
Active maintenance of genome stability is a prerequisite for the development and function of the nervous system. The high replication index during neurogenesis and the long life of mature neurons highlight the need for efficient cellular programs to safeguard genetic fidelity. Multiple DNA damage response pathways ensure that replication stress and other types of DNA lesions, such as oxidative damage, do not affect neural homeostasis. Numerous human neurologic syndromes result from defective DNA damage signaling and compromised genome integrity. These syndromes can involve different neuropathology, which highlights the diverse maintenance roles that are required for genome stability in the nervous system. Understanding how DNA damage signaling pathways promote neural development and preserve homeostasis is essential for understanding fundamental brain function.
Collapse
Affiliation(s)
- Peter J. McKinnon
- Department of Genetics, St Jude Children’s Research Hospital, Memphis TN, USA
| |
Collapse
|
34
|
Rodrigues PMG, Grigaravicius P, Remus M, Cavalheiro GR, Gomes AL, Martins MR, Frappart L, Reuss D, McKinnon PJ, von Deimling A, Martins RAP, Frappart PO. Nbn and atm cooperate in a tissue and developmental stage-specific manner to prevent double strand breaks and apoptosis in developing brain and eye. PLoS One 2013; 8:e69209. [PMID: 23935957 PMCID: PMC3728324 DOI: 10.1371/journal.pone.0069209] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 06/06/2013] [Indexed: 01/30/2023] Open
Abstract
Nibrin (NBN or NBS1) and ATM are key factors for DNA Double Strand Break (DSB) signaling and repair. Mutations in NBN or ATM result in Nijmegen Breakage Syndrome and Ataxia telangiectasia. These syndromes share common features such as radiosensitivity, neurological developmental defects and cancer predisposition. However, the functional synergy of Nbn and Atm in different tissues and developmental stages is not yet understood. Here, we show in vivo consequences of conditional inactivation of both genes in neural stem/progenitor cells using Nestin-Cre mice. Genetic inactivation of Atm in the central nervous system of Nbn-deficient mice led to reduced life span and increased DSBs, resulting in increased apoptosis during neural development. Surprisingly, the increase of DSBs and apoptosis was found only in few tissues including cerebellum, ganglionic eminences and lens. In sharp contrast, we showed that apoptosis associated with Nbn deletion was prevented by simultaneous inactivation of Atm in developing retina. Therefore, we propose that Nbn and Atm collaborate to prevent DSB accumulation and apoptosis during development in a tissue- and developmental stage-specific manner.
Collapse
Affiliation(s)
- Paulo M. G. Rodrigues
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulius Grigaravicius
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Remus
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gabriel R. Cavalheiro
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anielle L. Gomes
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mauricio R. Martins
- Programa de Pós Graduação em Biofísica, IBCCF, Universidade Federal do Rio de Janeiro, CCS, Rio de Janeiro, Brazil
| | - Lucien Frappart
- Leibniz Institute for Age Research – Fritz Lipmann Institute (FLI), Jena, Germany
| | - David Reuss
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Peter J. McKinnon
- Department of Genetics, St.Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Rodrigo A. P. Martins
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail: (POF); (RAPM)
| | - Pierre-Olivier Frappart
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- * E-mail: (POF); (RAPM)
| |
Collapse
|
35
|
Shokolenko IN, Fayzulin RZ, Katyal S, McKinnon PJ, Wilson GL, Alexeyev MF. Mitochondrial DNA ligase is dispensable for the viability of cultured cells but essential for mtDNA maintenance. J Biol Chem 2013; 288:26594-605. [PMID: 23884459 DOI: 10.1074/jbc.m113.472977] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Multiple lines of evidence support the notion that DNA ligase III (LIG3), the only DNA ligase found in mitochondria, is essential for viability in both whole organisms and in cultured cells. Previous attempts to generate cells devoid of mitochondrial DNA ligase failed. Here, we report, for the first time, the derivation of viable LIG3-deficient mouse embryonic fibroblasts. These cells lack mtDNA and are auxotrophic for uridine and pyruvate, which may explain the apparent lethality of the Lig3 knock-out observed in cultured cells in previous studies. Cells with severely reduced expression of LIG3 maintain normal mtDNA copy number and respiration but show reduced viability in the face of alkylating and oxidative damage, increased mtDNA degradation in response to oxidative damage, and slow recovery from mtDNA depletion. Our findings clarify the cellular role of LIG3 and establish that the loss of viability in LIG3-deficient cells is conditional and secondary to the ρ(0) phenotype.
