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Chakraborty A, Sreenivasmurthy SG, Miller W, Huai W, Biswas T, Mandal SM, Boscá L, Krishnan B, Ghosh G, Hazra T. A glycolytic metabolite restores DNA repair and ameliorates neuropathology in Huntington's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.26.564220. [PMID: 37961108 PMCID: PMC10634858 DOI: 10.1101/2023.10.26.564220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Huntington's disease (HD) and spinocerebellar ataxia type 3 (SCA3) are the most prevalent polyglutamine (polyQ) diseases, where the activity of an essential DNA repair enzyme, polynucleotide kinase 3'-phosphatase (PNKP), is severely abrogated resulting in accumulation of double-strand breaks in patients' brain genome leading to neuronal death. However, the mechanistic basis for such loss of PNKP activity is not known. Here we report that PNKP interacts with the nuclear isoform of 6-phosphofructo-2-kinase fructose-2,6-bisphosphatase 3 (PFKFB3), which converts fructose-6-phosphate (F6P) into fructose-2,6-bisphosphate (F2,6BP), a potent allosteric modulator of glycolysis. Depletion of PFKFB3 markedly abrogates PNKP activity. Notably, both PFKFB3 and F2,6BP levels are significantly lower in the nuclear extracts of HD and SCA3 post-mortem patients' brains. Exogenous F2,6BP, but neither F1,6BP nor F6P, restored PNKP activity in the patients' brain nuclear extracts. Moreover, intracellular delivery of F2,6BP into HD mouse striatum-derived neuronal cells restored PNKP activity and transcribed genome integrity. Importantly, supplementing F2,6BP effectively rescued the HD phenotype in Drosophila, suggesting F2,6BP to serve in vivo as a cofactor for the proper functionality of PNKP and thereby, of brain health. Our results thus provide a compelling rationale for exploring the therapeutic use of F2,6BP and structurally related compounds for treating polyQ diseases. Significance To unravel the biological basis for the loss of DNA repair activity of PNKP in both HD and SCA3, we analyzed PNKP interactome and found that the nuclear isoform of a glycolytic enzyme PFKFB3 associated with PNKP and other repair proteins forming a multiprotein complex. Surprisingly, we found that PFKFB3 and its biosynthetic product, F2,6BP are significantly low in the affected region of patients' brain. Exogenous addition of F2,6BP fully restored PNKP activity in patients' brain nuclear extract. Moreover, supplementing F2,6BP in cells and HD fruit flies restored genome integrity and rescued the disease symptoms. While there is no curative therapy for HD and SCA3, except symptom management, our discovery suggests that F2,6BP supplementation would be a promising therapeutic option.
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Tayanloo-Beik A, Hamidpour SK, Nikkhah A, Arjmand R, Mafi AR, Rezaei-Tavirani M, Larijani B, Gilany K, Arjmand B. DNA Damage Responses, the Trump Card of Stem Cells in the Survival Game. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023. [PMID: 37923882 DOI: 10.1007/5584_2023_791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Stem cells, as a group of undifferentiated cells, are enriched with self-renewal and high proliferative capacity, which have attracted the attention of many researchers as a promising approach in the treatment of many diseases over the past years. However, from the cellular and molecular point of view, the DNA repair system is one of the biggest challenges in achieving therapeutic goals through stem cell technology. DNA repair mechanisms are an advantage for stem cells that are constantly multiplying to deal with various types of DNA damage. However, this mechanism can be considered a trump card in the game of cell survival and treatment resistance in cancer stem cells, which can hinder the curability of various types of cancer. Therefore, getting a deep insight into the DNA repair system can bring researchers one step closer to achieving major therapeutic goals. The remarkable thing about the DNA repair system is that this system is not only under the control of genetic factors, but also under the control of epigenetic factors. Therefore, it is necessary to investigate the role of the DNA repair system in maintaining the survival of cancer stem cells from both aspects.
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Affiliation(s)
- Akram Tayanloo-Beik
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Amirabbas Nikkhah
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Rasta Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Rezazadeh Mafi
- Department of Radiation Oncology, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical sciences, Tehran, Iran
| | - Kambiz Gilany
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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Ribeiro JH, Altinisik N, Rajan N, Verslegers M, Baatout S, Gopalakrishnan J, Quintens R. DNA damage and repair: underlying mechanisms leading to microcephaly. Front Cell Dev Biol 2023; 11:1268565. [PMID: 37881689 PMCID: PMC10597653 DOI: 10.3389/fcell.2023.1268565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023] Open
Abstract
DNA-damaging agents and endogenous DNA damage constantly harm genome integrity. Under genotoxic stress conditions, the DNA damage response (DDR) machinery is crucial in repairing lesions and preventing mutations in the basic structure of the DNA. Different repair pathways are implicated in the resolution of such lesions. For instance, the non-homologous DNA end joining and homologous recombination pathways are central cellular mechanisms by which eukaryotic cells maintain genome integrity. However, defects in these pathways are often associated with neurological disorders, indicating the pivotal role of DDR in normal brain development. Moreover, the brain is the most sensitive organ affected by DNA-damaging agents compared to other tissues during the prenatal period. The accumulation of lesions is believed to induce cell death, reduce proliferation and premature differentiation of neural stem and progenitor cells, and reduce brain size (microcephaly). Microcephaly is mainly caused by genetic mutations, especially genes encoding proteins involved in centrosomes and DNA repair pathways. However, it can also be induced by exposure to ionizing radiation and intrauterine infections such as the Zika virus. This review explains mammalian cortical development and the major DNA repair pathways that may lead to microcephaly when impaired. Next, we discuss the mechanisms and possible exposures leading to DNA damage and p53 hyperactivation culminating in microcephaly.
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Affiliation(s)
- Jessica Honorato Ribeiro
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Nazlican Altinisik
- Laboratory for Centrosome and Cytoskeleton Biology, Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Nicholas Rajan
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Mieke Verslegers
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jay Gopalakrishnan
- Laboratory for Centrosome and Cytoskeleton Biology, Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Roel Quintens
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
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Gohil D, Sarker AH, Roy R. Base Excision Repair: Mechanisms and Impact in Biology, Disease, and Medicine. Int J Mol Sci 2023; 24:14186. [PMID: 37762489 PMCID: PMC10531636 DOI: 10.3390/ijms241814186] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Base excision repair (BER) corrects forms of oxidative, deamination, alkylation, and abasic single-base damage that appear to have minimal effects on the helix. Since its discovery in 1974, the field has grown in several facets: mechanisms, biology and physiology, understanding deficiencies and human disease, and using BER genes as potential inhibitory targets to develop therapeutics. Within its segregation of short nucleotide (SN-) and long patch (LP-), there are currently six known global mechanisms, with emerging work in transcription- and replication-associated BER. Knockouts (KOs) of BER genes in mouse models showed that single glycosylase knockout had minimal phenotypic impact, but the effects were clearly seen in double knockouts. However, KOs of downstream enzymes showed critical impact on the health and survival of mice. BER gene deficiency contributes to cancer, inflammation, aging, and neurodegenerative disorders. Medicinal targets are being developed for single or combinatorial therapies, but only PARP and APE1 have yet to reach the clinical stage.
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Affiliation(s)
- Dhara Gohil
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA;
| | - Altaf H. Sarker
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA;
| | - Rabindra Roy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA;
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Islam A, Chakraborty A, Gambardella S, Campopiano R, Sarker AH, Boldogh I, Hazra T. Functional analysis of a conserved site mutation in the DNA processing enzyme PNKP leading to Ataxia with Oculomotor Apraxia type 4 (AOA4) in humans. J Biol Chem 2023; 299:104714. [PMID: 37061005 DOI: 10.1016/j.jbc.2023.104714] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 04/17/2023] Open
Abstract
Polynucleotide kinase 3'-phosphatase (PNKP), an essential DNA end-processing enzyme in mammals with 3'-phosphatase and 5'-kinase activities, plays a pivotal role in multiple DNA repair pathways. Its functional deficiency has been etiologically linked to various neurological disorders. Recent reports have shown that mutation at a conserved Glutamine (Gln) in PNKP leads to late-onset Ataxia with Oculomotor Apraxia type 4 (AOA4) in humans, and embryonic lethality in pigs. However, the molecular mechanism underlying such phenotypes remains elusive. Here, we report that the enzymatic activities of the mutant vs. wild-type PNKP are comparable; however, cells expressing mutant PNKP as well as Peripheral Blood Mononuclear Cells (PBMCs) of AOA4 patients showed a significant amount of DNA double-strand break (DSB) accumulation and consequent activation of the DNA damage response (DDR). Further investigation revealed that the nuclear localization of mutant PNKP is severely abrogated, and the mutant proteins remain primarily in the cytoplasm. Western blot analysis of AOA4 patient-derived PBMCs also revealed the presence of mutated PNKP predominantly in the cytoplasm. To understand the molecular determinants, we identified that mutation at a conserved Gln residue impedes the interaction of PNKP with importin alpha, but not with importin beta, two highly conserved proteins that mediate the import of proteins from the cytoplasm into the nucleus. Collectively, our data suggest that the absence of PNKP in the nucleus leads to constant activation of the DDR due to persistent accumulation of DSBs in the mutant cells, triggering death of vulnerable brain cells-a potential cause of neurodegeneration in AOA4 patients.
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Affiliation(s)
- Azharul Islam
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Anirban Chakraborty
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Stefano Gambardella
- IRCCS Neuromed & Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Rosa Campopiano
- IRCCS Neuromed & Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Altaf H Sarker
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Tapas Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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Barbu MC, Harris M, Shen X, Aleks S, Green C, Amador C, Walker R, Morris S, Adams M, Sandu A, McNeil C, Waiter G, Evans K, Campbell A, Wardlaw J, Steele D, Murray A, Porteous D, McIntosh A, Whalley H. Epigenome-wide association study of global cortical volumes in generation Scotland: Scottish family health study. Epigenetics 2022; 17:1143-1158. [PMID: 34738878 PMCID: PMC9542280 DOI: 10.1080/15592294.2021.1997404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 01/22/2023] Open
Abstract
A complex interplay of genetic and environmental risk factors influence global brain structural alterations associated with brain health and disease. Epigenome-wide association studies (EWAS) of global brain imaging phenotypes have the potential to reveal the mechanisms of brain health and disease and can lead to better predictive analytics through the development of risk scores.We perform an EWAS of global brain volumes in Generation Scotland using peripherally measured whole blood DNA methylation (DNAm) from two assessments, (i) at baseline recruitment, ~6 years prior to MRI assessment (N = 672) and (ii) concurrent with MRI assessment (N=565). Four CpGs at baseline were associated with global cerebral white matter, total grey matter, and whole-brain volume (Bonferroni p≤7.41×10-8, βrange = -1.46x10-6 to 9.59 × 10-7). These CpGs were annotated to genes implicated in brain-related traits, including psychiatric disorders, development, and ageing. We did not find significant associations in the meta-analysis of the EWAS of the two sets concurrent with imaging at the corrected level.These findings reveal global brain structural changes associated with DNAm measured ~6 years previously, indicating a potential role of early DNAm modifications in brain structure. Although concurrent DNAm was not associated with global brain structure, the nominally significant findings identified here present a rationale for future investigation of associations between DNA methylation and structural brain phenotypes in larger population-based samples.
