1
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Yu XN, Guo Y, Yang Q, Yu H, Lu MJ, Zhao L, Jin ZS, Xu XN, Feng JY, Wen YQ. Chimeric mutations in grapevine ENHANCED DISEASE RESISTANCE1 improve resistance to powdery mildew without growth penalty. PLANT PHYSIOLOGY 2024; 195:1995-2015. [PMID: 38507576 DOI: 10.1093/plphys/kiae169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 03/22/2024]
Abstract
Grapevine (Vitis vinifera L.) incurs severe quality degradation and yield loss from powdery mildew, a major fungal disease caused by Erysiphe necator. ENHANCED DISEASE RESISTANCE1 (EDR1), a Raf-like mitogen-activated protein kinase kinase kinase, negatively regulates defense responses against powdery mildew in Arabidopsis (Arabidopsis thaliana). However, little is known about the role of the putatively orthologous EDR1 gene in grapevine. In this study, we obtained grapevine VviEDR1-edited lines using CRISPR/Cas9. Plantlets containing homozygous and bi-allelic indels in VviEDR1 developed leaf lesions shortly after transplanting into the soil and died at the seedling stage. Transgenic plants expressing wild-type VviEDR1 and mutant Vviedr1 alleles as chimera (designated as VviEDR1-chi) developed normally and displayed enhanced resistance to powdery mildew. Interestingly, VviEDR1-chi plants maintained a spatiotemporally distinctive pattern of VviEDR1 mutagenesis: while almost no mutations were detected from terminal buds, ensuring normal function of the apical meristem, mutations occurred in young leaves and increased as leaves matured, resulting in resistance to powdery mildew. Further analysis showed that the resistance observed in VviEDR1-chi plants was associated with callose deposition, increased production of salicylic acid and ethylene, H2O2 production and accumulation, and host cell death. Surprisingly, no growth penalty was observed with VviEDR1-chi plants. Hence, this study demonstrated a role of VviEDR1 in the negative regulation of resistance to powdery mildew in grapevine and provided an avenue for engineering powdery mildew resistance in grapevine.
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Affiliation(s)
- Xue-Na Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Ye Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Qianling Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Haiyan Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Meng-Jiao Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Liang Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Zhuo-Shuai Jin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Xiang-Nan Xu
- Institute of Plant Nutrition, Resource and Environment, Beijing Academy of Agriculture and Forestry Sciences, Shuguanghuayuan Mid Road 9, Haidian District, Beijing 100097, China
| | - Jia-Yue Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Ying-Qiang Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
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2
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Sun X, Liu L, Wu C, Li X, Guo J, Zhang J, Guan J, Wang N, Gu L, Yang XW, Li GM. Mutant huntingtin protein induces MLH1 degradation, DNA hyperexcision, and cGAS-STING-dependent apoptosis. Proc Natl Acad Sci U S A 2024; 121:e2313652121. [PMID: 38498709 PMCID: PMC10990133 DOI: 10.1073/pnas.2313652121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/27/2024] [Indexed: 03/20/2024] Open
Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder caused by an expanded CAG repeat in the huntingtin (HTT) gene. The repeat-expanded HTT encodes a mutated HTT (mHTT), which is known to induce DNA double-strand breaks (DSBs), activation of the cGAS-STING pathway, and apoptosis in HD. However, the mechanism by which mHTT triggers these events is unknown. Here, we show that HTT interacts with both exonuclease 1 (Exo1) and MutLα (MLH1-PMS2), a negative regulator of Exo1. While the HTT-Exo1 interaction suppresses the Exo1-catalyzed DNA end resection during DSB repair, the HTT-MutLα interaction functions to stabilize MLH1. However, mHTT displays a significantly reduced interaction with Exo1 or MutLα, thereby losing the ability to regulate Exo1. Thus, cells expressing mHTT exhibit rapid MLH1 degradation and hyperactive DNA excision, which causes severe DNA damage and cytosolic DNA accumulation. This activates the cGAS-STING pathway to mediate apoptosis. Therefore, we have identified unique functions for both HTT and mHTT in modulating DNA repair and the cGAS-STING pathway-mediated apoptosis by interacting with MLH1. Our work elucidates the mechanism by which mHTT causes HD.
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Affiliation(s)
- Xiao Sun
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX75390
- The Ministry of Education Key Laboratory of Reproductive Genetics, Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou310006, China
| | - Lu Liu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Chao Wu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Xueying Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Jinzhen Guo
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Junqiu Zhang
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Junhong Guan
- Cui-ying Experimental Center, Lanzhou University Second Hospital, Lanzhou730030, China
| | - Nan Wang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human behavior, University of California, Los Angeles, CA90095
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Liya Gu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - X. Willian Yang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human behavior, University of California, Los Angeles, CA90095
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX75390
- Institute for Cancer Research, Chinese Institutes for Medical Research, Beijing100069, China
- School of Basic Medical Sciences, Capital Medical University, Beijing100069, China
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3
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Hill RJ, Bona N, Smink J, Webb HK, Crisp A, Garaycoechea JI, Crossan GP. p53 regulates diverse tissue-specific outcomes to endogenous DNA damage in mice. Nat Commun 2024; 15:2518. [PMID: 38514641 PMCID: PMC10957910 DOI: 10.1038/s41467-024-46844-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
DNA repair deficiency can lead to segmental phenotypes in humans and mice, in which certain tissues lose homeostasis while others remain seemingly unaffected. This may be due to different tissues facing varying levels of damage or having different reliance on specific DNA repair pathways. However, we find that the cellular response to DNA damage determines different tissue-specific outcomes. Here, we use a mouse model of the human XPF-ERCC1 progeroid syndrome (XFE) caused by loss of DNA repair. We find that p53, a central regulator of the cellular response to DNA damage, regulates tissue dysfunction in Ercc1-/- mice in different ways. We show that ablation of p53 rescues the loss of hematopoietic stem cells, and has no effect on kidney, germ cell or brain dysfunction, but exacerbates liver pathology and polyploidisation. Mechanistically, we find that p53 ablation led to the loss of cell-cycle regulation in the liver, with reduced p21 expression. Eventually, p16/Cdkn2a expression is induced, serving as a fail-safe brake to proliferation in the absence of the p53-p21 axis. Taken together, our data show that distinct and tissue-specific functions of p53, in response to DNA damage, play a crucial role in regulating tissue-specific phenotypes.
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Affiliation(s)
- Ross J Hill
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK
| | - Nazareno Bona
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK
| | - Job Smink
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands
| | - Hannah K Webb
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK
| | - Alastair Crisp
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK
| | - Juan I Garaycoechea
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands.
| | - Gerry P Crossan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK.
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4
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Wang YJ, Cao JB, Yang J, Liu T, Yu HL, He ZX, Bao SL, He XX, Zhu XJ. PRMT5-mediated homologous recombination repair is essential to maintain genomic integrity of neural progenitor cells. Cell Mol Life Sci 2024; 81:123. [PMID: 38459149 PMCID: PMC10923982 DOI: 10.1007/s00018-024-05154-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/25/2024] [Accepted: 02/05/2024] [Indexed: 03/10/2024]
Abstract
Maintaining genomic stability is a prerequisite for proliferating NPCs to ensure genetic fidelity. Though histone arginine methylation has been shown to play important roles in safeguarding genomic stability, the underlying mechanism during brain development is not fully understood. Protein arginine N-methyltransferase 5 (PRMT5) is a type II protein arginine methyltransferase that plays a role in transcriptional regulation. Here, we identify PRMT5 as a key regulator of DNA repair in response to double-strand breaks (DSBs) during NPC proliferation. Prmt5F/F; Emx1-Cre (cKO-Emx1) mice show a distinctive microcephaly phenotype, with partial loss of the dorsal medial cerebral cortex and complete loss of the corpus callosum and hippocampus. This phenotype is resulted from DSBs accumulation in the medial dorsal cortex followed by cell apoptosis. Both RNA sequencing and in vitro DNA repair analyses reveal that PRMT5 is required for DNA homologous recombination (HR) repair. PRMT5 specifically catalyzes H3R2me2s in proliferating NPCs in the developing mouse brain to enhance HR-related gene expression during DNA repair. Finally, overexpression of BRCA1 significantly rescues DSBs accumulation and cell apoptosis in PRMT5-deficient NSCs. Taken together, our results show that PRMT5 maintains genomic stability by regulating histone arginine methylation in proliferating NPCs.
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Affiliation(s)
- Ya-Jun Wang
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Jian-Bo Cao
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Jing Yang
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Tong Liu
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Hua-Li Yu
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Zi-Xuan He
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Shi-Lai Bao
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiao-Xiao He
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China.
| | - Xiao-Juan Zhu
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China.
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5
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Abugable AA, Antar S, El-Khamisy SF. Chromosomal single-strand break repair and neurological disease: Implications on transcription and emerging genomic tools. DNA Repair (Amst) 2024; 135:103629. [PMID: 38266593 DOI: 10.1016/j.dnarep.2024.103629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Cells are constantly exposed to various sources of DNA damage that pose a threat to their genomic integrity. One of the most common types of DNA breaks are single-strand breaks (SSBs). Mutations in the repair proteins that are important for repairing SSBs have been reported in several neurological disorders. While several tools have been utilised to investigate SSBs in cells, it was only through recent advances in genomics that we are now beginning to understand the architecture of the non-random distribution of SSBs and their impact on key cellular processes such as transcription and epigenetic remodelling. Here, we discuss our current understanding of the genome-wide distribution of SSBs, their link to neurological disorders and summarise recent technologies to investigate SSBs at the genomic level.
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Affiliation(s)
- Arwa A Abugable
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Sarah Antar
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK; Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Mansoura University, Egypt
| | - Sherif F El-Khamisy
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK; Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, Bradford, UK.
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6
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Huang LC, McKeown CR, He HY, Ta AC, Cline HT. BRCA1 and ELK-1 regulate neural progenitor cell fate in the optic tectum in response to visual experience in Xenopus laevis tadpoles. Proc Natl Acad Sci U S A 2024; 121:e2316542121. [PMID: 38198524 PMCID: PMC10801852 DOI: 10.1073/pnas.2316542121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/05/2023] [Indexed: 01/12/2024] Open
Abstract
In developing Xenopus tadpoles, the optic tectum begins to receive patterned visual input while visuomotor circuits are still undergoing neurogenesis and circuit assembly. This visual input regulates neural progenitor cell fate decisions such that maintaining tadpoles in the dark increases proliferation, expanding the progenitor pool, while visual stimulation promotes neuronal differentiation. To identify regulators of activity-dependent neural progenitor cell fate, we profiled the transcriptomes of proliferating neural progenitor cells and newly differentiated neurons using RNA-Seq. We used advanced bioinformatic analysis of 1,130 differentially expressed transcripts to identify six differentially regulated transcriptional regulators, including Breast Cancer 1 (BRCA1) and the ETS-family transcription factor, ELK-1, which are predicted to regulate the majority of the other differentially expressed transcripts. BRCA1 is known for its role in cancers, but relatively little is known about its potential role in regulating neural progenitor cell fate. ELK-1 is a multifunctional transcription factor which regulates immediate early gene expression. We investigated the potential functions of BRCA1 and ELK-1 in activity-regulated neurogenesis in the tadpole visual system using in vivo time-lapse imaging to monitor the fate of GFP-expressing SOX2+ neural progenitor cells in the optic tectum. Our longitudinal in vivo imaging analysis showed that knockdown of either BRCA1 or ELK-1 altered the fates of neural progenitor cells and furthermore that the effects of visual experience on neurogenesis depend on BRCA1 and ELK-1 expression. These studies provide insight into the potential mechanisms by which neural activity affects neural progenitor cell fate.