Collapse
|
36
|
Rangachari M, Zhu C, Sakuishi K, Xiao S, Karman J, Chen A, Angin M, Wakeham A, Greenfield EA, Sobel RA, Okada H, McKinnon PJ, Mak TW, Addo MM, Anderson AC, Kuchroo VK. Bat3 promotes T cell responses and autoimmunity by repressing Tim-3–mediated cell death and exhaustion. Nat Med 2012; 18:1394-400. [PMID: 22863785 DOI: 10.1038/nm.2871] [Citation(s) in RCA: 270] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 06/14/2012] [Indexed: 12/14/2022]
Abstract
T cell immunoglobulin and mucin domain–containing 3 (Tim-3) is an inhibitory receptor that is expressed on exhausted T cells during infection with HIV-1 and hepatitis C virus. By contrast, Tim-3 expression and function are defective in multiple human autoimmune diseases. However, the molecular mechanisms modulating Tim-3 function are not well understood. Here we show that human leukocyte antigen B (HLA-B)-associated transcript 3 (Bat3) binds to, and represses the function of, Tim-3. Bat3 protects T helper type 1 (TH1) cells from galectin-9–mediated cell death and promotes both proliferation and proinflammatory cytokine production. Bat3-deficient T cells have elevated expression of exhaustion-associated molecules such as Tim-3, Lag3, Prdm1 and Pbx3, and Bat3 knockdown in myelin-antigen–specific CD4+ T cells markedly inhibits the development of experimental autoimmune encephalomyelitis while promoting the expansion of a dysfunctional Tim-3hi, interferon-γ (IFN-γ)loCD4+ cell population. Furthermore, expression of Bat3 is reduced in exhausted Tim-3+ T cells from mouse tumors and HIV-1–infected individuals. These data indicate that Bat3 acts as an inhibitor of Tim-3–dependent exhaustion and cell death. Bat3 may thus represent a viable therapeutic target in autoimmune disorders, chronic infections and cancers.
Collapse
Affiliation(s)
- Manu Rangachari
- Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Lee Y, Katyal S, Downing SM, Zhao J, Russell HR, McKinnon PJ. Neurogenesis requires TopBP1 to prevent catastrophic replicative DNA damage in early progenitors. Nat Neurosci 2012; 15:819-26. [PMID: 22522401 PMCID: PMC3404252 DOI: 10.1038/nn.3097] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 03/29/2012] [Indexed: 12/14/2022]
Abstract
The rapid proliferation of progenitors during neurogenesis requires a stringent genomic maintenance program to ensure transmission of genetic fidelity. However the essential factors that govern neural progenitor genome integrity are unknown. Here we report that conditional inactivation of mouse TopBP1, a protein linked to DNA replication, and a key activator of the DNA damage response kinase ATR (ataxia telangiectasia and rad3-related) is critical for maintenance of early-born neural progenitors. During cortical development TopBP1 prevented replication-associated DNA damage in Emx1-progenitors which otherwise resulted in profound tissue ablation. Notably, disrupted neurogenesis in TopBP1-depleted tissues was substantially rescued by inactivation of p53 but not of ATM. Our data establish that TopBP1 is essential for preventing replication-associated DNA strand breaks, but is not essential per se for DNA replication. Thus, TopBP1 is crucial for maintaining genome integrity in the early progenitors that drive neurogenesis.