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Affiliation(s)
- Miruna Carmen Barbu
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Mat Harris
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Xueyi Shen
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Stolicyn Aleks
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Claire Green
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Carmen Amador
- Mrc Human Genetics Unit, Institute of Genetics and Cancer, the University of Edinburgh, UK
| | - Rosie Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, the University of Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | - Stewart Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, the University of Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | - Mark Adams
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Anca Sandu
- Aberdeen Biomedical Imaging Centre, The Institute of Medical Sciences, University of Aberdeen, UK
| | - Christopher McNeil
- Aberdeen Biomedical Imaging Centre, The Institute of Medical Sciences, University of Aberdeen, UK
| | - Gordon Waiter
- Aberdeen Biomedical Imaging Centre, The Institute of Medical Sciences, University of Aberdeen, UK
| | - Kathryn Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, the University of Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | - Archie Campbell
- Mrc Human Genetics Unit, Institute of Genetics and Cancer, the University of Edinburgh, UK
| | - Joanna Wardlaw
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | - Douglas Steele
- Imaging Science and Technology, School of Medicine, University of Dundee, DundeeUK
| | - Alison Murray
- Aberdeen Biomedical Imaging Centre, The Institute of Medical Sciences, University of Aberdeen, UK
| | - David Porteous
- Mrc Human Genetics Unit, Institute of Genetics and Cancer, the University of Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, UK
| | - Andrew McIntosh
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, School of Philosophy, Psychology and Language Sciences, The University of Edinburgh, UK
| | - Heather Whalley
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
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Li X, Cao G, Liu X, Tang TS, Guo C, Liu H. Polymerases and DNA Repair in Neurons: Implications in Neuronal Survival and Neurodegenerative Diseases. Front Cell Neurosci 2022; 16:852002. [PMID: 35846567 PMCID: PMC9279898 DOI: 10.3389/fncel.2022.852002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/23/2022] [Indexed: 12/22/2022] Open
Abstract
Most of the neurodegenerative diseases and aging are associated with reactive oxygen species (ROS) or other intracellular damaging agents that challenge the genome integrity of the neurons. As most of the mature neurons stay in G0/G1 phase, replication-uncoupled DNA repair pathways including BER, NER, SSBR, and NHEJ, are pivotal, efficient, and economic mechanisms to maintain genomic stability without reactivating cell cycle. In these progresses, polymerases are prominent, not only because they are responsible for both sensing and repairing damages, but also for their more diversified roles depending on the cell cycle phase and damage types. In this review, we summarized recent knowledge on the structural and biochemical properties of distinct polymerases, including DNA and RNA polymerases, which are known to be expressed and active in nervous system; the biological relevance of these polymerases and their interactors with neuronal degeneration would be most graphically illustrated by the neurological abnormalities observed in patients with hereditary diseases associated with defects in DNA repair; furthermore, the vicious cycle of the trinucleotide repeat (TNR) and impaired DNA repair pathway is also discussed. Unraveling the mechanisms and contextual basis of the role of the polymerases in DNA damage response and repair will promote our understanding about how long-lived postmitotic cells cope with DNA lesions, and why disrupted DNA repair contributes to disease origin, despite the diversity of mutations in genes. This knowledge may lead to new insight into the development of targeted intervention for neurodegenerative diseases.
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Affiliation(s)
- Xiaoling Li
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Xiaoling Li
| | - Guanghui Cao
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
| | - Xiaokang Liu
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Caixia Guo
- Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- *Correspondence: Caixia Guo
| | - Hongmei Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Hongmei Liu
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Zika Virus Induces Mitotic Catastrophe in Human Neural Progenitors by Triggering Unscheduled Mitotic Entry in the Presence of DNA Damage While Functionally Depleting Nuclear PNKP. J Virol 2022; 96:e0033322. [PMID: 35412344 PMCID: PMC9093132 DOI: 10.1128/jvi.00333-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Vertical transmission of Zika virus (ZIKV) leads with high frequency to congenital ZIKV syndrome (CZS), whose worst outcome is microcephaly. However, the mechanisms of congenital ZIKV neurodevelopmental pathologies, including direct cytotoxicity to neural progenitor cells (NPC), placental insufficiency, and immune responses, remain incompletely understood. At the cellular level, microcephaly typically results from death or insufficient proliferation of NPC or cortical neurons. NPC replicate fast, requiring efficient DNA damage responses to ensure genome stability. Like congenital ZIKV infection, mutations in the polynucleotide 5′-kinase 3′-phosphatase (PNKP) gene, which encodes a critical DNA damage repair enzyme, result in recessive syndromes often characterized by congenital microcephaly with seizures (MCSZ). We thus tested whether there were any links between ZIKV and PNKP. Here, we show that two PNKP phosphatase inhibitors or PNKP knockout inhibited ZIKV replication. PNKP relocalized from the nucleus to the cytoplasm in infected cells, colocalizing with the marker of ZIKV replication factories (RF) NS1 and resulting in functional nuclear PNKP depletion. Although infected NPC accumulated DNA damage, they failed to activate the DNA damage checkpoint kinases Chk1 and Chk2. ZIKV also induced activation of cytoplasmic CycA/CDK1 complexes, which trigger unscheduled mitotic entry. Inhibition of CDK1 activity inhibited ZIKV replication and the formation of RF, supporting a role of cytoplasmic CycA/CDK1 in RF morphogenesis. In brief, ZIKV infection induces mitotic catastrophe resulting from unscheduled mitotic entry in the presence of DNA damage. PNKP and CycA/CDK1 are thus host factors participating in ZIKV replication in NPC, and pathogenesis to neural progenitor cells. IMPORTANCE The 2015–2017 Zika virus (ZIKV) outbreak in Brazil and subsequent international epidemic revealed the strong association between ZIKV infection and congenital malformations, mostly neurodevelopmental defects up to microcephaly. The scale and global expansion of the epidemic, the new ZIKV outbreaks (Kerala state, India, 2021), and the potential burden of future ones pose a serious ongoing risk. However, the cellular and molecular mechanisms resulting in microcephaly remain incompletely understood. Here, we show that ZIKV infection of neuronal progenitor cells results in cytoplasmic sequestration of an essential DNA repair protein itself associated with microcephaly, with the consequent accumulation of DNA damage, together with an unscheduled activation of cytoplasmic CDK1/Cyclin A complexes in the presence of DNA damage. These alterations result in mitotic catastrophe of neuronal progenitors, which would lead to a depletion of cortical neurons during development.
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9
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Jiang B, Murray C, Cole BL, Glover JNM, Chan GK, Deschenes J, Mani RS, Subedi S, Nerva JD, Wang AC, Lockwood CM, Mefford HC, Leary SES, Ojemann JG, Weinfeld M, Ene CI. Mutations of the DNA repair gene PNKP in a patient with microcephaly, seizures, and developmental delay (MCSZ) presenting with a high-grade brain tumor. Sci Rep 2022; 12:5386. [PMID: 35354845 PMCID: PMC8967877 DOI: 10.1038/s41598-022-09097-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 03/04/2022] [Indexed: 11/08/2022] Open
Abstract
Polynucleotide Kinase-Phosphatase (PNKP) is a bifunctional enzyme that possesses both DNA 3'-phosphatase and DNA 5'-kinase activities, which are required for processing termini of single- and double-strand breaks generated by reactive oxygen species (ROS), ionizing radiation and topoisomerase I poisons. Even though PNKP is central to DNA repair, there have been no reports linking PNKP mutations in a Microcephaly, Seizures, and Developmental Delay (MSCZ) patient to cancer. Here, we characterized the biochemical significance of 2 germ-line point mutations in the PNKP gene of a 3-year old male with MSCZ who presented with a high-grade brain tumor (glioblastoma multiforme) within the cerebellum. Functional and biochemical studies demonstrated these PNKP mutations significantly diminished DNA kinase/phosphatase activities, altered its cellular distribution, caused defective repair of DNA single/double stranded breaks, and were associated with a higher propensity for oncogenic transformation. Our findings indicate that specific PNKP mutations may contribute to tumor initiation within susceptible cells in the CNS by limiting DNA damage repair and increasing rates of spontaneous mutations resulting in pediatric glioma associated driver mutations such as ATRX and TP53.
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Affiliation(s)
- Bingcheng Jiang
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada
| | - Cameron Murray
- Department of Biochemistry, University of Alberta, Medical Sciences Building, Edmonton, AB, T6G 2H7, Canada
| | - Bonnie L Cole
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Medical Sciences Building, Edmonton, AB, T6G 2H7, Canada
| | - Gordon K Chan
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada
| | - Jean Deschenes
- Department of Laboratory Medicine and Pathology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada
| | - Rajam S Mani
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada
| | - Sudip Subedi
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada
| | - John D Nerva
- Department of Neurological Surgery, Tulane University, New Orleans, LA, USA
| | - Anthony C Wang
- Department of Neurological Surgery, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Heather C Mefford
- Division of Genetics Medicine, University of Washington, Seattle, WA, USA
| | - Sarah E S Leary
- Division of Pediatric Hematology/Oncology, Seattle Children's Hospital, Seattle, WA, USA
| | - Jeffery G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada.
| | - Chibawanye I Ene
- Department of Neurological Surgery, MD Anderson Cancer Center, Houston, TX, USA.
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10
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Prenatal phenotype of PNKP-related primary microcephaly associated with variants affecting both the FHA and phosphatase domain. Eur J Hum Genet 2021; 30:101-110. [PMID: 34697416 PMCID: PMC8738728 DOI: 10.1038/s41431-021-00982-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/05/2021] [Accepted: 10/04/2021] [Indexed: 11/20/2022] Open
Abstract
Biallelic PNKP variants cause heterogeneous disorders ranging from neurodevelopmental disorder with microcephaly/seizures to adult-onset Charcot–Marie–Tooth disease. To date, only postnatal descriptions exist. We present the first prenatal diagnosis of PNKP-related primary microcephaly. Pathological examination of a male fetus in the 18th gestational week revealed micrencephaly with extracerebral malformations and thus presumed syndromic microcephaly. A recessive disorder was suspected because of previous pregnancy termination for similar abnormalities. Prenatal trio-exome sequencing identified compound heterozygosity for the PNKP variants c.498G>A, p.[(=),0?] and c.302C>T, p.(Pro101Leu). Segregation confirmed both variants in the sister fetus. Through RNA analyses, we characterized exon 4 skipping affecting the PNKP forkhead-associated (FHA) and phosphatase domains (p.Leu67_Lys166del) as the predominant effect of the paternal c.498G>A variant. We retrospectively investigated two unrelated individuals diagnosed with biallelic PNKP-variants to compare prenatal/postnatal phenotypes. Both carry the splice donor variant c.1029+2T>C intrans with a variant in the FHA domain (c.311T>C, p.(Leu104Pro); c.151G>C, p.(Val51Leu)). RNA-seq showed complex splicing for c.1029+2T>C and c.151G>C. Structural modeling revealed significant clustering of missense variants in the FHA domain with variants generating structural damage. Our clinical description extends the PNKP-continuum to the prenatal stage. Investigating possible PNKP-variant effects using RNA and structural modeling, we highlight the mutational complexity and exemplify a PNKP-variant characterization framework.