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Affiliation(s)
- Lin-Chien Huang
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA92037
| | - Caroline R. McKeown
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA92037
| | - Hai-Yan He
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA92037
| | - Aaron C. Ta
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA92037
| | - Hollis T. Cline
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA92037
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7
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Bery A, Etienne O, Mouton L, Mokrani S, Granotier-Beckers C, Gauthier LR, Feat-Vetel J, Kortulewski T, Pérès EA, Desmaze C, Lestaveal P, Barroca V, Laugeray A, Boumezbeur F, Abramovski V, Mortaud S, Menuet A, Le Bihan D, Villartay JPD, Boussin FD. XLF/Cernunnos loss impairs mouse brain development by altering symmetric proliferative divisions of neural progenitors. Cell Rep 2023; 42:112342. [PMID: 37027298 DOI: 10.1016/j.celrep.2023.112342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/20/2022] [Accepted: 03/19/2023] [Indexed: 04/08/2023] Open
Abstract
XLF/Cernunnos is a component of the ligation complex used in classical non-homologous end-joining (cNHEJ), a major DNA double-strand break (DSB) repair pathway. We report neurodevelopmental delays and significant behavioral alterations associated with microcephaly in Xlf-/- mice. This phenotype, reminiscent of clinical and neuropathologic features in humans deficient in cNHEJ, is associated with a low level of apoptosis of neural cells and premature neurogenesis, which consists of an early shift of neural progenitors from proliferative to neurogenic divisions during brain development. We show that premature neurogenesis is related to an increase in chromatid breaks affecting mitotic spindle orientation, highlighting a direct link between asymmetric chromosome segregation and asymmetric neurogenic divisions. This study reveals thus that XLF is required for maintaining symmetric proliferative divisions of neural progenitors during brain development and shows that premature neurogenesis may play a major role in neurodevelopmental pathologies caused by NHEJ deficiency and/or genotoxic stress.
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Affiliation(s)
- Amandine Bery
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France
| | - Olivier Etienne
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France
| | - Laura Mouton
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France
| | - Sofiane Mokrani
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France
| | - Christine Granotier-Beckers
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France
| | - Laurent R Gauthier
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France
| | - Justyne Feat-Vetel
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France
| | - Thierry Kortulewski
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France
| | - Elodie A Pérès
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France; NeuroSpin, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Chantal Desmaze
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France
| | - Philippe Lestaveal
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED, 92262 Fontenay-aux-Roses, France
| | - Vilma Barroca
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France
| | - Antony Laugeray
- Immunologie et Neurogénétique Expérimentales et Moléculaires - UMR7355 CNRS - 3B, rue de la Férollerie, 45071 Orléans, France
| | - Fawzi Boumezbeur
- NeuroSpin, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Vincent Abramovski
- Université Paris Cité, Imagine Institute, Laboratory "Genome Dynamics in the Immune System", Equipe labellisée La LIGUE, INSERM UMR 1163, 75015 Paris, France
| | - Stéphane Mortaud
- Immunologie et Neurogénétique Expérimentales et Moléculaires - UMR7355 CNRS - 3B, rue de la Férollerie, 45071 Orléans, France; Université d'Orléans, Orléans, France
| | - Arnaud Menuet
- Immunologie et Neurogénétique Expérimentales et Moléculaires - UMR7355 CNRS - 3B, rue de la Férollerie, 45071 Orléans, France; Université d'Orléans, Orléans, France
| | - Denis Le Bihan
- NeuroSpin, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jean-Pierre de Villartay
- Université Paris Cité, Imagine Institute, Laboratory "Genome Dynamics in the Immune System", Equipe labellisée La LIGUE, INSERM UMR 1163, 75015 Paris, France
| | - François D Boussin
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations/iRCM, 92265 Fontenay-aux-Roses, France.
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8
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Shadfar S, Parakh S, Jamali MS, Atkin JD. Redox dysregulation as a driver for DNA damage and its relationship to neurodegenerative diseases. Transl Neurodegener 2023; 12:18. [PMID: 37055865 PMCID: PMC10103468 DOI: 10.1186/s40035-023-00350-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/16/2023] [Indexed: 04/15/2023] Open
Abstract
Redox homeostasis refers to the balance between the production of reactive oxygen species (ROS) as well as reactive nitrogen species (RNS), and their elimination by antioxidants. It is linked to all important cellular activities and oxidative stress is a result of imbalance between pro-oxidants and antioxidant species. Oxidative stress perturbs many cellular activities, including processes that maintain the integrity of DNA. Nucleic acids are highly reactive and therefore particularly susceptible to damage. The DNA damage response detects and repairs these DNA lesions. Efficient DNA repair processes are therefore essential for maintaining cellular viability, but they decline considerably during aging. DNA damage and deficiencies in DNA repair are increasingly described in age-related neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and Huntington's disease. Furthermore, oxidative stress has long been associated with these conditions. Moreover, both redox dysregulation and DNA damage increase significantly during aging, which is the biggest risk factor for neurodegenerative diseases. However, the links between redox dysfunction and DNA damage, and their joint contributions to pathophysiology in these conditions, are only just emerging. This review will discuss these associations and address the increasing evidence for redox dysregulation as an important and major source of DNA damage in neurodegenerative disorders. Understanding these connections may facilitate a better understanding of disease mechanisms, and ultimately lead to the design of better therapeutic strategies based on preventing both redox dysregulation and DNA damage.
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Affiliation(s)
- Sina Shadfar
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, 2109, Australia.
| | - Sonam Parakh
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, 2109, Australia
| | - Md Shafi Jamali
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, 2109, Australia
| | - Julie D Atkin
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, 2109, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia.
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9
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Bočkaj I, Martini TEI, Smit MJ, Armandari I, Bakker B, Wardenaar R, Meeuwsen-de Boer TGJ, Bakker PL, Spierings DCJ, Hoving EW, Guryev V, Foijer F, Bruggeman SWM. Chromosomal Instability Characterizes Pediatric Medulloblastoma but Is Not Tolerated in the Developing Cerebellum. Int J Mol Sci 2022; 23:ijms23179852. [PMID: 36077248 PMCID: PMC9456393 DOI: 10.3390/ijms23179852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/21/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Medulloblastoma is a pediatric brain malignancy that consists of four transcriptional subgroups. Structural and numerical aneuploidy are common in all subgroups, although they are particularly profound in Group 3 and Group 4 medulloblastoma and in a subtype of SHH medulloblastoma termed SHHα. This suggests that chromosomal instability (CIN), the process leading to aneuploidy, is an important player in medulloblastoma pathophysiology. However, it is not known if there is ongoing CIN in medulloblastoma or if CIN affects the developing cerebellum and promotes tumor formation. To investigate this, we performed karyotyping of single medulloblastoma cells and demonstrated the presence of distinct tumor cell clones harboring unique copy number alterations, which is suggestive of ongoing CIN. We also found enrichment for processes related to DNA replication, repair, and mitosis in both SHH medulloblastoma and in the highly proliferative compartment of the presumed tumor cell lineage-of-origin, the latter also being sensitive to genotoxic stress. However, when challenging these tumor cells-of-origin with genetic lesions inducing CIN using transgenic mouse modeling, we found no evidence for large chromosomal aberrations in the cerebellum or for medulloblastoma formation. We therefore conclude that without a background of specific genetic mutations, CIN is not tolerated in the developing cerebellum in vivo and, thus, by itself is not sufficient to initiate medulloblastoma.
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Affiliation(s)
- Irena Bočkaj
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Tosca E. I. Martini
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Marlinde J. Smit
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Inna Armandari
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - René Wardenaar
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Tiny G. J. Meeuwsen-de Boer
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Petra L. Bakker
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Diana C. J. Spierings
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Eelco W. Hoving
- Princess Máxima Center for Pediatric Oncology, 3584 EA Utrecht, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
- Correspondence: (F.F.); (S.W.M.B.)
| | - Sophia W. M. Bruggeman
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands
- Correspondence: (F.F.); (S.W.M.B.)
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10
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Jaylet T, Quintens R, Benotmane MA, Luukkonen J, Tanaka IB, Ibanez C, Durand C, Sachana M, Azimzadeh O, Adam-Guillermin C, Tollefsen KE, Laurent O, Audouze K, Armant O. Development of an Adverse Outcome Pathway for radiation-induced microcephaly via expert consultation and machine learning. Int J Radiat Biol 2022; 98:1752-1762. [PMID: 35947014 DOI: 10.1080/09553002.2022.2110312] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Brain development during embryogenesis and in early postnatal life is particularly complex and involves the interplay of many cellular processes and molecular mechanisms, making it extremely vulnerable to exogenous insults, including ionizing radiation (IR). Microcephaly is one of the most frequent neurodevelopmental abnormalities that is characterized by small brain size, and is often associated with intellectual deficiency. Decades of research span from epidemiological data on in utero exposure of the A-bomb survivors, to studies on animal and cellular models that allowed deciphering the most prominent molecular mechanisms leading to microcephaly. The Adverse Outcome Pathway (AOP) framework is used to organize, evaluate and portray the scientific knowledge of toxicological effects spanning different biological levels of organizations, from the initial interaction with molecular targets to the occurrence of a disease or adversity. In the present study, the framework was used in an attempt to organize the current scientific knowledge on microcephaly progression in the context of ionizing radiation (IR) exposure. This work was performed by a group of experts formed during a recent workshop organized jointly by the Multidisciplinary European Low Dose Initiative (MELODI) and the European Radioecology Alliance (ALLIANCE) associations to present the AOP approach and tools. Here we report on the development of a putative AOP for congenital microcephaly resulting from IR exposure based on discussions of the working group and we emphasize the use of a novel machine-learning approach to assist in the screening of the available literature to develop AOPs. CONCLUSION The expert consultation led to the identification of crucial biological events for the progression of microcephaly upon exposure to IR, and highlighted current knowledge gaps. The machine learning approach was successfully used to screen the existing knowledge and helped to rapidly screen the body of evidence and in particular the epidemiological data. This systematic review approach also ensured that the analysis was sufficiently comprehensive to identify the most relevant data and facilitate rapid and consistent AOP development. We anticipate that as machine learning approaches become more user-friendly through easy-to-use web interface, this would allow AOP development to become more efficient and less time consuming.