Collapse
Affiliation(s)
- Youngsoo Lee
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | | | | | | | | | | |
Collapse
|
38
|
DeWire MD, Beltran C, Boop FA, Helton KJ, Ellison DW, McKinnon PJ, Gajjar A, Pai Panandiker AS. Radiation therapy and adjuvant chemotherapy in a patient with a malignant glioneuronal tumor and underlying ataxia telangiectasia: a case report and review of the literature. J Clin Oncol 2012; 31:e12-4. [PMID: 22689803 DOI: 10.1200/jco.2011.40.1430] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Mariko D DeWire
- St. Jude Children's Research Hospital, Memphis, TN 38105-2794, USA.
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Lee Y, Shull ERP, Frappart PO, Katyal S, Enriquez-Rios V, Zhao J, Russell HR, Brown EJ, McKinnon PJ. ATR maintains select progenitors during nervous system development. EMBO J 2012; 31:1177-89. [PMID: 22266795 DOI: 10.1038/emboj.2011.493] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 12/19/2011] [Indexed: 01/09/2023] Open
Abstract
The ATR (ATM (ataxia telangiectasia mutated) and rad3-related) checkpoint kinase is considered critical for signalling DNA replication stress and its dysfunction can lead to the neurodevelopmental disorder, ATR-Seckel syndrome. To understand how ATR functions during neurogenesis, we conditionally deleted Atr broadly throughout the murine nervous system, or in a restricted manner in the dorsal telencephalon. Unexpectedly, in both scenarios, Atr loss impacted neurogenesis relatively late during neural development involving only certain progenitor populations. Whereas the Atr-deficient embryonic cerebellar external germinal layer underwent p53- (and p16(Ink4a/Arf))-independent proliferation arrest, other brain regions suffered apoptosis that was partially p53 dependent. In contrast to other organs, in the nervous system, p53 loss did not worsen the outcome of Atr inactivation. Coincident inactivation of Atm also did not affect the phenotype after Atr deletion, supporting non-overlapping physiological roles for these related DNA damage-response kinases in the brain. Rather than an essential general role in preventing replication stress, our data indicate that ATR functions to monitor genomic integrity in a selective spatiotemporal manner during neurogenesis.
Collapse
Affiliation(s)
- Youngsoo Lee
- Department of Genetics, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Abstract
Ataxia telangiectasia (A-T) results from inactivation of the ATM protein kinase. DNA-damage signaling is a prime function of this kinase, although other roles have been ascribed to ATM. Identifying the primary ATM function(s) for tissue homeostasis is key to understanding how these functions contribute to the prevention of A-T-related pathology. In this regard, because A-T is primarily a neurodegenerative disease, it is essential to understand how ATM loss results in degenerative effects on the nervous system. In addition to delineating the biochemistry and cell biology of ATM, important insights into the molecular basis for neurodegeneration in A-T come from a spectrum of phenotypically related neurodegenerative diseases that directly result from DNA-repair deficiency. Together with A-T, these syndromes indicate that neurodegeneration can be caused by the failure to appropriately respond to DNA damage. This review focuses on defective DNA-damage signaling as the underlying cause of A-T.
Collapse
Affiliation(s)
- Peter J McKinnon
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.
| |
Collapse
|
41
|
Caldecott KW, Bohr VA, McKinnon PJ. 3rd International Genome Dynamics in Neuroscience Conference: "DNA repair and neurological disease". Mech Ageing Dev 2011; 132:353-4. [PMID: 21820005 DOI: 10.1016/j.mad.2011.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
42
|
Abstract
DNA strand break repair is essential for the prevention of multiple human diseases, particularly those which feature neuropathology. To further understand the pathogenesis of these syndromes, we recently developed animal models in which the DNA single-strand break repair (SSBR) components, XRCC1 and DNA Ligase III (LIG3), were inactivated in the developing nervous system. Although biochemical evidence suggests that inactivation of XRCC1 and LIG3 should share common biological defects, we found profound phenotypic differences between these two models, implying distinct biological roles for XRCC1 and LIG3 during DNA repair. Rather than a key role in nuclear DNA repair, we found LIG3 function was central to mitochondrial DNA maintenance. Instead, our data indicate that DNA Ligase 1 is the main DNA ligase for XRCC1-mediated DNA repair. These studies refine our understanding of DNA SSBR and the etiology of neurological disease.