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11
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Shin W, Alpaugh W, Hallihan LJ, Sinha S, Crowther E, Martin GR, Scheidl-Yee T, Yang X, Yoon G, Goldsmith T, Berger ND, de Almeida LG, Dufour A, Dobrinski I, Weinfeld M, Jirik FR, Biernaskie J. PNKP is required for maintaining the integrity of progenitor cell populations in adult mice. Life Sci Alliance 2021; 4:4/9/e202000790. [PMID: 34226276 PMCID: PMC8321660 DOI: 10.26508/lsa.202000790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 11/24/2022] Open
Abstract
Knockout of Pnkp in adult mice impairs the growth of hair follicle, spermatogonial, and neural progenitor populations. DNA repair proteins are critical to the maintenance of genomic integrity. Specific types of genotoxic factors, including reactive oxygen species generated during normal cellular metabolism or as a result of exposure to exogenous oxidative agents, frequently leads to “ragged” single-strand DNA breaks. The latter exhibits abnormal free DNA ends containing either a 5′-hydroxyl or 3′-phosphate requiring correction by the dual function enzyme, polynucleotide kinase phosphatase (PNKP), before DNA polymerase and ligation reactions can occur to seal the break. Pnkp gene deletion during early murine development leads to lethality; in contrast, the role of PNKP in adult mice is unknown. To investigate the latter, we used an inducible conditional mutagenesis approach to cause global disruption of the Pnkp gene in adult mice. This resulted in a premature aging-like phenotype, characterized by impaired growth of hair follicles, seminiferous tubules, and neural progenitor cell populations. These results point to an important role for PNKP in maintaining the normal growth and survival of these murine progenitor populations.
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Affiliation(s)
- Wisoo Shin
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | - Whitney Alpaugh
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | - Laura J Hallihan
- McCaig Institute for Bone and Joint Health, Calgary, Canada.,Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Sarthak Sinha
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | - Emilie Crowther
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | - Gary R Martin
- McCaig Institute for Bone and Joint Health, Calgary, Canada.,Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | | | - Xiaoyan Yang
- Department of Oncology, University of Alberta, and Cross Cancer Institute, Edmonton, Canada
| | - Grace Yoon
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | - Taylor Goldsmith
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | - Nelson D Berger
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Luiz Gn de Almeida
- McCaig Institute for Bone and Joint Health, Calgary, Canada.,Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Antoine Dufour
- McCaig Institute for Bone and Joint Health, Calgary, Canada.,Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada.,Department of Physiology and Pharmacology, University of Calgary, Calgary, Canada
| | - Ina Dobrinski
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, and Cross Cancer Institute, Edmonton, Canada
| | - Frank R Jirik
- McCaig Institute for Bone and Joint Health, Calgary, Canada .,Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, Calgary, Canada
| | - Jeff Biernaskie
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada .,Department of Physiology and Pharmacology, University of Calgary, Calgary, Canada.,Department of Surgery, University of Calgary, Calgary, Canada.,Hotchkiss Brain Institute, Calgary, Canada
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12
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Morozko EL, Smith-Geater C, Monteys AM, Pradhan S, Lim RG, Langfelder P, Kachemov M, Kulkarni JA, Zaifman J, Hill A, Stocksdale JT, Cullis PR, Wu J, Ochaba J, Miramontes R, Chakraborty A, Hazra TK, Lau A, St-Cyr S, Orellana I, Kopan L, Wang KQ, Yeung S, Leavitt BR, Reidling JC, Yang XW, Steffan JS, Davidson BL, Sarkar PS, Thompson LM. PIAS1 modulates striatal transcription, DNA damage repair, and SUMOylation with relevance to Huntington's disease. Proc Natl Acad Sci U S A 2021; 118:e2021836118. [PMID: 33468657 PMCID: PMC7848703 DOI: 10.1073/pnas.2021836118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DNA damage repair genes are modifiers of disease onset in Huntington's disease (HD), but how this process intersects with associated disease pathways remains unclear. Here we evaluated the mechanistic contributions of protein inhibitor of activated STAT-1 (PIAS1) in HD mice and HD patient-derived induced pluripotent stem cells (iPSCs) and find a link between PIAS1 and DNA damage repair pathways. We show that PIAS1 is a component of the transcription-coupled repair complex, that includes the DNA damage end processing enzyme polynucleotide kinase-phosphatase (PNKP), and that PIAS1 is a SUMO E3 ligase for PNKP. Pias1 knockdown (KD) in HD mice had a normalizing effect on HD transcriptional dysregulation associated with synaptic function and disease-associated transcriptional coexpression modules enriched for DNA damage repair mechanisms as did reduction of PIAS1 in HD iPSC-derived neurons. KD also restored mutant HTT-perturbed enzymatic activity of PNKP and modulated genomic integrity of several transcriptionally normalized genes. The findings here now link SUMO modifying machinery to DNA damage repair responses and transcriptional modulation in neurodegenerative disease.
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Affiliation(s)
- Eva L Morozko
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697
| | - Charlene Smith-Geater
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
| | - Alejandro Mas Monteys
- Raymond G. Perelman Center for Cell and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Subrata Pradhan
- Department of Neurology, University of Texas Medical Branch, Galveston, TX 77555
| | - Ryan G Lim
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
| | - Peter Langfelder
- Department of Human Genetics, David Geffen School of Medicine at University of California, Los Angeles, CA 90095
| | - Marketta Kachemov
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697
| | - Jayesh A Kulkarni
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Josh Zaifman
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
| | - Austin Hill
- Incisive Genetics Inc., Vancouver, BC, Canada V6A 0H9
| | | | - Pieter R Cullis
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
- NanoMedicines Innovation Network, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, CA 92697
| | - Joseph Ochaba
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697
| | - Ricardo Miramontes
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
| | - Anirban Chakraborty
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555
| | - Tapas K Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555
| | - Alice Lau
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
| | - Sophie St-Cyr
- Raymond G. Perelman Center for Cell and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Iliana Orellana
- Sue and Bill Gross Stem Cell Institute, University of California, Irvine, CA 92697
| | - Lexi Kopan
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
| | - Keona Q Wang
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
| | - Sylvia Yeung
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Jack C Reidling
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
| | - X William Yang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095
| | - Joan S Steffan
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
| | - Beverly L Davidson
- Raymond G. Perelman Center for Cell and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Partha S Sarkar
- Department of Neurology, University of Texas Medical Branch, Galveston, TX 77555
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Leslie M Thompson
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697;
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
- Department of Biological Chemistry, University of California, Irvine, CA 92697
- Sue and Bill Gross Stem Cell Institute, University of California, Irvine, CA 92697
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13
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Bermúdez-Guzmán L, Jimenez-Huezo G, Arguedas A, Leal A. Mutational survivorship bias: The case of PNKP. PLoS One 2020; 15:e0237682. [PMID: 33332469 PMCID: PMC7746193 DOI: 10.1371/journal.pone.0237682] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/23/2020] [Indexed: 01/21/2023] Open
Abstract
The molecular function of a protein relies on its structure. Understanding how variants alter structure and function in multidomain proteins is key to elucidate the generation of a pathological phenotype. However, one may fall into the logical bias of assessing protein damage only based on the variants that are visible (survivorship bias), which can lead to partial conclusions. This is the case of PNKP, an important nuclear and mitochondrial DNA repair enzyme with both kinase and phosphatase function. Most variants in PNKP are confined to the kinase domain, leading to a pathological spectrum of three apparently distinct clinical entities. Since proteins and domains may have a different tolerability to variation, we evaluated whether variants in PNKP are under survivorship bias. Here, we provide the evidence that supports a higher tolerance in the kinase domain even when all variants reported are deleterious. Instead, the phosphatase domain is less tolerant due to its lower variant rates, a higher degree of sequence conservation, lower dN/dS ratios, and the presence of more disease-propensity hotspots. Together, our results support previous experimental evidence that demonstrated that the phosphatase domain is functionally more necessary and relevant for DNA repair, especially in the context of the development of the central nervous system. Finally, we propose the term "Wald’s domain" for future studies analyzing the possible survivorship bias in multidomain proteins.
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Affiliation(s)
- Luis Bermúdez-Guzmán
- Section of Genetics and Biotechnology, School of Biology, University de Costa Rica, San Pedro, San José, Costa Rica
| | - Gabriel Jimenez-Huezo
- Section of Genetics and Biotechnology, School of Biology, University de Costa Rica, San Pedro, San José, Costa Rica
| | - Andrés Arguedas
- School of Statistics, University de Costa Rica, San Pedro, San José, Costa Rica
| | - Alejandro Leal
- Section of Genetics and Biotechnology, School of Biology, University de Costa Rica, San Pedro, San José, Costa Rica
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14
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Garrelfs MR, Takada S, Kamsteeg EJ, Pegge S, Mancini G, Engelen M, van de Warrenburg B, Rennings A, van Gaalen J, Peters I, Weemaes C, van der Burg M, Willemsen MA. The Phenotypic Spectrum of PNKP-Associated Disease and the Absence of Immunodeficiency and Cancer Predisposition in a Dutch Cohort. Pediatr Neurol 2020; 113:26-32. [PMID: 32980744 DOI: 10.1016/j.pediatrneurol.2020.07.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/19/2020] [Accepted: 07/23/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND We aimed to expand the number of currently known pathogenic PNKP mutations, to study the phenotypic spectrum, including radiological characteristics and genotype-phenotype correlations, and to assess whether immunodeficiency and increased cancer risk are part of the DNA repair disorder caused by mutations in the PNKP gene. METHODS We evaluated nine patients with PNKP mutations. A neurological history and examination was obtained. All patients had undergone neuroimaging and genetic testing as part of the prior diagnostic process. Laboratory measurements included potential biomarkers, and, in the context of a DNA repair disorder, we performed a detailed immunologic evaluation, including B cell repertoire analysis. RESULTS We identified three new mutations in the PNKP gene and confirm the phenotypic spectrum of PNKP-associated disease, ranging from microcephaly, seizures, and developmental delay to ataxia with oculomotor apraxia type 4. Irrespective of the phenotype, alpha-fetoprotein is a biochemical marker and increases with age and progression of the disease. On neuroimaging, (progressive) cerebellar atrophy was a universal feature. No clinical signs of immunodeficiency were present, and immunologic assessment was unremarkable. One patient developed cancer, but this was attributed to a concurrent von Hippel-Lindau mutation. CONCLUSIONS Immunodeficiency and cancer predisposition do not appear to be part of PNKP-associated disease, contrasting many other DNA repair disorders. Furthermore, our study illustrates that the previously described syndromes microcephaly, seizures, and developmental delay, and ataxia with oculomotor apraxia type 4, represent the extremes of an overlapping spectrum of disease. Cerebellar atrophy and elevated serum alpha-fetoprotein levels are early diagnostic findings across the entire phenotypical spectrum.