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Affiliation(s)
- Thomas Jaylet
- Université Paris Cité, T3S, Inserm UMRS 1124, Paris, France
| | - Roel Quintens
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK-CEN, Mol, Belgium
| | | | - Jukka Luukkonen
- University of Eastern Finland, Kuopio Campus, Department of Environmental and Biological Sciences, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Ignacia Braga Tanaka
- Department of Radiobiology, Institute for Environmental Sciences, 1-7 lenomae, Obuchi, Rokkasho-mura, Kamikita-gun, Aomori 039-3212, Japan
| | - Chrystelle Ibanez
- PSE-SANTE/SESANE/LRTOX Institut de Radioprotection et de Sûreté Nucléaire (IRSN), F-92262, Fontenay-aux-Roses, France
| | - Christelle Durand
- PSE-SANTE/SESANE/LRTOX Institut de Radioprotection et de Sûreté Nucléaire (IRSN), F-92262, Fontenay-aux-Roses, France
| | - Magdalini Sachana
- Organisation for Economic Co-operation and Development (OECD), Environment Health and Safety Division, 75775 CEDEX 16 Paris, France
| | - Omid Azimzadeh
- Federal Office for Radiation Protection (Bfs), Section Radiation Biology, 85764 Neuherberg, Germany
| | - Christelle Adam-Guillermin
- PSE-SANTE/SDOS/LMDN, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Cadarache, 13115 Saint-Paul-Lez-Durance, France
| | - Knut Erik Tollefsen
- Norwegian Institute for Water Research (NIVA), Økernveien 94, N-0579, Oslo, Norway.,Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway.,Centre for Environmental Radioactivity, Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Olivier Laurent
- PSE-SANTE/SESANE/LEPID, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), F-92262, Fontenay-aux-Roses, France
| | - Karine Audouze
- Université Paris Cité, T3S, Inserm UMRS 1124, Paris, France
| | - Olivier Armant
- PSE-ENV/SRTE/LECO, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Cadarache, 13115 Saint-Paul-Lez-Durance, France
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11
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Qin N, Geng A, Xue R. Activated or Impaired: An Overview of DNA Repair in Neurodegenerative Diseases. Aging Dis 2022; 13:987-1004. [PMID: 35855336 PMCID: PMC9286913 DOI: 10.14336/ad.2021.1212] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/08/2021] [Indexed: 11/06/2022] Open
Abstract
As the population ages, age-related neurodegenerative diseases have become a major challenge in health science. Currently, the pathology of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and Huntington's disease, is still not fully understood. Remarkably, emerging evidence indicates a role of genomic DNA damage and repair in various neurodegenerative disorders. Here, we summarized the current understanding of the function of DNA damage repair, especially base excision repair and double strand break repair pathways, in a variety of neurodegenerative diseases. We concluded that exacerbation of DNA lesions is found in almost all types of neurodegenerative diseases, whereas the activities of different DNA repair pathways demonstrate distinct trends, depending on disease type and even brain region. Specifically, key enzymes involved in base excision repair are likely impaired in Alzheimer's disease and amyotrophic lateral sclerosis but activated in Parkinson's disease, while nonhomologous end joining is likely downregulated in most types of neurodegenerative diseases. Hence, impairment of nonhomologous end joining is likely a common etiology for most neurodegenerative diseases, while defects in base excision repair are likely involved in the pathology of Alzheimer's disease and amyotrophic lateral sclerosis but are Parkinson's disease, based on current findings. Although there are still discrepancies and further studies are required to completely elucidate the exact roles of DNA repair in neurodegeneration, the current studies summarized here provide crucial insights into the pathology of neurodegenerative diseases and may reveal novel drug targets for corresponding neurodegenerative diseases.
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Affiliation(s)
- Nan Qin
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Anke Geng
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Renhao Xue
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
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12
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Cuartas J, Gangwani L. R-loop Mediated DNA Damage and Impaired DNA Repair in Spinal Muscular Atrophy. Front Cell Neurosci 2022; 16:826608. [PMID: 35783101 PMCID: PMC9243258 DOI: 10.3389/fncel.2022.826608] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/23/2022] [Indexed: 12/02/2022] Open
Abstract
Defects in DNA repair pathways are a major cause of DNA damage accumulation leading to genomic instability and neurodegeneration. Efficient DNA damage repair is critical to maintain genomicstability and support cell function and viability. DNA damage results in the activation of cell death pathways, causing neuronal death in an expanding spectrum of neurological disorders, such as amyotrophic lateral sclerosis (ALS), Parkinson’s disease (PD), Alzheimer’s disease (AD), and spinal muscular atrophy (SMA). SMA is a neurodegenerative disorder caused by mutations in the Survival Motor Neuron 1 (SMN1) gene. SMA is characterized by the degeneration of spinal cord motor neurons due to low levels of the SMN protein. The molecular mechanism of selective motor neuron degeneration in SMA was unclear for about 20 years. However, several studies have identified biochemical and molecular mechanisms that may contribute to the predominant degeneration of motor neurons in SMA, including the RhoA/ROCK, the c-Jun NH2-terminal kinase (JNK), and p53-mediated pathways, which are involved in mediating DNA damage-dependent cell death. Recent studies provided insight into selective degeneration of motor neurons, which might be caused by accumulation of R-loop-mediated DNA damage and impaired non-homologous end joining (NHEJ) DNA repair pathway leading to genomic instability. Here, we review the latest findings involving R-loop-mediated DNA damage and defects in neuron-specific DNA repair mechanisms in SMA and discuss these findings in the context of other neurodegenerative disorders linked to DNA damage.
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Affiliation(s)
- Juliana Cuartas
- Center of Emphasis in Neurosciences, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Laxman Gangwani
- Center of Emphasis in Neurosciences, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
- Francis Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
- *Correspondence: Laxman Gangwani
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13
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Qing X, Zhang G, Wang Z. DNA
damage response in neurodevelopment and neuromaintenance. FEBS J 2022. [DOI: 10.1111/febs.16535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/24/2022] [Indexed: 01/01/2023]
Affiliation(s)
- Xiaobing Qing
- Leibniz Institute on Aging – Fritz Lipmann Institute (FLI) Jena Germany
| | - Guangyu Zhang
- Leibniz Institute on Aging – Fritz Lipmann Institute (FLI) Jena Germany
| | - Zhao‐Qi Wang
- Leibniz Institute on Aging – Fritz Lipmann Institute (FLI) Jena Germany
- Faculty of Biological Sciences Friedrich‐Schiller‐University of Jena Germany
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14
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McSwain LF, Parwani KK, Shahab SW, Hambardzumyan D, MacDonald TJ, Spangle JM, Kenney AM. Medulloblastoma and the DNA Damage Response. Front Oncol 2022; 12:903830. [PMID: 35747808 PMCID: PMC9209741 DOI: 10.3389/fonc.2022.903830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/10/2022] [Indexed: 12/04/2022] Open
Abstract
Medulloblastoma (MB) is the most common malignant brain tumor in children with standard of care consisting of surgery, radiation, and chemotherapy. Recent molecular profiling led to the identification of four molecularly distinct MB subgroups – Wingless (WNT), Sonic Hedgehog (SHH), Group 3, and Group 4. Despite genomic MB characterization and subsequent tumor stratification, clinical treatment paradigms are still largely driven by histology, degree of surgical resection, and presence or absence of metastasis rather than molecular profile. Patients usually undergo resection of their tumor followed by craniospinal radiation (CSI) and a 6 month to one-year multi-agent chemotherapeutic regimen. While there is clearly a need for development of targeted agents specific to the molecular alterations of each patient, targeting proteins responsible for DNA damage repair could have a broader impact regardless of molecular subgrouping. DNA damage response (DDR) protein inhibitors have recently emerged as targeted agents with potent activity as monotherapy or in combination in different cancers. Here we discuss the molecular underpinnings of genomic instability in MB and potential avenues for exploitation through DNA damage response inhibition.
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Affiliation(s)
- Leon F. McSwain
- Department of Pediatrics, Emory University, Atlanta, GA, United States
| | - Kiran K. Parwani
- Winship Cancer Institute, Emory University, Atlanta, GA, United States
- Department of Radiation Oncology, Emory University, Atlanta, GA, United States
| | - Shubin W. Shahab
- Winship Cancer Institute, Emory University, Atlanta, GA, United States
| | - Dolores Hambardzumyan
- Departments of Neurosurgery and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Tobey J. MacDonald
- Department of Pediatrics, Emory University, Atlanta, GA, United States
- Winship Cancer Institute, Emory University, Atlanta, GA, United States
| | - Jennifer M. Spangle
- Winship Cancer Institute, Emory University, Atlanta, GA, United States
- Department of Radiation Oncology, Emory University, Atlanta, GA, United States
| | - Anna Marie Kenney
- Department of Pediatrics, Emory University, Atlanta, GA, United States
- *Correspondence: Anna Marie Kenney,
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15
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Fielder SM, Rosenfeld JA, Burrage LC, Emrick L, Lalani S, Attali R, Bembenek JN, Hoang H, Baldridge D, Silverman GA, Schedl T, Pak SC. Functional analysis of a novel de novo variant in PPP5C associated with microcephaly, seizures, and developmental delay. Mol Genet Metab 2022; 136:65-73. [PMID: 35361529 DOI: 10.1016/j.ymgme.2022.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/13/2022] [Indexed: 11/27/2022]
Abstract
We describe a proband evaluated through the Undiagnosed Diseases Network (UDN) who presented with microcephaly, developmental delay, and refractory epilepsy with a de novo p.Ala47Thr missense variant in the protein phosphatase gene, PPP5C. This gene has not previously been associated with a Mendelian disease, and based on the population database, gnomAD, the gene has a low tolerance for loss-of-function variants (pLI = 1, o/e = 0.07). We functionally evaluated the PPP5C variant in C. elegans by knocking the variant into the orthologous gene, pph-5, at the corresponding residue, Ala48Thr. We employed assays in three different biological processes where pph-5 was known to function through opposing the activity of genes, mec-15 and sep-1. We demonstrated that, in contrast to control animals, the pph-5 Ala48Thr variant suppresses the neurite growth phenotype and the GABA signaling defects of mec-15 mutants, and the embryonic lethality of sep-1 mutants. The Ala48Thr variant did not display dominance and behaved similarly to the reference pph-5 null, indicating that the variant is likely a strong hypomorph or complete loss-of-function. We conclude that pph-5 Ala48Thr is damaging in C. elegans. By extension in the proband, PPP5C p.Ala47Thr is likely damaging, the de novo dominant presentation is consistent with haplo-insufficiency, and the PPP5C variant is likely responsible for one or more of the proband's phenotypes.