Collapse
Affiliation(s)
- Sachin Katyal
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN USA
| | | |
Collapse
|
43
|
Simsek D, Brunet E, Wong SYW, Katyal S, Gao Y, McKinnon PJ, Lou J, Zhang L, Li J, Rebar EJ, Gregory PD, Holmes MC, Jasin M. DNA ligase III promotes alternative nonhomologous end-joining during chromosomal translocation formation. PLoS Genet 2011; 7:e1002080. [PMID: 21655080 PMCID: PMC3107202 DOI: 10.1371/journal.pgen.1002080] [Citation(s) in RCA: 226] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 03/28/2011] [Indexed: 12/03/2022] Open
Abstract
Nonhomologous end-joining (NHEJ) is the primary DNA repair pathway thought to underlie chromosomal translocations and other genomic rearrangements in somatic cells. The canonical NHEJ pathway, including DNA ligase IV (Lig4), suppresses genomic instability and chromosomal translocations, leading to the notion that a poorly defined, alternative NHEJ (alt-NHEJ) pathway generates these rearrangements. Here, we investigate the DNA ligase requirement of chromosomal translocation formation in mouse cells. Mammals have two other DNA ligases, Lig1 and Lig3, in addition to Lig4. As deletion of Lig3 results in cellular lethality due to its requirement in mitochondria, we used recently developed cell lines deficient in nuclear Lig3 but rescued for mitochondrial DNA ligase activity. Further, zinc finger endonucleases were used to generate DNA breaks at endogenous loci to induce translocations. Unlike with Lig4 deficiency, which causes an increase in translocation frequency, translocations are reduced in frequency in the absence of Lig3. Residual translocations in Lig3-deficient cells do not show a bias toward use of pre-existing microhomology at the breakpoint junctions, unlike either wild-type or Lig4-deficient cells, consistent with the notion that alt-NHEJ is impaired with Lig3 loss. By contrast, Lig1 depletion in otherwise wild-type cells does not reduce translocations or affect microhomology use. However, translocations are further reduced in Lig3-deficient cells upon Lig1 knockdown, suggesting the existence of two alt-NHEJ pathways, one that is biased toward microhomology use and requires Lig3 and a back-up pathway which does not depend on microhomology and utilizes Lig1. Chromosomal rearrangements are associated with many tumor types, as they are one way in which genes affecting cancer initiation and progression become mutated. One type of rearrangement is a chromosomal translocation, in which parts of two different chromosomes join together. Although infrequent, translocations occur when both chromosomes undergo breakage and the ends from different chromosomes join rather than the two ends from the same chromosome. Human and mouse cells have three known DNA ligases which catalyze the joining of DNA ends (Lig1, Lig3, and Lig4). Lig4 is important for joining the correct ends together, thereby suppressing translocations. In this report, the role of the other two DNA ligases is examined in a novel mouse cell system. Lig3 is found to be required for efficient chromosomal translocation formation, but in its absence Lig1 can substitute, although less efficiently and although the joining characteristics of the two DNA ligases differ. These studies define the hierarchy of the three DNA ligases in this type of genomic rearrangement.