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Affiliation(s)
- Mark R Garrelfs
- Department of Pediatrics, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Sanami Takada
- Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sjoert Pegge
- Department of Radiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Grazia Mancini
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marc Engelen
- Department of Pediatric Neurology, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Bart van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition, and Behaviour, Nijmegen, the Netherlands
| | - Alexander Rennings
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Judith van Gaalen
- Department of Neurology, Donders Institute for Brain, Cognition, and Behaviour, Nijmegen, the Netherlands
| | - Ivo Peters
- Department of Neurology, Donders Institute for Brain, Cognition, and Behaviour, Nijmegen, the Netherlands
| | - Corry Weemaes
- Department of Pediatrics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mirjam van der Burg
- Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Michèl A Willemsen
- Department of Pediatrics, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Pediatric Neurology, Radboud University Medical Center, Amalia Children's Hospital and Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
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15
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The FHA domain of PNKP is essential for its recruitment to DNA damage sites and maintenance of genome stability. Mutat Res 2020; 822:111727. [PMID: 33220551 DOI: 10.1016/j.mrfmmm.2020.111727] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/28/2020] [Accepted: 10/26/2020] [Indexed: 01/08/2023]
Abstract
Polynucleotide kinase phosphatase (PNKP) has dual enzymatic activities as kinase and phosphatase for DNA ends, which are the prerequisite for the ligation, and thus is involved in base excision repair, single-strand break repair and non-homologous end joining for double-strand break (DSB) repair. In this study, we examined mechanisms for the recruitment of PNKP to DNA damage sites by laser micro-irradiation and live-cell imaging analysis using confocal microscope. We show that the forkhead-associated (FHA) domain of PNKP is essential for the recruitment of PNKP to DNA damage sites. Arg35 and Arg48 within the FHA domain are required for interactions with XRCC1 and XRCC4. PNKP R35A/R48A mutant failed to accumulate on the laser track and siRNA-mediated depletion of XRCC1 and/or XRCC4 reduced PNKP accumulation on the laser track, indicating that PNKP is recruited to DNA damage sites via the interactions between its FHA domain and XRCC1 or XRCC4. Furthermore, cells expressing PNKP R35A/R48A mutant exhibited increased sensitivity toward ionizing radiation in association with delayed SSB and DSB repair and genome instability, represented by micronuclei and chromosome bridges. Taken together, these findings revealed the importance of PNKP recruitment to DNA damage sites via its FHA domain for DNA repair and maintenance of genome stability.
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16
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Tsukada K, Matsumoto Y, Shimada M. Linker region is required for efficient nuclear localization of polynucleotide kinase phosphatase. PLoS One 2020; 15:e0239404. [PMID: 32970693 PMCID: PMC7514006 DOI: 10.1371/journal.pone.0239404] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 09/05/2020] [Indexed: 01/10/2023] Open
Abstract
Polynucleotide kinase phosphatase (PNKP) is a DNA repair factor with dual enzymatic functions, i.e., phosphorylation of 5’-end and dephosphorylation of 3’-end, which are prerequisites for DNA ligation and, thus, is involved in multiple DNA repair pathways, i.e., base excision repair, single-strand break repair and double-strand break repair through non-homologous end joining. Mutations in PNKP gene causes inherited diseases, such as microcephaly and seizure (MCSZ) by neural developmental failure and ataxia with oculomotor apraxia 4 (AOA4) and Charcot-Marie-Tooth disease 2B2 (CMT2B2) by neurodegeneration. PNKP consists of the Forkhead-associated (FHA) domain, linker region, phosphatase domain and kinase domain. Although the functional importance of PNKP interaction with XRCC1 and XRCC4 through the FHA domain and that of phosphatase and kinase enzyme activities have been well established, little is known about the function of linker region. In this study, we identified a functional putative nuclear localization signal (NLS) of PNKP located in the linker region, and showed that lysine 138 (K138), arginine 139 (R139) and arginine 141 (R141) residues therein are critically important for nuclear localization. Furthermore, double mutant of K138A and R35A, the latter of which mutates arginine 35, central amino acid of FHA domain, showed additive effect on nuclear localization, indicating that the FHA domain as well as the NLS is important for PNKP nuclear localization. Thus, this study revealed two distinct mechanisms regulating nuclear localization and subnuclear distribution of PNKP. These findings would contribute to deeper understanding of a variety of DNA repair pathway, i.e., base excision repair, single-strand break repair and double-strand break repair.
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Affiliation(s)
- Kaima Tsukada
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Yoshihisa Matsumoto
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Mikio Shimada
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
- * E-mail:
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17
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Kalasova I, Hailstone R, Bublitz J, Bogantes J, Hofmann W, Leal A, Hanzlikova H, Caldecott KW. Pathological mutations in PNKP trigger defects in DNA single-strand break repair but not DNA double-strand break repair. Nucleic Acids Res 2020; 48:6672-6684. [PMID: 32504494 PMCID: PMC7337934 DOI: 10.1093/nar/gkaa489] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/30/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022] Open
Abstract
Hereditary mutations in polynucleotide kinase-phosphatase (PNKP) result in a spectrum of neurological pathologies ranging from neurodevelopmental dysfunction in microcephaly with early onset seizures (MCSZ) to neurodegeneration in ataxia oculomotor apraxia-4 (AOA4) and Charcot-Marie-Tooth disease (CMT2B2). Consistent with this, PNKP is implicated in the repair of both DNA single-strand breaks (SSBs) and DNA double-strand breaks (DSBs); lesions that can trigger neurodegeneration and neurodevelopmental dysfunction, respectively. Surprisingly, however, we did not detect a significant defect in DSB repair (DSBR) in primary fibroblasts from PNKP patients spanning the spectrum of PNKP-mutated pathologies. In contrast, the rate of SSB repair (SSBR) is markedly reduced. Moreover, we show that the restoration of SSBR in patient fibroblasts collectively requires both the DNA kinase and DNA phosphatase activities of PNKP, and the fork-head associated (FHA) domain that interacts with the SSBR protein, XRCC1. Notably, however, the two enzymatic activities of PNKP appear to affect different aspects of disease pathology, with reduced DNA phosphatase activity correlating with neurodevelopmental dysfunction and reduced DNA kinase activity correlating with neurodegeneration. In summary, these data implicate reduced rates of SSBR, not DSBR, as the source of both neurodevelopmental and neurodegenerative pathology in PNKP-mutated disease, and the extent and nature of this reduction as the primary determinant of disease severity.
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Affiliation(s)
- Ilona Kalasova
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic
| | - Richard Hailstone
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Janin Bublitz
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Jovel Bogantes
- Servicio de Cirugía Reconstructiva, Hospital Rafael Ángel Calderón Guardia, Caja Costarricense de Seguro Social, San José, Costa Rica
| | - Winfried Hofmann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Alejandro Leal
- Section of Genetics and Biotechnology, School of Biology, University of Costa Rica, San José, Costa Rica
| | - Hana Hanzlikova
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic.,Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Keith W Caldecott
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic.,Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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18
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Kim J, Kim K, Mo JS, Lee Y. Atm deficiency in the DNA polymerase β null cerebellum results in cerebellar ataxia and Itpr1 reduction associated with alteration of cytosine methylation. Nucleic Acids Res 2020; 48:3678-3691. [PMID: 32123907 PMCID: PMC7144915 DOI: 10.1093/nar/gkaa140] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 02/20/2020] [Accepted: 02/27/2020] [Indexed: 12/13/2022] Open
Abstract
Genomic instability resulting from defective DNA damage responses or repair causes several abnormalities, including progressive cerebellar ataxia, for which the molecular mechanisms are not well understood. Here, we report a new murine model of cerebellar ataxia resulting from concomitant inactivation of POLB and ATM. POLB is one of key enzymes for the repair of damaged or chemically modified bases, including methylated cytosine, but selective inactivation of Polb during neurogenesis affects only a subpopulation of cortical interneurons despite the accumulation of DNA damage throughout the brain. However, dual inactivation of Polb and Atm resulted in ataxia without significant neuropathological defects in the cerebellum. ATM is a protein kinase that responds to DNA strand breaks, and mutations in ATM are responsible for Ataxia Telangiectasia, which is characterized by progressive cerebellar ataxia. In the cerebella of mice deficient for both Polb and Atm, the most downregulated gene was Itpr1, likely because of misregulated DNA methylation cycle. ITPR1 is known to mediate calcium homeostasis, and ITPR1 mutations result in genetic diseases with cerebellar ataxia. Our data suggest that dysregulation of ITPR1 in the cerebellum could be one of contributing factors to progressive ataxia observed in human genomic instability syndromes.
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Affiliation(s)
- Jusik Kim
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea.,Department of Biomedical Sciences, The Graduate School of Ajou University, Suwon 16499, Korea
| | - Keeeun Kim
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea.,Department of Biomedical Sciences, The Graduate School of Ajou University, Suwon 16499, Korea
| | - Jung-Soon Mo
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea.,Department of Biomedical Sciences, The Graduate School of Ajou University, Suwon 16499, Korea
| | - Youngsoo Lee
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea.,Department of Biomedical Sciences, The Graduate School of Ajou University, Suwon 16499, Korea
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19
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Kafer GR, Cesare AJ. A Survey of Essential Genome Stability Genes Reveals That Replication Stress Mitigation Is Critical for Peri-Implantation Embryogenesis. Front Cell Dev Biol 2020; 8:416. [PMID: 32548123 PMCID: PMC7274024 DOI: 10.3389/fcell.2020.00416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/05/2020] [Indexed: 12/16/2022] Open
Abstract
Murine development demands that pluripotent epiblast stem cells in the peri-implantation embryo increase from approximately 120 to 14,000 cells between embryonic days (E) 4.5 and E7.5. This is possible because epiblast stem cells can complete cell cycles in under 3 h in vivo. To ensure conceptus fitness, epiblast cells must undertake this proliferative feat while maintaining genome integrity. How epiblast cells maintain genome health under such an immense proliferation demand remains unclear. To illuminate the contribution of genome stability pathways to early mammalian development we systematically reviewed knockout mouse data from 347 DDR and repair associated genes. Cumulatively, the data indicate that while many DNA repair functions are dispensable in embryogenesis, genes encoding replication stress response and homology directed repair factors are essential specifically during the peri-implantation stage of early development. We discuss the significance of these findings in the context of the unique proliferative demands placed on pluripotent epiblast stem cells.
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Affiliation(s)
- Georgia R Kafer
- Genome Integrity Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
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Marcilla Vázquez C, Carrascosa Romero MDC, Martínez Gutiérrez A, Baquero Cano M, Alfaro Ponce B, Dabad Moreno MJ. A Novel c.968C > T homozygous Mutation in the Polynucleotide Kinase 3' - Phosphatase Gene Related to the Syndrome of Microcephaly, Seizures, and Developmental Delay. J Pediatr Genet 2020; 10:164-172. [PMID: 34040816 DOI: 10.1055/s-0040-1710540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/12/2020] [Indexed: 10/24/2022]
Abstract
Microcephaly is defined by a head circumference that is at least two standard deviations below the mean for age and sex of the general population in a specific race. Primary microcephaly may occur as an isolated inborn error, which may damage to the central nervous system or as part of the congenital abnormalities associated with genetic syndrome, affecting multiple organ systems. One of the syndromic forms consists of microcephaly, seizures, and developmental delay caused by biallelic mutations in the gene that encode polynucleotide kinase 3' - phosphatase protein (PNKP). In this article, we reported a newborn male who presented with microcephaly, severe developmental delay, and early-onset refractories seizures, caused by a novel homozygous mutation of the PNKP gene.