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Affiliation(s)
- Sara M Fielder
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Lisa Emrick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Seema Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Ruben Attali
- Genomic Research Department, Emedgene Technologies, 6744332 Tel Aviv, Israel
| | - Joshua N Bembenek
- Department of Obstetrics and Gynecology, C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Hieu Hoang
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Dustin Baldridge
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Gary A Silverman
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Tim Schedl
- Department of Genetics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA
| | - Stephen C Pak
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO 63110, USA.
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16
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Yoon YS, You JS, Kim TK, Ahn WJ, Kim MJ, Son KH, Ricarte D, Ortiz D, Lee SJ, Lee HJ. Senescence and impaired DNA damage responses in alpha-synucleinopathy models. Exp Mol Med 2022; 54:115-128. [PMID: 35136202 PMCID: PMC8894476 DOI: 10.1038/s12276-022-00727-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 10/11/2021] [Accepted: 11/09/2021] [Indexed: 02/06/2023] Open
Abstract
α-Synuclein is a crucial element in the pathogenesis of Parkinson’s disease (PD) and related neurological diseases. Although numerous studies have presented potential mechanisms underlying its pathogenesis, the understanding of α-synuclein-mediated neurodegeneration remains far from complete. Here, we show that overexpression of α-synuclein leads to impaired DNA repair and cellular senescence. Transcriptome analysis showed that α-synuclein overexpression led to cellular senescence with activation of the p53 pathway and DNA damage responses (DDRs). Chromatin immunoprecipitation analyses using p53 and γH2AX, chromosomal markers of DNA damage, revealed that these proteins bind to promoters and regulate the expression of DDR and cellular senescence genes. Cellular marker analyses confirmed cellular senescence and the accumulation of DNA double-strand breaks. The non-homologous end joining (NHEJ) DNA repair pathway was activated in α-synuclein-overexpressing cells. However, the expression of MRE11, a key component of the DSB repair system, was reduced, suggesting that the repair pathway induction was incomplete. Neuropathological examination of α-synuclein transgenic mice showed increased levels of phospho-α-synuclein and DNA double-strand breaks, as well as markers of cellular senescence, at an early, presymptomatic stage. These results suggest that the accumulation of DNA double-strand breaks (DSBs) and cellular senescence are intermediaries of α-synuclein-induced pathogenesis in PD. Excess levels of a protein involved in Parkinson’s disease can impair the brain’s capacity to repair DNA damage, leading to a state of cellular aging that accelerates neuronal death. When aggregated, the α-synuclein protein plays a major role in Parkinson’s disease and other neurodegenerative disorders. A team from South Korea, led by He-Jin Lee of Konkuk University, Seoul, and Seung-Jae Lee of Seoul National University College of Medicine, showed that human neuronal cells and mouse models with elevated expression of α-synuclein develop double-stranded breaks in their genomes as a consequence of deficient quality control mechanisms. The accumulated DNA damage spurs the cells to enter a state in which they show canonical signs of cellular aging but remain metabolically active in ways that fuel neurodegeneration. Therapies that target these processes could help prevent or treat α-synuclein–linked diseases.
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Affiliation(s)
- Ye-Seul Yoon
- Department of Anatomy, Konkuk University, Seoul, 05029, Korea
| | - Jueng Soo You
- Department of Biochemistry, Konkuk University, Seoul, 05029, Korea.,Research Institute of Medical Science, Seoul, 05029, Korea.,IBST, Konkuk University, Seoul, 05029, Korea
| | - Tae-Kyung Kim
- Department of Biomedical Sciences and Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, Korea.,Departments of Exercise Physiology and Biochemistry, Korea National Sport University, Seoul, Korea
| | | | - Myoung Jun Kim
- Department of Biochemistry, Konkuk University, Seoul, 05029, Korea
| | - Keun Hong Son
- Department of Microbiology, College of Natural Sciences, Dankook University, Seoul, Korea
| | - Diadem Ricarte
- Department of Anatomy, Konkuk University, Seoul, 05029, Korea
| | - Darlene Ortiz
- Department of Anatomy, Konkuk University, Seoul, 05029, Korea
| | - Seung-Jae Lee
- Department of Biomedical Sciences and Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, Korea.
| | - He-Jin Lee
- Department of Anatomy, Konkuk University, Seoul, 05029, Korea. .,Research Institute of Medical Science, Seoul, 05029, Korea. .,IBST, Konkuk University, Seoul, 05029, Korea.
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17
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Zada D, Sela Y, Matosevich N, Monsonego A, Lerer-Goldshtein T, Nir Y, Appelbaum L. Parp1 promotes sleep, which enhances DNA repair in neurons. Mol Cell 2021; 81:4979-4993.e7. [PMID: 34798058 PMCID: PMC8688325 DOI: 10.1016/j.molcel.2021.10.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 10/18/2021] [Accepted: 10/26/2021] [Indexed: 10/19/2022]
Abstract
The characteristics of the sleep drivers and the mechanisms through which sleep relieves the cellular homeostatic pressure are unclear. In flies, zebrafish, mice, and humans, DNA damage levels increase during wakefulness and decrease during sleep. Here, we show that 6 h of consolidated sleep is sufficient to reduce DNA damage in the zebrafish dorsal pallium. Induction of DNA damage by neuronal activity and mutagens triggered sleep and DNA repair. The activity of the DNA damage response (DDR) proteins Rad52 and Ku80 increased during sleep, and chromosome dynamics enhanced Rad52 activity. The activity of the DDR initiator poly(ADP-ribose) polymerase 1 (Parp1) increased following sleep deprivation. In both larva zebrafish and adult mice, Parp1 promoted sleep. Inhibition of Parp1 activity reduced sleep-dependent chromosome dynamics and repair. These results demonstrate that DNA damage is a homeostatic driver for sleep, and Parp1 pathways can sense this cellular pressure and facilitate sleep and repair activity.
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Affiliation(s)
- David Zada
- The Faculty of Life Sciences and the Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Yaniv Sela
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv-Yafo 69978, Israel
| | - Noa Matosevich
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv-Yafo 69978, Israel
| | - Adir Monsonego
- The Faculty of Life Sciences and the Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Tali Lerer-Goldshtein
- The Faculty of Life Sciences and the Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Yuval Nir
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv-Yafo 69978, Israel
| | - Lior Appelbaum
- The Faculty of Life Sciences and the Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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18
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Cardinale A, Saladini S, Lupacchini L, Ruspantini I, De Dominicis C, Papale M, Silvagno F, Garaci E, Mollinari C, Merlo D. DNA repair protein DNA-PK protects PC12 cells from oxidative stress-induced apoptosis involving AKT phosphorylation. Mol Biol Rep 2021; 49:1089-1101. [PMID: 34797489 PMCID: PMC8825611 DOI: 10.1007/s11033-021-06934-5] [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] [Received: 03/24/2021] [Accepted: 11/05/2021] [Indexed: 11/30/2022]
Abstract
Background Emerging evidence suggest that DNA-PK complex plays a role in the cellular response to oxidative stress, in addition to its function of double strand break (DSB) repair. In this study we evaluated whether DNA-PK participates in oxidative stress response and whether this role is independent of its function in DNA repair. Methods and results We used a model of H2O2-induced DNA damage in PC12 cells (rat pheochromocytoma), a well-known neuronal tumor cell line. We found that H2O2 treatment of PC12 cells induces an increase in DNA-PK protein complex levels, along with an elevation of DNA damage, measured both by the formation of γΗ2ΑX foci, detected by immunofluorescence, and γH2AX levels detected by western blot analysis. After 24 h of cell recovery, γΗ2ΑX foci are repaired both in the absence and presence of DNA-PK kinase inhibitor NU7026, while an increase of apoptotic cells is observed when DNA-PK activity is inhibited, as revealed by counting pycnotic nuclei and confirmed by FACS analysis. Our results suggest a role of DNA-PK as an anti-apoptotic factor in proliferating PC12 cells under oxidative stress conditions. The anti-apoptotic role of DNA-PK is associated with AKT phosphorylation in Ser473. On the contrary, in differentiated PC12 cells, were the main pathway to repair DSBs is DNA-PK-mediated, the inhibition of DNA-PK activity causes an accumulation of DNA damage. Conclusions Taken together, our results show that DNA-PK can protect cells from oxidative stress induced-apoptosis independently from its function of DSB repair enzyme. Graphical Abstract ![]()
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Affiliation(s)
- Alessio Cardinale
- Molecular and Cellular Neurobiology, IRCCS San Raffaele Roma, Via di Val Cannuta 247, 00166, Rome, Italy
| | - Serena Saladini
- Molecular and Cellular Neurobiology, IRCCS San Raffaele Roma, Via di Val Cannuta 247, 00166, Rome, Italy
| | - Leonardo Lupacchini
- Molecular and Cellular Neurobiology, IRCCS San Raffaele Roma, Via di Val Cannuta 247, 00166, Rome, Italy
| | - Irene Ruspantini
- FAST. Istituto Superiore di Sanita', Viale Regina Elena 299, 00161, Rome, Italy
| | - Chiara De Dominicis
- Molecular and Cellular Neurobiology, IRCCS San Raffaele Roma, Via di Val Cannuta 247, 00166, Rome, Italy.,Department of Neuroscience, Istituto Superiore di Sanita', Viale Regina Elena 299, 00161, Rome, Italy
| | - Marco Papale
- Molecular and Cellular Neurobiology, IRCCS San Raffaele Roma, Via di Val Cannuta 247, 00166, Rome, Italy
| | - Francesca Silvagno
- Department of Oncology, University Torino, via Santena 5 bis, 10126, Torino, Italy
| | - Enrico Garaci
- University San Raffaele, Via di Val Cannuta 247, 00166, Rome, Italy
| | - Cristiana Mollinari
- Department of Neuroscience, Istituto Superiore di Sanita', Viale Regina Elena 299, 00161, Rome, Italy.,Institute of Translational Pharmacology, National Research Council, Via Fosso del Cavaliere 100, 00133, Rome, Italy
| | - Daniela Merlo
- Department of Neuroscience, Istituto Superiore di Sanita', Viale Regina Elena 299, 00161, Rome, Italy.