Collapse
Affiliation(s)
- Deniz Simsek
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- Weill Cornell Graduate School of Medical Sciences, New York, New York, United States of America
| | - Erika Brunet
- Museum National d'Histoire Naturelle, Paris, France
- CNRS, UMR7196, Paris, France
- Inserm, U565, Paris, France
| | | | - Sachin Katyal
- Department of Genetics and Tumor Cell Biology, St Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Yankun Gao
- Department of Genetics and Tumor Cell Biology, St Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Peter J. McKinnon
- Department of Genetics and Tumor Cell Biology, St Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Jacqueline Lou
- Sangamo BioSciences, Richmond, California, United States of America
| | - Lei Zhang
- Sangamo BioSciences, Richmond, California, United States of America
| | - James Li
- Sangamo BioSciences, Richmond, California, United States of America
| | - Edward J. Rebar
- Sangamo BioSciences, Richmond, California, United States of America
| | | | | | - Maria Jasin
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- Weill Cornell Graduate School of Medical Sciences, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
44
|
Gibson P, Tong Y, Robinson G, Poppleton H, Thompson MC, Currle DS, Eden C, Hogg TL, Finkelstein D, Pounds S, Patay Z, Scoggins M, Pei Y, Ogg R, Lee Y, Zindy F, Lindsey JC, Boop FA, Gajjar A, Clifford SC, Roussel MF, McKinnon PJ, Ellison DW, Wechsler-Reya R, Gutmann DH, Gilbertson RJ. Abstract 3448: Subtypes of medulloblastoma have distinct developmental origins. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-3448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Medulloblastoma encompasses a collection of clinically and molecularly diverse tumor subtypes that together comprise the most common malignant childhood brain tumor. These tumors are thought to arise within the cerebellum, with approximately 25% originating from granule neuron precursor cells (GNPCs) following aberrant activation of the Sonic Hedgehog pathway (hereafter, SHH-subtype). The pathological processes that drive heterogeneity among the other medulloblastoma subtypes are not known, hindering the development of much needed new therapies. Here, we provide evidence that a discrete subtype of medulloblastoma that contains activating mutations in the WNT pathway effector CTNNB1 (hereafter, WNT-subtype), arises outside the cerebellum from cells of the lower rhombic lip (LRL). We found that genes marking human WNT-subtype medulloblastomas are more frequently expressed in the LRL and embryonic dorsal brainstem than in the upper rhombic lip (URL) and developing cerebellum. Magnetic resonance imaging (MRI) and intra-operative reports showed that human WNT-subtype tumors infiltrate the dorsal brainstem, while SHH-subtype tumors are located within the cerebellar hemispheres. Activating mutations in Ctnnb1 had little impact on progenitor cell populations in the cerebellum, but caused an aberrant accumulation of proliferating precursor cells within the LRL. These lesions persisted in the dorsal brainstem of all mutant adult mice and in 15% of cases in which Tp53 was concurrently deleted, progressed to form medulloblastomas that modeled faithfully the anatomy and gene expression profiles of human WNT-subtype medulloblastoma. We provide the first evidence that subtypes of medulloblastoma have distinct cellular origins. Our data provide an explanation for the marked molecular and clinical differences between SHH and WNT-subtype medulloblastomas and have profound implications for future research and treatment of this important childhood cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3448. doi:10.1158/1538-7445.AM2011-3448
Collapse
Affiliation(s)
- Paul Gibson
- 1St. Jude Children's Research Hospital, Memphis, TN
| | - Yiai Tong
- 1St. Jude Children's Research Hospital, Memphis, TN
| | | | | | | | | | | | | | | | | | - Zoltan Patay
- 1St. Jude Children's Research Hospital, Memphis, TN
| | | | - Yanxin Pei
- 3Duke University Medical Center, Durham, NC
| | - Robert Ogg
- 1St. Jude Children's Research Hospital, Memphis, TN
| | - Youngsoo Lee
- 1St. Jude Children's Research Hospital, Memphis, TN
| | | | - Janet C. Lindsey
- 4Northern Institute For Cancer Research, Newcastle, United Kingdom
| | | | - Amar Gajjar
- 1St. Jude Children's Research Hospital, Memphis, TN
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Lindsey JC, Schwalbe EC, Kawauchi D, Olson JM, McKinnon PJ, Gilbertson RJ, Roussel MF, Ellison DW, Bailey S, Clifford SC. Abstract 3449: Epigenomics identifies conserved DNA methylation events associated with medulloblastoma development in humans and mice. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-3449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Medulloblastoma, an invasive embryonal tumor of the cerebellum, is the most common malignant brain tumor of childhood. Genome-wide technologies have recently shown that gene-specific changes in DNA methylation status are a significant feature of medulloblastoma development. Mouse models of medulloblastoma may provide important systems in which to study the impact of these DNA methylation changes, however the epigenetic basis of these models has not been widely investigated. We therefore adopted a cross-species approach to identify epigenetic events of relevance in human and mouse tumors, and investigate their impact on medulloblastoma development.