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Deficiency in classical nonhomologous end-joining-mediated repair of transcribed genes is linked to SCA3 pathogenesis. Proc Natl Acad Sci U S A 2020; 117:8154-8165. [PMID: 32205441 DOI: 10.1073/pnas.1917280117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Spinocerebellar ataxia type 3 (SCA3) is a dominantly inherited neurodegenerative disease caused by CAG (encoding glutamine) repeat expansion in the Ataxin-3 (ATXN3) gene. We have shown previously that ATXN3-depleted or pathogenic ATXN3-expressing cells abrogate polynucleotide kinase 3'-phosphatase (PNKP) activity. Here, we report that ATXN3 associates with RNA polymerase II (RNAP II) and the classical nonhomologous end-joining (C-NHEJ) proteins, including PNKP, along with nascent RNAs under physiological conditions. Notably, ATXN3 depletion significantly decreased global transcription, repair of transcribed genes, and error-free double-strand break repair of a 3'-phosphate-containing terminally gapped, linearized reporter plasmid. The missing sequence at the terminal break site was restored in the recircularized plasmid in control cells by using the endogenous homologous transcript as a template, indicating ATXN3's role in PNKP-mediated error-free C-NHEJ. Furthermore, brain extracts from SCA3 patients and mice show significantly lower PNKP activity, elevated p53BP1 level, more abundant strand-breaks in the transcribed genes, and degradation of RNAP II relative to controls. A similar RNAP II degradation is also evident in mutant ATXN3-expressing Drosophila larval brains and eyes. Importantly, SCA3 phenotype in Drosophila was completely amenable to PNKP complementation. Hence, salvaging PNKP's activity can be a promising therapeutic strategy for SCA3.
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Shimada M, Tsukada K, Kagawa N, Matsumoto Y. Reprogramming and differentiation-dependent transcriptional alteration of DNA damage response and apoptosis genes in human induced pluripotent stem cells. JOURNAL OF RADIATION RESEARCH 2019; 60:719-728. [PMID: 31665364 PMCID: PMC7357234 DOI: 10.1093/jrr/rrz057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/25/2019] [Accepted: 06/25/2019] [Indexed: 05/22/2023]
Abstract
Pluripotent stem cells (PSCs), such as embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), have a dual capability to self-renew and differentiate into all cell types necessary to develop an entire organism. Differentiation is associated with dynamic epigenetic alteration and transcriptional change, while self-renewal depends on maintaining the genome DNA accurately. Genome stability of PSCs is strictly regulated to maintain pluripotency. However, the DNA damage response (DDR) mechanism in PSCs is still unclear. There is accumulating evidence that genome stability and pluripotency are regulated by a transcriptional change in undifferentiated and differentiated states. iPSCs are ideal for analyzing transcriptional regulation during reprogramming and differentiation. This study aimed to elucidate the transcriptional alteration surrounding genome stability maintenance, including DNA repair, cell cycle checkpoints and apoptosis in fibroblasts, iPSCs and neural progenitor cells (NPCs) derived from iPSCs as differentiated cells. After ionizing radiation exposure, foci for the DNA double-stranded break marker γ-H2AX increased, peaking at 0.5 h in all cells (>90%), decreasing after 4 h in fibroblasts (32.3%) and NPCs (22.3%), but still remaining at 52.5% (NB1RGB C2 clone) and 54.7% (201B7 cells) in iPSCs. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL)-positive cells were detected, indicating that iPSCs' apoptosis increases. In addition, RNA sequencing (RNA-Seq) analysis showed high expression of apoptosis genes (TP53, CASP3 and BID) in iPSCs. Results suggested that increased apoptosis activity maintains accurate, undifferentiated genome DNA in the cell population.
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Affiliation(s)
- Mikio Shimada
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1, Oookayaka, Meguro-ku, 152-8550, Tokyo, Japan
- Corresponding author: Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1, Oookayaka, Meguro-ku, 152-8550, Tokyo, Japan. Tel: +81-3-5734-3703; Fax: +81-3-5734-3703.
| | - Kaima Tsukada
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1, Oookayaka, Meguro-ku, 152-8550, Tokyo, Japan
| | - Nozomi Kagawa
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1, Oookayaka, Meguro-ku, 152-8550, Tokyo, Japan
| | - Yoshihisa Matsumoto
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1, Oookayaka, Meguro-ku, 152-8550, Tokyo, Japan
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23
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Previtali SC, Zhao E, Lazarevic D, Pipitone GB, Fabrizi GM, Manganelli F, Mazzeo A, Pareyson D, Schenone A, Taroni F, Vita G, Bellone E, Ferrarini M, Garibaldi M, Magri S, Padua L, Pennisi E, Pisciotta C, Riva N, Scaioli V, Scarlato M, Tozza S, Geroldi A, Jordanova A, Ferrari M, Molineris I, Reilly MM, Comi G, Carrera P, Devoto M, Bolino A. Expanding the spectrum of genes responsible for hereditary motor neuropathies. J Neurol Neurosurg Psychiatry 2019; 90:1171-1179. [PMID: 31167812 DOI: 10.1136/jnnp-2019-320717] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/24/2019] [Accepted: 05/17/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Inherited peripheral neuropathies (IPNs) represent a broad group of genetically and clinically heterogeneous disorders, including axonal Charcot-Marie-Tooth type 2 (CMT2) and hereditary motor neuropathy (HMN). Approximately 60%-70% of cases with HMN/CMT2 still remain without a genetic diagnosis. Interestingly, mutations in HMN/CMT2 genes may also be responsible for motor neuron disorders or other neuromuscular diseases, suggesting a broad phenotypic spectrum of clinically and genetically related conditions. Thus, it is of paramount importance to identify novel causative variants in HMN/CMT2 patients to better predict clinical outcome and progression. METHODS We designed a collaborative study for the identification of variants responsible for HMN/CMT2. We collected 15 HMN/CMT2 families with evidence for autosomal recessive inheritance, who had tested negative for mutations in 94 known IPN genes, who underwent whole-exome sequencing (WES) analyses. Candidate genes identified by WES were sequenced in an additional cohort of 167 familial or sporadic HMN/CMT2 patients using next-generation sequencing (NGS) panel analysis. RESULTS Bioinformatic analyses led to the identification of novel or very rare variants in genes, which have not been previously associated with HMN/CMT2 (ARHGEF28, KBTBD13, AGRN and GNE); in genes previously associated with HMN/CMT2 but in combination with different clinical phenotypes (VRK1 and PNKP), and in the SIGMAR1 gene, which has been linked to HMN/CMT2 in only a few cases. These findings were further validated by Sanger sequencing, segregation analyses and functional studies. CONCLUSIONS These results demonstrate the broad spectrum of clinical phenotypes that can be associated with a specific disease gene, as well as the complexity of the pathogenesis of neuromuscular disorders.
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Affiliation(s)
- Stefano C Previtali
- Institute of Experimental Neurology (InSpe), Division of Neuroscience, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Edward Zhao
- Division of Genetics, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dejan Lazarevic
- Center for Translational Genomics and Bioinformatics, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Giovanni Battista Pipitone
- Laboratory of Clinical and Molecular Biology and Unit of Genomics for Diagnosis of Genetic Diseases, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Gian Maria Fabrizi
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Fiore Manganelli
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University Federico II of Naples, Napoli, Italy
| | - Anna Mazzeo
- Unit of Neurology and Neuromuscular Diseases, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Davide Pareyson
- Unit of Rare Neurodegenerative and Neurometabolic Diseases, Department of Clinical Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Angelo Schenone
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal Infantile Sciences, University of Genoa, and IRCCS Policlinico San Martino, Genova, Italy
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Giuseppe Vita
- Unit of Neurology and Neuromuscular Diseases, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Emilia Bellone
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal Infantile Sciences, University of Genoa, and IRCCS Policlinico San Martino, Genova, Italy
| | - Moreno Ferrarini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Matteo Garibaldi
- Unit of Neuromuscular Disorders, Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Sapienza University of Rome, Sant'Andrea Hospital, Roma, Italy
| | - Stefania Magri
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Luca Padua
- Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica, Roma, Italy
| | | | - Chiara Pisciotta
- Unit of Rare Neurodegenerative and Neurometabolic Diseases, Department of Clinical Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Nilo Riva
- Institute of Experimental Neurology (InSpe), Division of Neuroscience, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Vidmer Scaioli
- Neurophysiopathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Marina Scarlato
- Institute of Experimental Neurology (InSpe), Division of Neuroscience, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Stefano Tozza
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University Federico II of Naples, Napoli, Italy
| | - Alessandro Geroldi
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal Infantile Sciences, University of Genoa, and IRCCS Policlinico San Martino, Genova, Italy
| | - Albena Jordanova
- VIB-UAntwerp Center for Molecular Neurology, Antwerp, Belgium
- Department of Medical Chemistry and Biochemistry, Medical University-Sofia, Sofia, Bulgaria
| | - Maurizio Ferrari
- Laboratory of Clinical and Molecular Biology and Unit of Genomics for Diagnosis of Genetic Diseases, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Ivan Molineris
- Center for Translational Genomics and Bioinformatics, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Mary M Reilly
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Giancarlo Comi
- Institute of Experimental Neurology (InSpe), Division of Neuroscience, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Paola Carrera
- Laboratory of Clinical and Molecular Biology and Unit of Genomics for Diagnosis of Genetic Diseases, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Marcella Devoto
- Division of Genetics, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Translational and Precision Medicine, University La Sapienza, Roma, Italy
| | - Alessandra Bolino
- Institute of Experimental Neurology (InSpe), Division of Neuroscience, IRCCS Ospedale San Raffaele, Milano, Italy
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Gatti M, Magri S, Nanetti L, Sarto E, Di Bella D, Salsano E, Pantaleoni C, Mariotti C, Taroni F. From congenital microcephaly to adult onset cerebellar ataxia: Distinct and overlapping phenotypes in patients with PNKP gene mutations. Am J Med Genet A 2019; 179:2277-2283. [PMID: 31436889 DOI: 10.1002/ajmg.a.61339] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/07/2019] [Accepted: 08/09/2019] [Indexed: 12/23/2022]
Abstract
Pathogenic variants in polynucleotide kinase 3'-phosphatase (PNKP) gene have been associated with two distinct clinical presentations: autosomal recessive microcephaly, seizures, and developmental delay (MCSZ; MIM 613402) and ataxia with oculomotor apraxia type 4 (AOA4; MIM 616267). More than 40 patients have been reported so far, and their clinical presentations revealed a continuum phenotypic spectrum ranging from congenital microcephaly and early-onset intractable seizures, to adult onset slowly progressive sensory-motor neuropathy and cerebellar ataxia. We describe three unrelated Italian patients with different phenotypes and novel or recurrent pathogenic variants in PNKP gene. Patient 1, homozygous for the recurrent frameshift variant (p.Thr424Glyfs*49), had an early-onset MCSZ phenotype. Late in the disease progression, cerebellar ataxia and peripheral neuropathy were recognized. Patient 2, homozygous for a frameshift variant (p.Ala429Thrfs*42), presented a phenotype partially consistent with MCSZ including microcephaly and developmental delay, but without seizures. Patient 3 is one of the oldest patients described to date and presented polyneuropathy, and cerebellar signs. Biochemical tests showed abnormalities of cholesterol, albumin, or alpha-fetoprotein plasma levels. The clinical presentation of our patients encompassed early-to-adult-onset manifestations. For these cases, the long clinical follow-up allowed an in-depth phenotypic characterization and a better delineation of the natural history of patients carrying PNKP pathogenic variants.