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19
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Prakash R, Freyer L, Saiz N, Gavrilov S, Wang RQ, Romanienko PJ, Lacy E, Hadjantonakis AK, Jasin M. XRCC3 loss leads to midgestational embryonic lethality in mice. DNA Repair (Amst) 2021; 108:103227. [PMID: 34601382 DOI: 10.1016/j.dnarep.2021.103227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
RAD51 paralogs are key components of the homologous recombination (HR) machinery. Mouse mutants have been reported for four of the canonical RAD51 paralogs, and each of these mutants exhibits embryonic lethality, although at different gestational stages. However, the phenotype of mice deficient in the fifth RAD51 paralog, XRCC3, has not been reported. Here we report that Xrcc3 knockout mice exhibit midgestational lethality, with mild phenotypes beginning at about E8.25 but severe developmental abnormalities evident by E9.0-9.5. The most obvious phenotypes are small size and a failure of the embryo to turn to a fetal position. A knockin mutation at a key ATPase residue in the Walker A box results in embryonic lethality at a similar stage. Death of knockout mice can be delayed a few days for some embryos by homozygous or heterozygous Trp53 mutation, in keeping with an important role for XRCC3 in promoting genome integrity. Given that XRCC3 is a unique member of one of two RAD51 paralog complexes with RAD51C, these results demonstrate that both RAD51 paralog complexes are required for mouse development.
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Affiliation(s)
- Rohit Prakash
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 430 East 67 Street, New York, NY 10065, United States; Regeneron Pharmaceuticals, Tarrytown, New York, NY, United States
| | - Laina Freyer
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 430 East 67 Street, New York, NY 10065, United States; Institut Pasteur, Paris, France
| | - Néstor Saiz
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 430 East 67 Street, New York, NY 10065, United States; Rockefeller University Press, New York, NY, United States
| | - Svetlana Gavrilov
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 430 East 67 Street, New York, NY 10065, United States; Bristol-Myers Squibb, New York, NY, United States
| | - Raymond Q Wang
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 430 East 67 Street, New York, NY 10065, United States
| | - Peter J Romanienko
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 430 East 67 Street, New York, NY 10065, United States; Rutgers-Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Elizabeth Lacy
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 430 East 67 Street, New York, NY 10065, United States
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 430 East 67 Street, New York, NY 10065, United States
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 430 East 67 Street, New York, NY 10065, United States.
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20
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Prakash R, Sandoval T, Morati F, Zagelbaum JA, Lim PX, White T, Taylor B, Wang R, Desclos ECB, Sullivan MR, Rein HL, Bernstein KA, Krawczyk PM, Gautier J, Modesti M, Vanoli F, Jasin M. Distinct pathways of homologous recombination controlled by the SWS1-SWSAP1-SPIDR complex. Nat Commun 2021; 12:4255. [PMID: 34253720 PMCID: PMC8275761 DOI: 10.1038/s41467-021-24205-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
Homology-directed repair (HDR), a critical DNA repair pathway in mammalian cells, is complex, leading to multiple outcomes with different impacts on genomic integrity. However, the factors that control these different outcomes are often not well understood. Here we show that SWS1-SWSAP1-SPIDR controls distinct types of HDR. Despite their requirement for stable assembly of RAD51 recombinase at DNA damage sites, these proteins are not essential for intra-chromosomal HDR, providing insight into why patients and mice with mutations are viable. However, SWS1-SWSAP1-SPIDR is critical for inter-homolog HDR, the first mitotic factor identified specifically for this function. Furthermore, SWS1-SWSAP1-SPIDR drives the high level of sister-chromatid exchange, promotes long-range loss of heterozygosity often involved with cancer initiation, and impels the poor growth of BLM helicase-deficient cells. The relevance of these genetic interactions is evident as SWSAP1 loss prolongs Blm-mutant embryo survival, suggesting a possible druggable target for the treatment of Bloom syndrome.
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Affiliation(s)
- Rohit Prakash
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Thomas Sandoval
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Florian Morati
- Cancer Research Center of Marseille, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Jennifer A Zagelbaum
- Department of Genetics and Development and Institute for Cancer Genetics, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Pei-Xin Lim
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Travis White
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brett Taylor
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Raymond Wang
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emilie C B Desclos
- Department of Medical Biology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Meghan R Sullivan
- Department of Microbiology and Molecular Genetics, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Hayley L Rein
- Department of Microbiology and Molecular Genetics, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kara A Bernstein
- Department of Microbiology and Molecular Genetics, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Przemek M Krawczyk
- Department of Medical Biology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Jean Gautier
- Department of Genetics and Development and Institute for Cancer Genetics, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Fabio Vanoli
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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21
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Kajitani GS, Nascimento LLDS, Neves MRDC, Leandro GDS, Garcia CCM, Menck CFM. Transcription blockage by DNA damage in nucleotide excision repair-related neurological dysfunctions. Semin Cell Dev Biol 2021; 114:20-35. [DOI: 10.1016/j.semcdb.2020.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 08/18/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022]
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22
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Mouse Models for Deciphering the Impact of Homologous Recombination on Tumorigenesis. Cancers (Basel) 2021; 13:cancers13092083. [PMID: 33923105 PMCID: PMC8123484 DOI: 10.3390/cancers13092083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/15/2022] Open
Abstract
Homologous recombination (HR) is a fundamental evolutionarily conserved process that plays prime role(s) in genome stability maintenance through DNA repair and through the protection and resumption of arrested replication forks. Many HR genes are deregulated in cancer cells. Notably, the breast cancer genes BRCA1 and BRCA2, two important HR players, are the most frequently mutated genes in familial breast and ovarian cancer. Transgenic mice constitute powerful tools to unravel the intricate mechanisms controlling tumorigenesis in vivo. However, the genes central to HR are essential in mammals, and their knockout leads to early embryonic lethality in mice. Elaborated strategies have been developed to overcome this difficulty, enabling one to analyze the consequences of HR disruption in vivo. In this review, we first briefly present the molecular mechanisms of HR in mammalian cells to introduce each factor in the HR process. Then, we present the different mouse models of HR invalidation and the consequences of HR inactivation on tumorigenesis. Finally, we discuss the use of mouse models for the development of targeted cancer therapies as well as perspectives on the future potential for understanding the mechanisms of HR inactivation-driven tumorigenesis in vivo.
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23
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Cicconi A, Rai R, Xiong X, Broton C, Al-Hiyasat A, Hu C, Dong S, Sun W, Garbarino J, Bindra RS, Schildkraut C, Chen Y, Chang S. Microcephalin 1/BRIT1-TRF2 interaction promotes telomere replication and repair, linking telomere dysfunction to primary microcephaly. Nat Commun 2020; 11:5861. [PMID: 33203878 PMCID: PMC7672075 DOI: 10.1038/s41467-020-19674-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 10/22/2020] [Indexed: 01/07/2023] Open
Abstract
Telomeres protect chromosome ends from inappropriately activating the DNA damage and repair responses. Primary microcephaly is a key clinical feature of several human telomere disorder syndromes, but how microcephaly is linked to dysfunctional telomeres is not known. Here, we show that the microcephalin 1/BRCT-repeats inhibitor of hTERT (MCPH1/BRIT1) protein, mutated in primary microcephaly, specifically interacts with the TRFH domain of the telomere binding protein TRF2. The crystal structure of the MCPH1-TRF2 complex reveals that this interaction is mediated by the MCPH1 330YRLSP334 motif. TRF2-dependent recruitment of MCPH1 promotes localization of DNA damage factors and homology directed repair of dysfunctional telomeres lacking POT1-TPP1. Additionally, MCPH1 is involved in the replication stress response, promoting telomere replication fork progression and restart of stalled telomere replication forks. Our work uncovers a previously unrecognized role for MCPH1 in promoting telomere replication, providing evidence that telomere replication defects may contribute to the onset of microcephaly.
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Affiliation(s)
- Alessandro Cicconi
- grid.47100.320000000419368710Department of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA
| | - Rekha Rai
- grid.47100.320000000419368710Department of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA
| | - Xuexue Xiong
- grid.507739.fState Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Cayla Broton
- grid.47100.320000000419368710Department of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA ,grid.5386.8000000041936877XTri- Institutional MD/PhD Program, Weill Cornell Medical College, New York, NY 10065 USA
| | - Amer Al-Hiyasat
- grid.47100.320000000419368710Department of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA ,grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA
| | - Chunyi Hu
- grid.507739.fState Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Siying Dong
- grid.507739.fState Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Wenqi Sun
- grid.507739.fState Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Jennifer Garbarino
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA ,grid.47100.320000000419368710Department of Therapeutic Radiology, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA
| | - Ranjit S. Bindra
- grid.47100.320000000419368710Department of Therapeutic Radiology, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA ,grid.47100.320000000419368710Department of Experimental Pathology, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA
| | - Carl Schildkraut
- grid.251993.50000000121791997Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
| | - Yong Chen
- grid.507739.fState Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Sandy Chang
- grid.47100.320000000419368710Department of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA ,grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA ,grid.47100.320000000419368710Department of Pathology, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520 USA
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24
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Sinha A, Saleh A, Endersby R, Yuan SH, Chokshi CR, Brown KR, Kuzio B, Kauppinen T, Singh SK, Baker SJ, McKinnon PJ, Katyal S. RAD51-Mediated DNA Homologous Recombination Is Independent of PTEN Mutational Status. Cancers (Basel) 2020; 12:cancers12113178. [PMID: 33138032 PMCID: PMC7693555 DOI: 10.3390/cancers12113178] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 10/20/2020] [Indexed: 12/22/2022] Open
Abstract
Simple Summary PTEN is an important tumor suppressor that is frequently mutated in malignancy. PTEN mutational loss has been associated with reduced RAD51 expression and homologous recombination deficiency (HRD), however; recent studies have failed to recapitulate these findings. Here, we show that RAD51 expression, foci formation and homologous recombination repair activity are unaltered in normal and tumorigenic PTEN-deficient cells and patient samples. Furthermore, we show that PTEN-deficient tumor cell lines do not synergize with the clinical PARP inhibitor olaparib, underscoring a need to discontinue its use in treating patients with PTEN-deficient tumors that do not otherwise exhibit HRD. Abstract PTEN mutation occurs in a variety of aggressive cancers and is associated with poor patient outcomes. Recent studies have linked mutational loss of PTEN to reduced RAD51 expression and function, a key factor involved in the homologous recombination (HR) pathway. However, these studies remain controversial, as they fail to establish a definitive causal link to RAD51 expression that is PTEN-dependent, while other studies have not been able to recapitulate the relationship between the PTEN expression and the RAD51/HR function. Resolution of this apparent conundrum is essential due to the clinically-significant implication that PTEN-deficient tumors may be sensitive to poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) commonly used in the clinical management of BRCA-mutated and other HR-deficient (HRD) tumors. Methods: Primary Pten-deficient (and corresponding wild-type) mouse embryonic fibroblasts (MEFs) and astrocytes and PTEN-null human tumor cell lines and primary cells were assessed for RAD51 expression (via the Western blot analysis) and DNA damage repair analyses (via alkali comet and γH2AX foci assays). RAD51 foci analysis was used to measure HR-dependent DNA repair. Xrcc2-deficient MEFs served as an HR-deficient control, while the stable knockdown of RAD51 (shRAD51) served to control for the relative RAD51/HR-mediated repair and the phospho-53BP1 foci analysis served to confirm and measure non-homologous end joining (NHEJ) activity in PTEN-deficient and shRAD51-expressing (HRD) lines. Cell proliferation studies were used to measure any potential added sensitivity of PTEN-null cells to the clinically-relevant PARPi, olaparib. RAD51 levels and DNA damage response signaling were assessed in PTEN-mutant brain tumor initiating cells (BTICs) derived from primary and recurrent glioblastoma multiforme (GBM) patients, while expression of RAD51 and its paralogs were examined as a function of the PTEN status in the RNA expression datasets isolated from primary GBM tumor specimens and BTICs. Results: Pten knockout primary murine cells display unaltered RAD51 expression, endogenous and DNA strand break-induced RAD51 foci and robust DNA repair activity. Defective HR was only observed in the cells lacking Xrcc2. Likewise, human glioblastoma multiforme (GBM) cell lines with known PTEN deficiency (U87, PTEN-mutated; U251 and U373, PTEN-null) show apparent expression of RAD51 and display efficient DNA repair activity. Only GBM cells stably expressing shRNAs against RAD51 (shRAD51) display dysfunctional DNA repair activity and reduced proliferative capacity, which is exacerbated by PARPi treatment. Furthermore, GBM patient-derived BTICs displayed robust RAD51 expression and intact DNA damage response signaling in spite of PTEN-inactivating mutations. RNA expression analysis of primary GBM tissue specimens and BTICs demonstrate stable levels of RAD51 and its paralogs (RAD51B, RAD51C, RAD51D, XRCC2, XRCC3, and DMC1), regardless of the PTEN mutational status. Conclusions: Our findings demonstrate definitively that PTEN loss does not alter the RAD51 expression, its paralogs, or the HR activity. Furthermore, deficiency in PTEN alone is not sufficient to impart enhanced sensitivity to PARPi associated with HRD. This study is the first to unequivocally demonstrate that PTEN deficiency is not linked to the RAD51 expression or the HR activity amongst primary neural and non-neural Pten-null cells, PTEN-deficient tumor cell lines, and primary PTEN-mutant GBM patient-derived tissue specimens and BTICs.