Using Illumina Goldengate DNA methylation arrays, we first identified a series of tumor-specific DNA methylation changes (measured relative to the normal cerebellum) which are strongly associated with activation of the Sonic hedgehog (SHH) signalling pathway, which occurs in approximately 25% of human primary tumors. From these, 12 candidate CpG sites, which lay within regions orthologous to the mouse genome, were selected for further investigation, alongside RASSF1A and COL1A2 CpG sites, which show frequent methylation in human primary tumors. The methylation status of these CpG sites was confirmed to be representative of their surrounding CpG islands in human primary tumors and control cerebellar samples, using bisulfite sequencing approaches.
We next assessed whether the DNA methylation status of orthologous regions was altered in tumors from four independent mouse models driven by Shh pathway activation (Ptc1+/- Ink4c-/-; Smo/Smo; Sufu+/- p53-/-; p53-/- Ink4c-/-), compared to strain-matched control mouse cerebella. Tissue-specific methylation patterns in the normal cerebellum were conserved between mouse and human, for 10/14 of the candidate regions investigated. Three regions which showed hypermethylation in human medulloblastomas (DSC2, RASSF1A and TAL1) also showed evidence of hypermethylation in mouse tumors and five regions showed evidence of hypomethylation in both human and mouse tumors (CYP2E1, MMP9, SPDEF, TGFB1, and VAV1). CYP2E1 and VAV1 showed the most similar frequencies and patterns of methylation changes in mouse and human tumors, while other changes were either less frequent (RASSF1A), affected fewer CpG sites (TAL1, TGFB1, SPDEF) or had different tissue-specific methylation patterns (DSC2, MMP9) in mice.
Ongoing work investigates the relationship of these methylation changes to gene expression and tumorigenesis. Assessment of the conservation of epigenetic changes between human tumors and disease relevant mouse models may help highlight those alterations most important in driving tumorigenesis, and identify candidate genes to take forward for further investigation.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3449. doi:10.1158/1538-7445.AM2011-3449
Collapse
Affiliation(s)
| | - Ed C. Schwalbe
- 1Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Jim M. Olson
- 3Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | | | - Simon Bailey
- 1Newcastle University, Newcastle upon Tyne, United Kingdom
| | | |
Collapse
|
46
|
Helmink BA, Tubbs AT, Dorsett Y, Bednarski JJ, M.Walker L, Feng Z, Sharma GG, McKinnon PJ, Zhang J, Bassing CH, Sleckman BP. Erratum: H2AX prevents CtIP-mediated DNA end resection and aberrant repair in G1-phase lymphocytes. Nature 2011. [DOI: 10.1038/nature09942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
47
|
Simsek D, Furda A, Gao Y, Artus J, Brunet E, Hadjantonakis AK, Van Houten B, Shuman S, McKinnon PJ, Jasin M. Crucial role for DNA ligase III in mitochondria but not in Xrcc1-dependent repair. Nature 2011; 471:245-8. [PMID: 21390132 PMCID: PMC3261757 DOI: 10.1038/nature09794] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 01/05/2011] [Indexed: 11/09/2022]
Abstract
Mammalian cells have three ATP-dependent DNA ligases, which are required for DNA replication and repair. Homologues of ligase I (Lig1) and ligase IV (Lig4) are ubiquitous in Eukarya, whereas ligase III (Lig3), which has nuclear and mitochondrial forms, appears to be restricted to vertebrates. Lig3 is implicated in various DNA repair pathways with its partner protein Xrcc1 (ref. 1). Deletion of Lig3 results in early embryonic lethality in mice, as well as apparent cellular lethality, which has precluded definitive characterization of Lig3 function. Here we used pre-emptive