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Affiliation(s)
- Marta Gatti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Stefania Magri
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Lorenzo Nanetti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Elisa Sarto
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniela Di Bella
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Ettore Salsano
- Unit of Neurodegenerative and Neurometabolic Rare Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Chiara Pantaleoni
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Caterina Mariotti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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25
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Bermúdez-Guzmán L, Leal A. DNA repair deficiency in neuropathogenesis: when all roads lead to mitochondria. Transl Neurodegener 2019; 8:14. [PMID: 31110700 PMCID: PMC6511134 DOI: 10.1186/s40035-019-0156-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/24/2019] [Indexed: 12/18/2022] Open
Abstract
Mutations in DNA repair enzymes can cause two neurological clinical manifestations: a developmental impairment and a degenerative disease. Polynucleotide kinase 3'-phosphatase (PNKP) is an enzyme that is actively involved in DNA repair in both single and double strand break repair systems. Mutations in this protein or others in the same pathway are responsible for a complex group of diseases with a broad clinical spectrum. Besides, mitochondrial dysfunction also has been consolidated as a hallmark of brain degeneration. Here we provide evidence that supports a shared role between mitochondrial dysfunction and DNA repair defects in the pathogenesis of the nervous system. As models, we analyze PNKP-related disorders, focusing on Charcot-Marie-Tooth disease and ataxia. A better understanding of the molecular dynamics of this relationship could provide improved diagnosis and treatment for neurological diseases.
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Affiliation(s)
- Luis Bermúdez-Guzmán
- Section of Genetics and Biotechnology, School of Biology, Universidad de Costa Rica, San José, 11501 Costa Rica
| | - Alejandro Leal
- Section of Genetics and Biotechnology, School of Biology, Universidad de Costa Rica, San José, 11501 Costa Rica
- Neuroscience Research Center, Universidad de Costa Rica, San José, Costa Rica
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26
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Kalasova I, Hanzlikova H, Gupta N, Li Y, Altmüller J, Reynolds JJ, Stewart GS, Wollnik B, Yigit G, Caldecott KW. Novel PNKP mutations causing defective DNA strand break repair and PARP1 hyperactivity in MCSZ. NEUROLOGY-GENETICS 2019; 5:e320. [PMID: 31041400 PMCID: PMC6454307 DOI: 10.1212/nxg.0000000000000320] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/07/2019] [Indexed: 11/29/2022]
Abstract
Objective To address the relationship between novel mutations in polynucleotide 5'-kinase 3'-phosphatase (PNKP), DNA strand break repair, and neurologic disease. Methods We have employed whole-exome sequencing, Sanger sequencing, and molecular/cellular biology. Results We describe here a patient with microcephaly with early onset seizures (MCSZ) from the Indian sub-continent harboring 2 novel mutations in PNKP, including a pathogenic mutation in the fork-head associated domain. In addition, we confirm that MCSZ is associated with hyperactivation of the single-strand break sensor protein protein poly (ADP-ribose) polymerase 1 (PARP1) following the induction of abortive topoisomerase I activity, a source of DNA strand breakage associated previously with neurologic disease. Conclusions These data expand the spectrum of PNKP mutations associated with MCSZ and show that PARP1 hyperactivation at unrepaired topoisomerase-induced DNA breaks is a molecular feature of this disease.
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Affiliation(s)
- Ilona Kalasova
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Hana Hanzlikova
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Neerja Gupta
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Yun Li
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Janine Altmüller
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - John J Reynolds
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Grant S Stewart
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Bernd Wollnik
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Gökhan Yigit
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Keith W Caldecott
- Department of Genome Dynamics (I.K., H.H., K.W.C.), Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Republic; Genome Damage and Stability Centre (H.H., K.W.C.), School of Life Sciences, University of Sussex, Falmer, Brighton, UK; Institute of Human Genetics (Y.L., B.W., G.Y.), University Medical Center Göttingen, Germany; Cologne Center for Genomics (J.A.), University of Cologne, Germany; Institute of Cancer and Genomic Sciences (J.J.R., G.S.S.), College of Medical and Dental Sciences, University of Birmingham, UK; and Division of Genetics (N.G.), Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
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Derks MFL, Gjuvsland AB, Bosse M, Lopes MS, van Son M, Harlizius B, Tan BF, Hamland H, Grindflek E, Groenen MAM, Megens HJ. Loss of function mutations in essential genes cause embryonic lethality in pigs. PLoS Genet 2019; 15:e1008055. [PMID: 30875370 PMCID: PMC6436757 DOI: 10.1371/journal.pgen.1008055] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 03/27/2019] [Accepted: 02/28/2019] [Indexed: 01/23/2023] Open
Abstract
Lethal recessive alleles cause pre- or postnatal death in homozygous affected individuals, reducing fertility. Especially in small size domestic and wild populations, those alleles might be exposed by inbreeding, caused by matings between related parents that inherited the same recessive lethal allele from a common ancestor. In this study we report five relatively common (up to 13.4% carrier frequency) recessive lethal haplotypes in two commercial pig populations. The lethal haplotypes have a large effect on carrier-by-carrier matings, decreasing litter sizes by 15.1 to 21.6%. The causal mutations are of different type including two splice-site variants (affecting POLR1B and TADA2A genes), one frameshift (URB1), and one missense (PNKP) variant, resulting in a complete loss-of-function of these essential genes. The recessive lethal alleles affect up to 2.9% of the litters within a single population and are responsible for the death of 0.52% of the total population of embryos. Moreover, we provide compelling evidence that the identified embryonic lethal alleles contribute to the observed heterosis effect for fertility (i.e. larger litters in crossbred offspring). Together, this work marks specific recessive lethal variation describing its functional consequences at the molecular, phenotypic, and population level, providing a unique model to better understand fertility and heterosis in livestock. Lethal recessives are mutations that cause early lethality in homozygous state that usually occur at very low frequency in wild and domestic populations. In livestock, however, those mutations might become more prevalent as a result of inbreeding. In this study, we report five such recessive lethal haplotypes that cause embryonic lethality in homozygous state in pigs. The causal mutations are of different type but all destroy the structure of essential genes involved in cellular housekeeping processes, essential for embryonic development. The lethal recessives have substantial impact on the population fitness affecting up to 3% of the population litters, causing the death of 0.52% of the total population of embryos. Moreover, these 'natural knockouts' can increase understanding of gene function within the mammalian clade. Together, our study will allow monitoring, and facilitate the purging and partial elimination of recessive lethal mutations in frequently used pig breeds.
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Affiliation(s)
- Martijn F. L. Derks
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands
- * E-mail:
| | | | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands
| | - Marcos S. Lopes
- Topigs Norsvin Research Center, Beuningen, the Netherlands
- Topigs Norsvin, Curitiba, Brazil
| | | | | | - Beatrice F. Tan
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands
| | | | | | - Martien A. M. Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands
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Apurinic endonuclease-1 preserves neural genome integrity to maintain homeostasis and thermoregulation and prevent brain tumors. Proc Natl Acad Sci U S A 2018; 115:E12285-E12294. [PMID: 30538199 DOI: 10.1073/pnas.1809682115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Frequent oxidative modification of the neural genome is a by-product of the high oxygen consumption of the nervous system. Rapid correction of oxidative DNA lesions is essential, as genome stability is a paramount determinant of neural homeostasis. Apurinic/apyrimidinic endonuclease 1 (APE1; also known as "APEX1" or "REF1") is a key enzyme for the repair of oxidative DNA damage, although the specific role(s) for this enzyme in the development and maintenance of the nervous system is largely unknown. Here, using conditional inactivation of murine Ape1, we identify critical roles for this protein in the brain selectively after birth, coinciding with tissue oxygenation shifting from a placental supply to respiration. While mice lacking APE1 throughout neurogenesis were viable with little discernible phenotype at birth, rapid and pronounced brain-wide degenerative changes associated with DNA damage were observed immediately after birth leading to early death. Unexpectedly, Ape1 Nes-cre mice appeared hypothermic with persistent shivering associated with the loss of thermoregulatory serotonergic neurons. We found that APE1 is critical for the selective regulation of Fos1-induced hippocampal immediate early gene expression. Finally, loss of APE1 in combination with p53 inactivation resulted in a profound susceptibility to brain tumors, including medulloblastoma and glioblastoma, implicating oxidative DNA lesions as an etiologic agent in these diseases. Our study reveals APE1 as a major suppressor of deleterious oxidative DNA damage and uncovers specific and broad pathogenic consequences of respiratory oxygenation in the postnatal nervous system.
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Bianchi FT, Berto GE, Di Cunto F. Impact of DNA repair and stability defects on cortical development. Cell Mol Life Sci 2018; 75:3963-3976. [PMID: 30116853 PMCID: PMC11105354 DOI: 10.1007/s00018-018-2900-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/16/2018] [Accepted: 08/08/2018] [Indexed: 02/07/2023]
Abstract
Maintenance of genome stability is a crucial cellular function for normal mammalian development and physiology. However, despite the general relevance of this process, genome stability alteration due to genetic or non-genetic conditions has a particularly profound impact on the developing cerebral cortex. In this review, we will analyze the main pathways involved in maintenance of genome stability, the consequences of their alterations with regard to central nervous system development, as well as the possible molecular and cellular basis of this specificity.
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Affiliation(s)
- Federico T Bianchi
- Neuroscience Institute Cavalieri Ottolenghi, Turin, Italy.
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy.
| | - Gaia E Berto
- Neuroscience Institute Cavalieri Ottolenghi, Turin, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Ferdinando Di Cunto
- Neuroscience Institute Cavalieri Ottolenghi, Turin, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
- Department of Neuroscience, University of Turin, Turin, Italy
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Ramaekers VT, Segers K, Sequeira JM, Koenig M, Van Maldergem L, Bours V, Kornak U, Quadros EV. Genetic assessment and folate receptor autoantibodies in infantile-onset cerebral folate deficiency (CFD) syndrome. Mol Genet Metab 2018; 124:87-93. [PMID: 29661558 DOI: 10.1016/j.ymgme.2018.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Cerebral folate deficiency (CFD) syndromes are defined as neuro-psychiatric conditions with low CSF folate and attributed to different causes such as autoantibodies against the folate receptor-alpha (FR) protein that can block folate transport across the choroid plexus, FOLR1 gene mutations or mitochondrial disorders. High-dose folinic acid treatment restores many neurologic deficits. STUDY AIMS AND METHODS Among 36 patients from 33 families the infantile-onset CFD syndrome was diagnosed based on typical clinical features and low CSF folate. All parents were healthy. Three families had 2 affected siblings, while parents from 4 families were first cousins. We analysed serum FR autoantibodies and the FOLR1 and FOLR2 genes. Among three consanguineous families homozygosity mapping attempted to identify a monogenetic cause. Whole exome sequencing (WES) was performed in the fourth consanguineous family, where two siblings also suffered from polyneuropathy as an atypical finding. RESULTS Boys (72%) outnumbered girls (28%). Most patients (89%) had serum FR autoantibodies fluctuating over 5-6 weeks. Two children had a genetic FOLR1 variant without pathological significance. Homozygosity mapping failed to detect a single autosomal recessive gene. WES revealed an autosomal recessive polynucleotide kinase 3´phosphatase (PNKP) gene abnormality in the siblings with polyneuropathy. DISCUSSION Infantile-onset CFD was characterized by serum FR autoantibodies as its predominant pathology whereas pathogenic FOLR1 gene mutations were absent. Homozygosity mapping excluded autosomal recessive inheritance of any single responsible gene. WES in one consanguineous family identified a PNKP gene abnormality that explained the polyneuropathy and also its contribution to the infantile CFD syndrome because the PNKP gene plays a dual role in both neurodevelopment and immune-regulatory function. Further research for candidate genes predisposing to FRα-autoimmunity is suggested to include X-chromosomal and non-coding DNA regions.