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Affiliation(s)
- Asha Sinha
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Ali Saleh
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Raelene Endersby
- Telethon Kids Institute, Perth Children’s Hospital, 15 Hospital Avenue, Perth, WA 6009, Australia;
- Centre for Child Health Research, University of Western Australia, 15 Hospital Avenue, Perth, WA 6009, Australia
| | - Shek H. Yuan
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Chirayu R. Chokshi
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8S 4L8, Canada; (C.R.C.); (S.K.S.)
| | - Kevin R. Brown
- Donnelly Centre, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada;
| | - Bozena Kuzio
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Tiina Kauppinen
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Health Sciences Centre, 710 William Avenue, Winnipeg, MB R3E 0Z3, Canada
| | - Sheila K. Singh
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8S 4L8, Canada; (C.R.C.); (S.K.S.)
- Department of Surgery, Faculty of Health Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Suzanne J. Baker
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA;
| | - Peter J. McKinnon
- Department of Genetics, St Jude Children’s Research Hospital, Memphis, TN 38105-3678, USA;
| | - Sachin Katyal
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E 0T6, Canada; (A.S.); (A.S.); (S.H.Y.); (B.K.); (T.K.)
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
- Correspondence: ; Tel.: +1-204-787-2765; Fax: +1-204-787-2190
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25
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Li J, Shang Y, Wang L, Zhao B, Sun C, Li J, Liu S, Li C, Tang M, Meng FL, Zheng P. Genome integrity and neurogenesis of postnatal hippocampal neural stem/progenitor cells require a unique regulator Filia. SCIENCE ADVANCES 2020; 6:6/44/eaba0682. [PMID: 33115731 PMCID: PMC7608785 DOI: 10.1126/sciadv.aba0682] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 09/01/2020] [Indexed: 05/03/2023]
Abstract
Endogenous DNA double-strand breaks (DSBs) formation and repair in neural stem/progenitor cells (NSPCs) play fundamental roles in neurogenesis and neurodevelopmental disorders. NSPCs exhibit heterogeneity in terms of lineage fates and neurogenesis activity. Whether NSPCs also have heterogeneous regulations on DSB formation and repair to accommodate region-specific neurogenesis has not been explored. Here, we identified a regional regulator Filia, which is predominantly expressed in mouse hippocampal NSPCs after birth and regulates DNA DSB formation and repair. On one hand, Filia protects stalling replication forks and prevents the replication stress-associated DNA DSB formation. On the other hand, Filia facilitates the homologous recombination-mediated DNA DSB repair. Consequently, Filia-/- mice had impaired hippocampal NSPC proliferation and neurogenesis and were deficient in learning, memory, and mood regulations. Thus, our study provided the first proof of concept demonstrating the region-specific regulations of DSB formation and repair in subtypes of NSPCs.
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Affiliation(s)
- Jingzheng Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yafang Shang
- University of Chinese Academy of Sciences, Beijing 101408, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Bo Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Chunli Sun
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Jiali Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650201, China
| | - Siling Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650201, China
| | - Cong Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Min Tang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
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26
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Pizzamiglio L, Focchi E, Antonucci F. ATM Protein Kinase: Old and New Implications in Neuronal Pathways and Brain Circuitry. Cells 2020; 9:E1969. [PMID: 32858941 PMCID: PMC7564642 DOI: 10.3390/cells9091969] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/14/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022] Open
Abstract
Despite that the human autosomal recessive disease ataxia telangiectasia (A-T) is a rare pathology, interest in the function of ataxia-telangiectasia mutated protein (ATM) is extensive. From a clinical point of view, the role of ATM in the central nervous system (CNS) is the most impacting, as motor disability is the predominant symptom affecting A-T patients. Coherently, spino-cerebellar neurodegeneration is the principal hallmark of A-T and other CNS regions such as dentate and olivary nuclei and brain stem are implicated in A-T pathophysiology. Recently, several preclinical studies also highlighted the involvement of ATM in the cerebral cortex and hippocampus, thus extending A-T symptomatology to new brain areas and pathways. Here, we review old and recent evidence that largely demonstrates not only the historical ATM account in DNA damage response and cell cycle regulation, but the multiple pathways through which ATM controls oxidative stress homeostasis, insulin signalling pathways, epigenetic regulation, synaptic transmission, and excitatory-inhibitory balance. We also summarise recent evidence on ATM implication in neurological and cognitive diseases beyond A-T, bringing out ATM as new pathological substrate and potential therapeutic target.
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Affiliation(s)
- Lara Pizzamiglio
- Institute of Molecular and Cellular Pharmacology (IPMC), Université Côte d’Azur (UCA), CNRS UMR7275, 06560 Valbonne-Sophia Antipolis, France;
| | - Elisa Focchi
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, 20100 Milan, Italy;
| | - Flavia Antonucci
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, 20100 Milan, Italy;
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27
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Symmetric neural progenitor divisions require chromatin-mediated homologous recombination DNA repair by Ino80. Nat Commun 2020; 11:3839. [PMID: 32737294 PMCID: PMC7395731 DOI: 10.1038/s41467-020-17551-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022] Open
Abstract
Chromatin regulates spatiotemporal gene expression during neurodevelopment, but it also mediates DNA damage repair essential to proliferating neural progenitor cells (NPCs). Here, we uncover molecularly dissociable roles for nucleosome remodeler Ino80 in chromatin-mediated transcriptional regulation and genome maintenance in corticogenesis. We find that conditional Ino80 deletion from cortical NPCs impairs DNA double-strand break (DSB) repair, triggering p53-dependent apoptosis and microcephaly. Using an in vivo DSB repair pathway assay, we find that Ino80 is selectively required for homologous recombination (HR) DNA repair, which is mechanistically distinct from Ino80 function in YY1-associated transcription. Unexpectedly, sensitivity to loss of Ino80-mediated HR is dependent on NPC division mode: Ino80 deletion leads to unrepaired DNA breaks and apoptosis in symmetric NPC-NPC divisions, but not in asymmetric neurogenic divisions. This division mode dependence is phenocopied following conditional deletion of HR gene Brca2. Thus, distinct modes of NPC division have divergent requirements for Ino80-dependent HR DNA repair.
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28
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Gabriel E, Ramani A, Altinisik N, Gopalakrishnan J. Human Brain Organoids to Decode Mechanisms of Microcephaly. Front Cell Neurosci 2020; 14:115. [PMID: 32457578 PMCID: PMC7225330 DOI: 10.3389/fncel.2020.00115] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
Brain organoids are stem cell-based self-assembling 3D structures that recapitulate early events of human brain development. Recent improvements with patient-specific 3D brain organoids have begun to elucidate unprecedented details of the defective mechanisms that cause neurodevelopmental disorders of congenital and acquired microcephaly. In particular, brain organoids derived from primary microcephaly patients have uncovered mechanisms that deregulate neural stem cell proliferation, maintenance, and differentiation. Not only did brain organoids reveal unknown aspects of neurogenesis but also have illuminated surprising roles of cellular structures of centrosomes and primary cilia in regulating neurogenesis during brain development. Here, we discuss how brain organoids have started contributing to decoding the complexities of microcephaly, which are unlikely to be identified in the existing non-human models. Finally, we discuss the yet unresolved questions and challenges that can be addressed with the use of brain organoids as in vitro models of neurodevelopmental disorders.
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Affiliation(s)
- Elke Gabriel
- Laboratory for Centrosome and Cytoskeleton Biology, Institute für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Anand Ramani
- Laboratory for Centrosome and Cytoskeleton Biology, Institute für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Nazlican Altinisik
- Laboratory for Centrosome and Cytoskeleton Biology, Institute für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Jay Gopalakrishnan
- Laboratory for Centrosome and Cytoskeleton Biology, Institute für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität, Düsseldorf, Germany
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29
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OKAWA A, MORIOKA T, IMAOKA T, KAKINUMA S, MATSUMOTO Y. Differential expression of DNA-dependent protein kinase catalytic subunit in the brain of neonatal mice and young adult mice. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2020; 96:171-179. [PMID: 32389917 PMCID: PMC7248211 DOI: 10.2183/pjab.96.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/10/2020] [Indexed: 06/11/2023]
Abstract
It is generally thought that younger people are more susceptible to cancer development after exposure to ionizing radiation in reference to epidemiological studies and animal experiments. However, little is known about the age-dependent alteration in DNA repair ability. In the present study, we examined the expression levels of proteins involved in the repair of DNA double-strand breaks through non-homologous end joining (NHEJ), i.e., DNA-dependent protein kinase catalytic subunit (DNA-PKcs), X-ray repair cross-complementing 4 (XRCC4) and XRCC4-like factor (XLF). We found that the expression of DNA-PKcs in brain tissues was higher in neonatal mice (1 week after birth) than in young adult mice (7 weeks after birth). In association with this, DNA double-strand breaks were repaired more rapidly in the brain tissues of neonatal mice than in those of young adult mice. The current results suggested a possible role for DNA-PKcs protecting developing brain tissues from DNA double-strand breaks.