complementation to determine the viability requirement for Lig3 in mammalian cells and its requirement in DNA repair. Various forms of Lig3 were introduced stably into mouse embryonic stem (mES) cells containing a conditional allele of Lig3 that could be deleted with Cre recombinase. With this approach, we find that the mitochondrial, but not nuclear, Lig3 is required for cellular viability. Although the catalytic function of Lig3 is required, the zinc finger (ZnF) and BRCA1 carboxy (C)-terminal-related (BRCT) domains of Lig3 are not. Remarkably, the viability requirement for Lig3 can be circumvented by targeting Lig1 to the mitochondria or expressing Chlorella virus DNA ligase, the minimal eukaryal nick-sealing enzyme, or Escherichia coli LigA, an NAD(+)-dependent ligase. Lig3-null cells are not sensitive to several DNA-damaging agents that sensitize Xrcc1-deficient cells. Our results establish a role for Lig3 in mitochondria, but distinguish it from its interacting protein Xrcc1.
Collapse
Affiliation(s)
- Deniz Simsek
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Gibson P, Tong Y, Robinson G, Thompson MC, Currle DS, Eden C, Kranenburg TA, Hogg T, Poppleton H, Martin J, Finkelstein D, Pounds S, Weiss A, Patay Z, Scoggins M, Ogg R, Pei Y, Yang ZJ, Brun S, Lee Y, Zindy F, Lindsey JC, Taketo MM, Boop FA, Sanford RA, Gajjar A, Clifford SC, Roussel MF, McKinnon PJ, Gutmann DH, Ellison DW, Wechsler-Reya R, Gilbertson RJ. Subtypes of medulloblastoma have distinct developmental origins. Nature 2010; 468:1095-9. [PMID: 21150899 PMCID: PMC3059767 DOI: 10.1038/nature09587] [Citation(s) in RCA: 589] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2009] [Accepted: 10/15/2010] [Indexed: 12/11/2022]
Abstract
Medulloblastoma encompasses a collection of clinically and molecularly diverse tumor subtypes that together comprise the most common malignant childhood brain tumor1–4. These tumors are thought to arise within the cerebellum, with approximately 25% originating from granule neuron precursor cells (GNPCs) following aberrant activation of the Sonic Hedgehog pathway (hereafter, SHH-subtype)3–8. The pathological processes that drive heterogeneity among the other medulloblastoma subtypes are not known, hindering the development of much needed new therapies. Here, we provide evidence that a discrete subtype of medulloblastoma that contains activating mutations in the WNT pathway effector CTNNB1 (hereafter, WNT-subtype)1,3,4, arises outside the cerebellum from cells of the dorsal brainstem. We found that genes marking human WNT-subtype medulloblastomas are more frequently expressed in the lower rhombic lip (LRL) and embryonic dorsal brainstem than in the upper rhombic lip (URL) and developing cerebellum. Magnetic resonance imaging (MRI) and intra-operative reports showed that human WNT-subtype tumors infiltrate the dorsal brainstem, while SHH-subtype tumors are located within the cerebellar hemispheres. Activating mutations in Ctnnb1 had little impact on progenitor cell populations in the cerebellum, but caused the abnormal accumulation of cells on the embryonic dorsal brainstem that included aberrantly proliferating Zic1+ precursor cells. These lesions persisted in all mutant adult mice and in 15% of cases in which Tp53 was concurrently deleted, progressed to form medulloblastomas that recapitulated the anatomy and gene expression profiles of human WNT-subtype medulloblastoma. We provide the first evidence that subtypes of medulloblastoma have distinct cellular origins. Our data provide an explanation for the marked molecular and clinical differences between SHH and WNT-subtype medulloblastomas and have profound implications for future research and treatment of this important childhood cancer.