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Affiliation(s)
- V Th Ramaekers
- Center of Autism and Department of Genetics, University Hospital Liège (CHU), Belgium.
| | - K Segers
- Center of Autism and Department of Genetics, University Hospital Liège (CHU), Belgium
| | - J M Sequeira
- Department of Medicine, SUNY-Downstate Medical Center, Brooklyn, New York, USA
| | - M Koenig
- EA7402 Institut Universitaire de Recherche Clinique, Montpellier, France
| | - L Van Maldergem
- Center Human Genetics, Université de Franche-Comté, Besançon, France
| | - V Bours
- Center of Autism and Department of Genetics, University Hospital Liège (CHU), Belgium
| | - U Kornak
- Institut für Humangenetik, Charité-University Berlin, Berlin, Germany
| | - E V Quadros
- Department of Medicine, SUNY-Downstate Medical Center, Brooklyn, New York, USA
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Oxidative stress and DNA damage after cerebral ischemia: Potential therapeutic targets to repair the genome and improve stroke recovery. Neuropharmacology 2017; 134:208-217. [PMID: 29128308 DOI: 10.1016/j.neuropharm.2017.11.011] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/02/2017] [Accepted: 11/05/2017] [Indexed: 12/12/2022]
Abstract
The past two decades have witnessed remarkable advances in oxidative stress research, particularly in the context of ischemic brain injury. Oxidative stress in ischemic tissues compromises the integrity of the genome, resulting in DNA lesions, cell death in neurons, glial cells, and vascular cells, and impairments in neurological recovery after stroke. As DNA is particularly vulnerable to oxidative attack, cells have evolved the ability to induce multiple DNA repair mechanisms, including base excision repair (BER), nucleotide excision repair (NER) and non-homogenous endpoint jointing (NHEJ). Defective DNA repair is tightly correlated with worse neurological outcomes after stroke, whereas upregulation of DNA repair enzymes, such as APE1, OGG1, and XRCC1, improves long-term functional recovery following stroke. Indeed, DNA damage and repair are now known to play critical roles in fundamental aspects of stroke recovery, such as neurogenesis, white matter recovery, and neurovascular unit remodeling. Several DNA repair enzymes are essential for comprehensive neural repair mechanisms after stroke, including Polβ and NEIL3 for neurogenesis, APE1 for white matter repair, Gadd45b for axonal regeneration, and DNA-PKs for neurovascular remodeling. This review discusses the emerging role of DNA damage and repair in functional recovery after stroke and highlights the contribution of DNA repair to regenerative elements after stroke. This article is part of the Special Issue entitled 'Cerebral Ischemia'.
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Sanchez A, Gadaleta MC, Limbo O, Russell P. Lingering single-strand breaks trigger Rad51-independent homology-directed repair of collapsed replication forks in the polynucleotide kinase/phosphatase mutant of fission yeast. PLoS Genet 2017; 13:e1007013. [PMID: 28922417 PMCID: PMC5626526 DOI: 10.1371/journal.pgen.1007013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 10/03/2017] [Accepted: 09/08/2017] [Indexed: 11/19/2022] Open
Abstract
The DNA repair enzyme polynucleotide kinase/phosphatase (PNKP) protects genome integrity by restoring ligatable 5'-phosphate and 3'-hydroxyl termini at single-strand breaks (SSBs). In humans, PNKP mutations underlie the neurological disease known as MCSZ, but these individuals are not predisposed for cancer, implying effective alternative repair pathways in dividing cells. Homology-directed repair (HDR) of collapsed replication forks was proposed to repair SSBs in PNKP-deficient cells, but the critical HDR protein Rad51 is not required in PNKP-null (pnk1Δ) cells of Schizosaccharomyces pombe. Here, we report that pnk1Δ cells have enhanced requirements for Rad3 (ATR/Mec1) and Chk1 checkpoint kinases, and the multi-BRCT domain protein Brc1 that binds phospho-histone H2A (γH2A) at damaged replication forks. The viability of pnk1Δ cells depends on Mre11 and Ctp1 (CtIP/Sae2) double-strand break (DSB) resection proteins, Rad52 DNA strand annealing protein, Mus81-Eme1 Holliday junction resolvase, and Rqh1 (BLM/WRN/Sgs1) DNA helicase. Coupled with increased sister chromatid recombination and Rad52 repair foci in pnk1Δ cells, these findings indicate that lingering SSBs in pnk1Δ cells trigger Rad51-independent homology-directed repair of collapsed replication forks. From these data, we propose models for HDR-mediated tolerance of persistent SSBs with 3' phosphate in pnk1Δ cells.
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Affiliation(s)
- Arancha Sanchez
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Mariana C. Gadaleta
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Oliver Limbo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Paul Russell
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
- * E-mail:
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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.
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Affiliation(s)
- Peter J McKinnon
- Department of Genetics, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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Breslin C, Mani RS, Fanta M, Hoch N, Weinfeld M, Caldecott KW. The Rev1 interacting region (RIR) motif in the scaffold protein XRCC1 mediates a low-affinity interaction with polynucleotide kinase/phosphatase (PNKP) during DNA single-strand break repair. J Biol Chem 2017; 292:16024-16031. [PMID: 28821613 PMCID: PMC5625035 DOI: 10.1074/jbc.m117.806638] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/15/2017] [Indexed: 11/22/2022] Open
Abstract
The scaffold protein X-ray repair cross-complementing 1 (XRCC1) interacts with multiple enzymes involved in DNA base excision repair and single-strand break repair (SSBR) and is important for genetic integrity and normal neurological function. One of the most important interactions of XRCC1 is that with polynucleotide kinase/phosphatase (PNKP), a dual-function DNA kinase/phosphatase that processes damaged DNA termini and that, if mutated, results in ataxia with oculomotor apraxia 4 (AOA4) and microcephaly with early-onset seizures and developmental delay (MCSZ). XRCC1 and PNKP interact via a high-affinity phosphorylation-dependent interaction site in XRCC1 and a forkhead-associated domain in PNKP. Here, we identified using biochemical and biophysical approaches a second PNKP interaction site in XRCC1 that binds PNKP with lower affinity and independently of XRCC1 phosphorylation. However, this interaction nevertheless stimulated PNKP activity and promoted SSBR and cell survival. The low-affinity interaction site required the highly conserved Rev1-interacting region (RIR) motif in XRCC1 and included three critical and evolutionarily invariant phenylalanine residues. We propose a bipartite interaction model in which the previously identified high-affinity interaction acts as a molecular tether, holding XRCC1 and PNKP together and thereby promoting the low-affinity interaction identified here, which then stimulates PNKP directly.
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Affiliation(s)
- Claire Breslin
- From the Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN19RQ, United Kingdom
| | - Rajam S Mani
- the Department of Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada, and
| | - Mesfin Fanta
- the Department of Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada, and
| | - Nicolas Hoch
- From the Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN19RQ, United Kingdom.,the CAPES Foundation, Ministry of Education of Brazil, Brasilia/DF 70040-020, Brazil
| | - Michael Weinfeld
- the Department of Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada, and
| | - Keith W Caldecott
- From the Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN19RQ, United Kingdom,
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Genome Stability by DNA Polymerase β in Neural Progenitors Contributes to Neuronal Differentiation in Cortical Development. J Neurosci 2017; 37:8444-8458. [PMID: 28765330 DOI: 10.1523/jneurosci.0665-17.2017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 07/06/2017] [Accepted: 07/27/2017] [Indexed: 01/21/2023] Open
Abstract
DNA repair is crucial for genome stability in the developing cortex, as somatic de novo mutations cause neurological disorders. However, how DNA repair contributes to neuronal development is largely unknown. To address this issue, we studied the spatiotemporal roles of DNA polymerase β (Polβ), a key enzyme in DNA base excision repair pathway, in the developing cortex using distinct forebrain-specific conditional knock-out mice, Emx1-Cre/Polβ fl/fl and Nex-Cre/Polβ fl/fl mice. Polβ expression was absent in both neural progenitors and postmitotic neurons in Emx1-Cre/Polβ fl/fl mice, whereas only postmitotic neurons lacked Polβ expression in Nex-Cre/Polβ fl/fl mice. We found that DNA double-strand breaks (DSBs) were frequently detected during replication in cortical progenitors of Emx1-Cre/Polβ fl/fl mice. Increased DSBs remained in postmitotic cells, which resulted in p53-mediated neuronal apoptosis. This neuronal apoptosis caused thinning of the cortical plate, although laminar structure was normal. In addition, accumulated DSBs also affected growth of corticofugal axons but not commissural axons. These phenotypes were not observed in Nex-Cre/Polβ fl/fl mice. Moreover, cultured Polβ-deficient neural progenitors exhibited higher sensitivity to the base-damaging agent methylmethanesulfonate, resulting in enhanced DSB formation. Similar damage was found by vitamin C treatment, which induces TET1-mediated DNA demethylation via 5-hydroxymethylcytosine. Together, genome stability mediated by Polβ-dependent base excision repair is crucial for the competence of neural progenitors, thereby contributing to neuronal differentiation in cortical development.SIGNIFICANCE STATEMENT DNA repair is crucial for development of the nervous system. However, how DNA polymerase β (Polβ)-dependent DNA base excision repair pathway contributes to the process is still unknown. We found that loss of Polβ in cortical progenitors rather than postmitotic neurons led to catastrophic DNA double-strand breaks (DSBs) during replication and p53-mediated neuronal apoptosis, which resulted in thinning of the cortical plate. The DSBs also affected corticofugal axon growth in surviving neurons. Moreover, induction of base damage and DNA demethylation intermediates in the genome increased DSBs in cultured Polβ-deficient neural progenitors. Thus, genome stability by Polβ-dependent base excision repair in neural progenitors is required for the viability and differentiation of daughter neurons in the developing nervous system.