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Affiliation(s)
- Aoi OKAWA
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Takamitsu MORIOKA
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Tatsuhiko IMAOKA
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Shizuko KAKINUMA
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Yoshihisa MATSUMOTO
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
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30
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Thadathil N, Hori R, Xiao J, Khan MM. DNA double-strand breaks: a potential therapeutic target for neurodegenerative diseases. Chromosome Res 2019; 27:345-364. [PMID: 31707536 PMCID: PMC7934912 DOI: 10.1007/s10577-019-09617-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/08/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022]
Abstract
The complexity of neurodegeneration restricts the ability to understand and treat the neurological disorders affecting millions of people worldwide. Therefore, there is an unmet need to develop new and more effective therapeutic strategies to combat these devastating conditions and that will only be achieved with a better understanding of the biological mechanism associated with disease conditions. Recent studies highlight the role of DNA damage, particularly, DNA double-strand breaks (DSBs), in the progression of neuronal loss in a broad spectrum of human neurodegenerative diseases. This is not unexpected because neurons are prone to DNA damage due to their non-proliferative nature and high metabolic activity. However, it is not clear if DSBs is a primary driver of neuronal loss in disease conditions or simply occurs concomitant with disease progression. Here, we provide evidence that supports a critical role of DSBs in the pathogenesis of the neurodegenerative diseases. Among different kinds of DNA damages, DSBs are the most harmful and perilous type of DNA damage and can lead to cell death if left unrepaired or repaired with error. In this review, we explore the current state of knowledge regarding the role of DSBs repair mechanisms in preserving neuronal function and survival and describe how DSBs could drive the molecular mechanisms resulting in neuronal death in neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. We also discuss the potential implications of DSBs as a novel therapeutic target and prognostic marker in patients with neurodegenerative conditions.
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Affiliation(s)
- Nidheesh Thadathil
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Roderick Hori
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jianfeng Xiao
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Mohammad Moshahid Khan
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
- Division of Rehabilitation Sciences and Department of Physical Therapy, College of Health Professions, University of Tennessee Health Science Center, Memphis, TN, USA.
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
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31
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Waisertreiger I, Popovich K, Block M, Anderson KR, Barlow JH. Visualizing locus-specific sister chromatid exchange reveals differential patterns of replication stress-induced fragile site breakage. Oncogene 2019; 39:1260-1272. [PMID: 31636383 PMCID: PMC7002298 DOI: 10.1038/s41388-019-1054-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 09/26/2019] [Accepted: 10/02/2019] [Indexed: 11/09/2022]
Abstract
Chromosomal fragile sites are genomic loci sensitive to replication stress which accumulate high levels of DNA damage, and are frequently mutated in cancers. Fragile site damage is thought to arise from the aberrant repair of spontaneous replication stress, however successful fragile site repair cannot be calculated using existing techniques. Here, we report a new assay measuring recombination-mediated repair at endogenous genomic loci by combining a sister chromatid exchange (SCE) assay with fluorescent in situ hybridization (SCE-FISH). Using SCE-FISH, we find that endogenous and exogenous replication stress generated unrepaired breaks and SCEs at fragile sites. We also find that distinct sources of replication stress induce distinct patterns of breakage: ATR inhibition induces more breaks at early replicating fragile sites (ERFS), while ERFS and late-replicating common fragile sites (CFS) are equally fragile in response to aphidicolin. Furthermore, SCEs were suppressed at fragile sites near centromeres in response to replication stress, suggesting that genomic location influences DNA repair pathway choice. SCE-FISH also measured successful recombination in human primary lymphocytes, and identificed the proto-oncogene BCL2 as a replication stress-induced fragile site. These findings demonstrate that SCE-FISH frequency at fragile sites is a sensitive indicator of replication stress, and that large-scale genome organization influences DNA repair pathway choice.
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Affiliation(s)
- Irina Waisertreiger
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA
| | - Katherine Popovich
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA
| | - Maya Block
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA
| | - Krista R Anderson
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA
| | - Jacqueline H Barlow
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA. .,Genome Center, University of California, Davis, CA, 95616, USA.
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32
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Bosshard S, Duroy PO, Mermod N. A role for alternative end-joining factors in homologous recombination and genome editing in Chinese hamster ovary cells. DNA Repair (Amst) 2019; 82:102691. [PMID: 31476574 DOI: 10.1016/j.dnarep.2019.102691] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 12/22/2022]
Abstract
CRISPR technologies greatly foster genome editing in mammalian cells through site-directed DNA double strand breaks (DSBs). However, precise editing outcomes, as mediated by homologous recombination (HR) repair, are typically infrequent and outnumbered by undesired genome alterations. By using knockdown and overexpression studies in Chinese hamster ovary (CHO) cells as well as characterizing repaired DNA junctions, we found that efficient HR-mediated genome editing depends on alternative end-joining (alt-EJ) DNA repair activities, a family of incompletely characterized DNA repair pathways traditionally considered to oppose HR. This dependency was influenced by the CRISPR nuclease type and the DSB-to-mutation distance, but not by the DNA sequence surrounding the DSBs or reporter cell line. We also identified elevated Mre11 and Pari, and low Rad51 expression levels as the most rate-limiting factors for HR in CHO cells. Counteracting these three bottlenecks improved precise genome editing by up to 75%. Altogether, our study provides novel insights into the complex interplay of alt-EJ and HR repair pathways, highlighting their relevance for developing improved genome editing strategies.
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Affiliation(s)
- Sandra Bosshard
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Pierre-Olivier Duroy
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Mermod
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland.
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33
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Abstract
XRCC2 is one of five somatic RAD51 paralogs, all of which have Walker A and B ATPase motifs. Each of the paralogs, including XRCC2, has a function in DNA double-strand break repair by homologous recombination (HR). However, their individual roles are not as well understood as that of RAD51 itself. The XRCC2 protein forms a complex (BCDX2) with three other RAD51 paralogs, RAD51B, RAD51C and RAD51D. It is believed that the BCDX2 complex mediates HR downstream of BRCA2 but upstream of RAD51, as XRCC2 is involved in the assembly of RAD51 into DNA damage foci. XRCC2 can bind DNA and, along with RAD51D, can promote homologous pairing in vitro. Consistent with its role in HR, XRCC2-deficient cells have increased levels of spontaneous chromosome instability, and exhibit hypersensitivity to DNA interstrand crosslinking agents such as mitomycin C and cisplatin as well as ionizing radiation, alkylating agents and aldehydes. XRCC2 also functions in promoting DNA replication and chromosome segregation. Biallelic mutation of XRCC2 (FANCU) causes the FA-U subtype of FA, while heterozygosity for deleterious mutations in XRCC2 may be associated with an increased breast cancer risk. XRCC2 appears to function 'downstream' in the FA pathway, since it is not required for FANCD2 monoubiquitination, which is the central step in the FA pathway. Clinically, the only known FA-U patient in the world exhibits severe congenital abnormalities, but had not developed, by seven years of age, the bone marrow failure and cancer that are often seen in patients from other FA complementation groups.
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Affiliation(s)
- Paul R Andreassen
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA; (PRA); Department of Pediatrics III, University Children's Hospital Essen, University Duisburg-Essen, Essen Germany; (HH)
| | - Helmut Hanenberg
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA; (PRA); Department of Pediatrics III, University Children's Hospital Essen, University Duisburg-Essen, Essen Germany; (HH)
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34
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Khan C, Muliyil S, Rao BJ. Genome Damage Sensing Leads to Tissue Homeostasis in Drosophila. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 345:173-224. [PMID: 30904193 DOI: 10.1016/bs.ircmb.2018.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA repair is a critical cellular process required for the maintenance of genomic integrity. It is now well appreciated that cells employ several DNA repair pathways to take care of distinct types of DNA damage. It is also well known that a cascade of signals namely DNA damage response or DDR is activated in response to DNA damage which comprise cellular responses, such as cell cycle arrest, DNA repair and cell death, if the damage is irreparable. There is also emerging literature suggesting a cross-talk between DNA damage signaling and several signaling networks within a cell. Moreover, cell death players themselves are also well known to engage in processes outside their canonical function of apoptosis. This chapter attempts to build a link between DNA damage, DDR and signaling from the studies mainly conducted in mammals and Drosophila model systems, with a special emphasis on their relevance in overall tissue homeostasis and development.
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Affiliation(s)
- Chaitali Khan
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Sonia Muliyil
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - B J Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India.
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35
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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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36
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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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37
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Kim J, Kim J, Lee Y. DNA polymerase β deficiency in the p53 null cerebellum leads to medulloblastoma formation. Biochem Biophys Res Commun 2018; 505:548-553. [PMID: 30274781 DOI: 10.1016/j.bbrc.2018.09.166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 09/26/2018] [Indexed: 10/28/2022]
Abstract
Defects in DNA damage response or repair mechanisms during neurogenesis result in genomic instability, which is causative for several neural defects. These include brain tumors, particularly medulloblastoma, which occurs in the cerebellum with a high incidence in children. We generated an animal model with defective base excision repair during brain development through selective inactivation of DNA polymerase β (Polb) in neuroprogenitor cells. All of Polb conditional knockout mice developed medulloblastoma in a p53 null background, similar to the Xrcc1 and p53 double deficient animal model. XRCC1 is a scaffolding protein which is involved in DNA damage repair and binds to POLB. In both animal models, the histopathological characteristics of the medulloblastoma were similar to those of human classic medulloblastoma. Brain tumor development was slower in the Polb and p53 double null animals than in the Xrcc1 and p53 double knockout animals. Molecular marker analysis suggested that Polb- and Xrcc1-deficient medulloblastomas belonged to the SHHα subtype, underscoring the important role of genomic stability in preventing this devastating pediatric cerebellar tumor.
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Affiliation(s)
- Jusik Kim
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Republic of Korea; Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, Republic of Korea
| | - Jaemi Kim
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Republic of Korea; Genome Stability Institute, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Youngsoo Lee
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Republic of Korea; Genome Stability Institute, Ajou University School of Medicine, Suwon, Republic of Korea; Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, Republic of Korea.