Collapse
Affiliation(s)
- Paul Gibson
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Kondo N, Takahashi A, Mori E, Noda T, Su X, Ohnishi K, McKinnon PJ, Sakaki T, Nakase H, Ono K, Ohnishi T. DNA ligase IV is a potential molecular target in ACNU sensitivity. Cancer Sci 2010; 101:1881-5. [PMID: 20487264 DOI: 10.1111/j.1349-7006.2010.01591.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Nimustine (ACNU) is a chloroethylating agent which was the most active chemotherapy agent used for patients with high-grade gliomas until the introduction of temozolomide, which became the standard of care for patients with newly diagnosed glioblastomas in Japan. Since temozolomide was established as the standard first-line therapy for glioblastoma multiforme (GBM), ACNU has been employed as a salvage chemotherapy agent for recurrent GBM in combination with other drugs. The acting molecular mechanism in ACNU has yet to be elucidated. ACNU is a cross-linking agent which induces DNA double-strand breaks (DSBs). The work described here was intended to clarify details in repair pathways which are active in the repair of DNA DSBs induced by ACNU. DSBs are repaired through the homologous recombination (HR) and non-homologous end-joining (NHEJ) pathways. Cultured mouse embryonic fibroblasts were used which have deficiencies in DNA DSB repair genes which are involved in HR repair (X-ray repair cross-complementing group 2 [XRCC2] and radiation sensitive mutant 54 [Rad54]), and in NHEJ repair (DNA ligase IV [Lig4]). Cellular sensitivity to ACNU treatment was evaluated with colony forming assays. The most effective molecular target which correlated with ACNU cell sensitivity was Lig4. In addition, it was found that Lig4 small-interference RNA (siRNA) efficiently enhanced cell lethality which was induced by ACNU in human glioblastoma A172 cells. These findings suggest that the down-regulation of Lig4 might provide a useful tool which can be used to increase cell sensitivity in response to ACNU chemotherapy.
Collapse
Affiliation(s)
- Natsuko Kondo
- Department of Biology, School of Medicine, Nara Medical University, Nara, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Becherel OJ, Jakob B, Cherry AL, Gueven N, Fusser M, Kijas AW, Peng C, Katyal S, McKinnon PJ, Chen J, Epe B, Smerdon SJ, Taucher-Scholz G, Lavin MF. CK2 phosphorylation-dependent interaction between aprataxin and MDC1 in the DNA damage response. Nucleic Acids Res 2009; 38:1489-503. [PMID: 20008512 PMCID: PMC2836575 DOI: 10.1093/nar/gkp1149] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aprataxin, defective in the neurodegenerative disorder ataxia oculomotor apraxia type 1, resolves abortive DNA ligation intermediates during DNA repair. Here, we demonstrate that aprataxin localizes at sites of DNA damage induced by high LET radiation and binds to mediator of DNA-damage checkpoint protein 1 (MDC1/NFBD1) through a phosphorylation-dependent interaction. This interaction is mediated via the aprataxin FHA domain and multiple casein kinase 2 di-phosphorylated S-D-T-D motifs in MDC1. X-ray structural and mutagenic analysis of aprataxin FHA domain, combined with modelling of the pSDpTD peptide interaction suggest an unusual FHA binding mechanism mediated by a cluster of basic residues at and around the canonical pT-docking site. Mutation of aprataxin FHA Arg29 prevented its interaction with MDC1 and recruitment to sites of DNA damage. These results indicate that aprataxin is involved not only in single strand break repair but also in the processing of a subset of double strand breaks presumably through its interaction with MDC1.
Collapse
Affiliation(s)
- Olivier J Becherel
- Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|