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DNA-PKcs, ATM, and ATR Interplay Maintains Genome Integrity during Neurogenesis. J Neurosci 2017; 37:893-905. [PMID: 28123024 DOI: 10.1523/jneurosci.4213-15.2016] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 11/14/2016] [Accepted: 11/26/2016] [Indexed: 12/15/2022] Open
Abstract
The DNA damage response (DDR) orchestrates a network of cellular processes that integrates cell-cycle control and DNA repair or apoptosis, which serves to maintain genome stability. DNA-PKcs (the catalytic subunit of the DNA-dependent kinase, encoded by PRKDC), ATM (ataxia telangiectasia, mutated), and ATR (ATM and Rad3-related) are related PI3K-like protein kinases and central regulators of the DDR. Defects in these kinases have been linked to neurodegenerative or neurodevelopmental syndromes. In all cases, the key neuroprotective function of these kinases is uncertain. It also remains unclear how interactions between the three DNA damage-responsive kinases coordinate genome stability, particularly in a physiological context. Here, we used a genetic approach to identify the neural function of DNA-PKcs and the interplay between ATM and ATR during neurogenesis. We found that DNA-PKcs loss in the mouse sensitized neuronal progenitors to apoptosis after ionizing radiation because of excessive DNA damage. DNA-PKcs was also required to prevent endogenous DNA damage accumulation throughout the adult brain. In contrast, ATR coordinated the DDR during neurogenesis to direct apoptosis in cycling neural progenitors, whereas ATM regulated apoptosis in both proliferative and noncycling cells. We also found that ATR controls a DNA damage-induced G2/M checkpoint in cortical progenitors, independent of ATM and DNA-PKcs. These nonoverlapping roles were further confirmed via sustained murine embryonic or cortical development after all three kinases were simultaneously inactivated. Thus, our results illustrate how DNA-PKcs, ATM, and ATR have unique and essential roles during the DDR, collectively ensuring comprehensive genome maintenance in the nervous system. SIGNIFICANCE STATEMENT The DNA damage response (DDR) is essential for prevention of a broad spectrum of different human neurologic diseases. However, a detailed understanding of the DDR at a physiological level is lacking. In contrast to many in vitro cellular studies, here we demonstrate independent biological roles for the DDR kinases DNA-PKcs, ATM, and ATR during neurogenesis. We show that DNA-PKcs is central to DNA repair in nonproliferating cells, and restricts DNA damage accumulation, whereas ATR controls damage-induced G2 checkpoint control and apoptosis in proliferating cells. Conversely, ATM is critical for controlling apoptosis in immature noncycling neural cells after DNA damage. These data demonstrate functionally distinct, but cooperative, roles for each kinase in preserving genome stability in the nervous system.
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Abbotts R, Wilson DM. Coordination of DNA single strand break repair. Free Radic Biol Med 2017; 107:228-244. [PMID: 27890643 PMCID: PMC5443707 DOI: 10.1016/j.freeradbiomed.2016.11.039] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/21/2016] [Accepted: 11/23/2016] [Indexed: 12/28/2022]
Abstract
The genetic material of all organisms is susceptible to modification. In some instances, these changes are programmed, such as the formation of DNA double strand breaks during meiotic recombination to generate gamete variety or class switch recombination to create antibody diversity. However, in most cases, genomic damage is potentially harmful to the health of the organism, contributing to disease and aging by promoting deleterious cellular outcomes. A proportion of DNA modifications are caused by exogenous agents, both physical (namely ultraviolet sunlight and ionizing radiation) and chemical (such as benzopyrene, alkylating agents, platinum compounds and psoralens), which can produce numerous forms of DNA damage, including a range of "simple" and helix-distorting base lesions, abasic sites, crosslinks and various types of phosphodiester strand breaks. More significant in terms of frequency are endogenous mechanisms of modification, which include hydrolytic disintegration of DNA chemical bonds, attack by reactive oxygen species and other byproducts of normal cellular metabolism, or incomplete or necessary enzymatic reactions (such as topoisomerases or repair nucleases). Both exogenous and endogenous mechanisms are associated with a high risk of single strand breakage, either produced directly or generated as intermediates of DNA repair. This review will focus upon the creation, consequences and resolution of single strand breaks, with a particular focus on two major coordinating repair proteins: poly(ADP-ribose) polymerase 1 (PARP1) and X-ray repair cross-complementing protein 1 (XRCC1).
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Affiliation(s)
- Rachel Abbotts
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
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Havali-Shahriari Z, Weinfeld M, Glover JNM. Characterization of DNA Substrate Binding to the Phosphatase Domain of the DNA Repair Enzyme Polynucleotide Kinase/Phosphatase. Biochemistry 2017; 56:1737-1745. [PMID: 28276686 DOI: 10.1021/acs.biochem.6b01236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Polynucleotide kinase/phosphatase (PNKP) is a DNA strand break repair enzyme that uses separate 5' kinase and 3' phosphatase active sites to convert damaged 5'-hydroxyl/3'-phosphate strand termini to ligatable 5'-phosphate/3'-hydroxyl ends. The phosphatase active site has received particular attention as a target of inhibition in cancer therapy development. The phosphatase domain dephosphorylates a range of single- and double-stranded substrates; however, structural studies have shown that the phosphatase catalytic cleft can bind only single-stranded substrates. Here we use a catalytically inactive but structurally intact phosphatase mutant to probe interactions between PNKP and a variety of single- and double-stranded DNA substrates using an electrophoretic mobility shift assay. This work indicates that the phosphatase domain binds 3'-phosphorylated single-stranded DNAs in a manner that is highly dependent on the presence of the 3'-phosphate. Double-stranded substrate binding, in contrast, is not as dependent on the 3'-phosphate. Experiments comparing blunt-end, 3'-overhanging, and frayed-end substrates indicate that the predicted loss of energy due to base pair disruption upon binding of the phosphatase active site is likely balanced by favorable interactions between the liberated complementary strand and PNKP. Comparison of the effects on substrate binding of mutations within the phosphatase active site cleft with mutations in surrounding positively charged surfaces suggests that the surrounding surfaces are important for binding to double-stranded substrates. We further show that while fluorescence polarization methods can detect specific binding of single-stranded DNAs with the phosphatase domain, this method does not detect specific interactions between the PNKP phosphatase and double-stranded substrates.
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Affiliation(s)
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, Cross Cancer Institute , 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta , Edmonton, Alberta T6G 2H7, Canada
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40
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Röhrig S, Schröpfer S, Knoll A, Puchta H. The RTR Complex Partner RMI2 and the DNA Helicase RTEL1 Are Both Independently Involved in Preserving the Stability of 45S rDNA Repeats in Arabidopsis thaliana. PLoS Genet 2016; 12:e1006394. [PMID: 27760121 PMCID: PMC5070779 DOI: 10.1371/journal.pgen.1006394] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/29/2016] [Indexed: 11/18/2022] Open
Abstract
The stability of repetitive sequences in complex eukaryotic genomes is safeguarded by factors suppressing homologues recombination. Prominent in this is the role of the RTR complex. In plants, it consists of the RecQ helicase RECQ4A, the topoisomerase TOP3α and RMI1. Like mammals, but not yeast, plants harbor an additional complex partner, RMI2. Here, we demonstrate that, in Arabidopsis thaliana, RMI2 is involved in the repair of aberrant replication intermediates in root meristems as well as in intrastrand crosslink repair. In both instances, RMI2 is involved independently of the DNA helicase RTEL1. Surprisingly, simultaneous loss of RMI2 and RTEL1 leads to loss of male fertility. As both the RTR complex and RTEL1 are involved in suppression of homologous recombination (HR), we tested the efficiency of HR in the double mutant rmi2-2 rtel1-1 and found a synergistic enhancement (80-fold). Searching for natural target sequences we found that RTEL1 is required for stabilizing 45S rDNA repeats. In the double mutant with rmi2-2 the number of 45S rDNA repeats is further decreased sustaining independent roles of both factors in this process. Thus, loss of suppression of HR does not only lead to a destabilization of rDNA repeats but might be especially deleterious for tissues undergoing multiple cell divisions such as the male germline. The Bloom syndrome and Hoyeraal Hreidarsson syndrome are severe diseases in humans that are correlated with genome instability. Interestingly, plants harbor homologs of factors that are defective in the respective diseases. In the model plant A. thaliana these proteins play important roles in various aspects of the repair of genetic information and the maintenance of repetitive elements. Here, we show that the concomitant loss of function of two specific factors that are representative for each syndrome leads in plants to male sterility, due to somatic catastrophe leading to instability and cell death. This defect is correlated with a massive loss of repetitive genes involved in general protein production. It has been shown before for mammals that loss of certain other factors involved in genome stability leads to a defect in neural development. Our results now demonstrate that genome instability can also result in organ-specific defects in plants, in our case during flower development, leading to a defect in the cell proliferation of the premeiotic male germline.
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Affiliation(s)
- Sarah Röhrig
- Botanical Institute II, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Susan Schröpfer
- Botanical Institute II, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Alexander Knoll
- Botanical Institute II, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, Karlsruhe, Germany
- * E-mail:
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Jiang B, Glover JNM, Weinfeld M. Neurological disorders associated with DNA strand-break processing enzymes. Mech Ageing Dev 2016; 161:130-140. [PMID: 27470939 DOI: 10.1016/j.mad.2016.07.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/21/2016] [Accepted: 07/23/2016] [Indexed: 12/24/2022]
Abstract
The termini of DNA strand breaks induced by reactive oxygen species or by abortive DNA metabolic intermediates require processing to enable subsequent gap filling and ligation to proceed. The three proteins, tyrosyl DNA-phosphodiesterase 1 (TDP1), aprataxin (APTX) and polynucleotide kinase/phosphatase (PNKP) each act on a discrete set of modified strand-break termini. Recently, a series of neurodegenerative and neurodevelopmental disorders have been associated with mutations in the genes coding for these proteins. Mutations in TDP1 and APTX have been linked to Spinocerebellar ataxia with axonal neuropathy (SCAN1) and Ataxia-ocular motor apraxia 1 (AOA1), respectively, while mutations in PNKP are considered to be responsible for Microcephaly with seizures (MCSZ) and Ataxia-ocular motor apraxia 4 (AOA4). Here we present an overview of the mechanisms of these proteins and how their impairment may give rise to their respective disorders.
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Affiliation(s)
- Bingcheng Jiang
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada.
| | - J N Mark Glover
- Department of Biochemistry, Medical Sciences Building, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada.
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada.
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End-processing nucleases and phosphodiesterases: An elite supporting cast for the non-homologous end joining pathway of DNA double-strand break repair. DNA Repair (Amst) 2016; 43:57-68. [PMID: 27262532 DOI: 10.1016/j.dnarep.2016.05.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/05/2016] [Indexed: 11/20/2022]
Abstract
Nonhomologous end joining (NHEJ) is an error-prone DNA double-strand break repair pathway that is active throughout the cell cycle. A substantial fraction of NHEJ repair events show deletions and, less often, insertions in the repair joints, suggesting an end-processing step comprising the removal of mismatched or damaged nucleotides by nucleases and other phosphodiesterases, as well as subsequent strand extension by polymerases. A wide range of nucleases, including Artemis, Metnase, APLF, Mre11, CtIP, APE1, APE2 and WRN, are biochemically competent to carry out such double-strand break end processing, and have been implicated in NHEJ by at least circumstantial evidence. Several additional DNA end-specific phosphodiesterases, including TDP1, TDP2 and aprataxin are available to resolve various non-nucleotide moieties at DSB ends. This review summarizes the biochemical specificities of these enzymes and the evidence for their participation in the NHEJ pathway.
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43
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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] [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.
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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.
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The Response to Oxidative DNA Damage in Neurons: Mechanisms and Disease. Neural Plast 2016; 2016:3619274. [PMID: 26942017 PMCID: PMC4752990 DOI: 10.1155/2016/3619274] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 12/24/2015] [Indexed: 11/26/2022] Open
Abstract
There is a growing body of evidence indicating that the mechanisms that control genome stability are of key importance in the development and function of the nervous system. The major threat for neurons is oxidative DNA damage, which is repaired by the base excision repair (BER) pathway. Functional mutations of enzymes that are involved in the processing of single-strand breaks (SSB) that are generated during BER have been causally associated with syndromes that present important neurological alterations and cognitive decline. In this review, the plasticity of BER during neurogenesis and the importance of an efficient BER for correct brain function will be specifically addressed paying particular attention to the brain region and neuron-selectivity in SSB repair-associated neurological syndromes and age-related neurodegenerative diseases.
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