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38
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Vesikansa A. Unraveling of Central Nervous System Disease Mechanisms Using CRISPR Genome Manipulation. J Cent Nerv Syst Dis 2018; 10:1179573518787469. [PMID: 30013417 PMCID: PMC6043941 DOI: 10.1177/1179573518787469] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 06/09/2018] [Indexed: 12/26/2022] Open
Abstract
The complex structure and highly variable gene expression profile of the brain makes it among the most challenging fields to study in both basic and translational biological research. Most of the brain diseases are multifactorial and despite the rapidly increasing genomic data, molecular pathways and causal links between genes and central nervous system (CNS) diseases are largely unknown. The advent of an easy and flexible CRISPR-Cas genome editing technology has rapidly revolutionized the field of functional genomics and opened unprecedented possibilities to dissect the mechanisms of CNS disease. CRISPR-Cas allows a plenitude of applications for both gene-focused and genome-wide approaches, ranging from original “gene scissors” making permanent modifications in the genome to the regulation of gene expression and epigenetics. CRISPR technology provides a unique opportunity to establish new cellular and animal models of CNS diseases and holds potential for breakthroughs in the CNS research and drug development.
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Affiliation(s)
- Aino Vesikansa
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.,Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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39
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Abstract
Primary microcephaly (MCPH, for "microcephaly primary hereditary") is a disorder of brain development that results in a head circumference more than 3 standard deviations below the mean for age and gender. It has a wide variety of causes, including toxic exposures, in utero infections, and metabolic conditions. While the genetic microcephaly syndromes are relatively rare, studying these syndromes can reveal molecular mechanisms that are critical in the regulation of neural progenitor cells, brain size, and human brain evolution. Many of the causative genes for MCPH encode centrosomal proteins involved in centriole biogenesis. However, other MCPH genes fall under different mechanistic categories, notably DNA replication and repair. Recent gene discoveries and functional studies have implicated novel cellular processes, such as cytokinesis, centromere and kinetochore function, transmembrane or intracellular transport, Wnt signaling, and autophagy, as well as the apical polarity complex. Thus, MCPH genes implicate a wide variety of molecular and cellular mechanisms in the regulation of cerebral cortical size during development.
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Affiliation(s)
- Divya Jayaraman
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Harvard-MIT MD-PhD Program, Harvard Medical School, Boston, Massachusetts 02115, USA.,Current affiliation: Boston Combined Residency Program (Child Neurology), Boston Children's Hospital, Boston, Massachusetts 02115, USA;
| | - Byoung-Il Bae
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06510, USA;
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Departments of Pediatrics and Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA;
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40
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Goffena J, Lefcort F, Zhang Y, Lehrmann E, Chaverra M, Felig J, Walters J, Buksch R, Becker KG, George L. Elongator and codon bias regulate protein levels in mammalian peripheral neurons. Nat Commun 2018; 9:889. [PMID: 29497044 PMCID: PMC5832791 DOI: 10.1038/s41467-018-03221-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 01/29/2018] [Indexed: 12/16/2022] Open
Abstract
Familial dysautonomia (FD) results from mutation in IKBKAP/ELP1, a gene encoding the scaffolding protein for the Elongator complex. This highly conserved complex is required for the translation of codon-biased genes in lower organisms. Here we investigate whether Elongator serves a similar function in mammalian peripheral neurons, the population devastated in FD. Using codon-biased eGFP sensors, and multiplexing of codon usage with transcriptome and proteome analyses of over 6,000 genes, we identify two categories of genes, as well as specific gene identities that depend on Elongator for normal expression. Moreover, we show that multiple genes in the DNA damage repair pathway are codon-biased, and that with Elongator loss, their misregulation is correlated with elevated levels of DNA damage. These findings link Elongator's function in the translation of codon-biased genes with both the developmental and neurodegenerative phenotypes of FD, and also clarify the increased risk of cancer associated with the disease.
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Affiliation(s)
- Joy Goffena
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT, 59101, USA
| | - Frances Lefcort
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, 59717, USA
| | - Yongqing Zhang
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Elin Lehrmann
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Marta Chaverra
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, 59717, USA
| | - Jehremy Felig
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT, 59101, USA
| | - Joseph Walters
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT, 59101, USA
| | - Richard Buksch
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT, 59101, USA
| | - Kevin G Becker
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Lynn George
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT, 59101, USA.
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41
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Thompson DB, Aboulhouda S, Hysolli E, Smith CJ, Wang S, Castanon O, Church GM. The Future of Multiplexed Eukaryotic Genome Engineering. ACS Chem Biol 2018; 13:313-325. [PMID: 29241002 PMCID: PMC5880278 DOI: 10.1021/acschembio.7b00842] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Multiplex genome editing is the simultaneous introduction of multiple distinct modifications to a given genome. Though in its infancy, maturation of this field will facilitate powerful new biomedical research approaches and will enable a host of far-reaching biological engineering applications, including new therapeutic modalities and industrial applications, as well as "genome writing" and de-extinction efforts. In this Perspective, we focus on multiplex editing of large eukaryotic genomes. We describe the current state of multiplexed genome editing, the current limits of our ability to multiplex edits, and provide perspective on the many applications that fully realized multiplex editing technologies would enable in higher eukaryotic genomes. We offer a broad look at future directions, covering emergent CRISPR-based technologies, advances in intracellular delivery, and new DNA assembly approaches that may enable future genome editing on a massively multiplexed scale.
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Affiliation(s)
- David B. Thompson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Soufiane Aboulhouda
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Eriona Hysolli
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Cory J. Smith
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Stan Wang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Oscar Castanon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay, 91128 Palaiseau, France
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
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42
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Newman EA, Chukkapalli S, Bashllari D, Thomas TT, Van Noord RA, Lawlor ER, Hoenerhoff MJ, Opipari AW, Opipari VP. Alternative NHEJ pathway proteins as components of MYCN oncogenic activity in human neural crest stem cell differentiation: implications for neuroblastoma initiation. Cell Death Dis 2017; 8:3208. [PMID: 29238067 PMCID: PMC5870584 DOI: 10.1038/s41419-017-0004-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 12/14/2022]
Abstract
Neuroblastoma is a cancer of neural crest stem cell (NCSC) lineage. Signaling pathways that regulate NCSC differentiation have been implicated in neuroblastoma tumorigenesis. This is exemplified by MYCN oncogene targets that balance proliferation, differentiation, and cell death similarly in normal NCSC and in high-risk neuroblastoma. Our previous work discovered a survival mechanism by which MYCN-amplified neuroblastoma circumvents cell death by upregulating components of the error-prone non-canonical alternative nonhomologous end-joining (alt-NHEJ) DNA repair pathway. Similar to proliferating stem cells, high-risk neuroblastoma cells have enhanced DNA repair capacity, overcoming DNA damage with higher repair efficiency than somatic cells. Adequate DNA maintenance is required for lineage protection as stem cells proliferate and during tumor progression to overcome oncogene-induced replication stress. On this basis, we hypothesized that alt-NHEJ overexpression in neuroblastoma is a cancer cell survival mechanism that originates from DNA repair systems of NCSC, the presumed progenitor cell of origin. A human NCSC model was generated in which inducible MYCN triggered an immortalized phenotype capable of forming metastatic neuroectodermal tumors in mice, resembling human neuroblastoma. Critical alt-NHEJ components (DNA Ligase III, DNA Ligase I, and Poly [ADP-ribose polymerase 1]) were highly expressed in normal early NCSC, and decreased as cells became terminally differentiated. Constitutive MYCN expression maintained high alt-NHEJ protein expression, preserving the expression pattern of the immature neural phenotype. siRNA knockdown of alt-NHEJ components reversed MYCN effects on NCSC proliferation, invasion, and migration. DNA Ligase III, Ligase I, and PARP1 silencing significantly decreased neuroblastoma markers expression (TH, Phox2b, and TRKB). These results utilized the first human NCSC model of neuroblastoma to uncover an important link between MYCN and alt-NHEJ expression in developmental tumor initiation, setting precedence to investigate alt-NHEJ repair mechanics in neuroblastoma DNA maintenance.
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Affiliation(s)
- Erika A Newman
- Department of Surgery, C.S. Mott Children and Women's Hospital, Mott Solid Tumor Oncology Program, The University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Sahiti Chukkapalli
- Department of Surgery, C.S. Mott Children and Women's Hospital, Mott Solid Tumor Oncology Program, The University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniela Bashllari
- Department of Surgery, C.S. Mott Children and Women's Hospital, Mott Solid Tumor Oncology Program, The University of Michigan Medical School, Ann Arbor, MI, USA
| | - Tina T Thomas
- Department of Surgery, C.S. Mott Children and Women's Hospital, Mott Solid Tumor Oncology Program, The University of Michigan Medical School, Ann Arbor, MI, USA
| | - Raelene A Van Noord
- Department of Surgery, C.S. Mott Children and Women's Hospital, Mott Solid Tumor Oncology Program, The University of Michigan Medical School, Ann Arbor, MI, USA
| | - Elizabeth R Lawlor
- Department of Pathology, The University of Michigan Medical School, Ann Arbor, MI, USA.,Department of Pediatrics, C.S. Mott Children and Women's Hospital, The University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mark J Hoenerhoff
- In Vivo Animal Core (IVAC), The University of Michigan Medical School, Ann Arbor, MI, USA
| | - Anthony W Opipari
- Department of Obstetrics and Gynecology, C.S. Mott Children and Women's Hospital, The University of Michigan Medical School, Ann Arbor, MI, USA
| | - Valerie P Opipari
- Department of Pediatrics, C.S. Mott Children and Women's Hospital, The University of Michigan Medical School, Ann Arbor, MI, USA
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43
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Kim J, Choi I, Lee Y. Involvement of Atm and Trp53 in neural cell loss due to Terf2 inactivation during mouse brain development. Histochem Cell Biol 2017. [PMID: 28620865 PMCID: PMC5641282 DOI: 10.1007/s00418-017-1591-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Maintenance of genomic integrity is one of the critical features for proper neurodevelopment and inhibition of neurological diseases. The signals from both ATM and ATR to TP53 are well-known mechanisms to remove neural cells with DNA damage during neurogenesis. Here we examined the involvement of Atm and Atr in genomic instability due to Terf2 inactivation during mouse brain development. Selective inactivation of Terf2 in neural progenitors induced apoptosis, resulting in a complete loss of the brain structure. This neural loss was rescued partially in both Atm and Trp53 deficiency, but not in an Atr-deficient background in the mouse. Atm inactivation resulted in incomplete brain structures, whereas p53 deficiency led to the formation of multinucleated giant neural cells and the disruption of the brain structure. These giant neural cells disappeared in Lig4 deficiency. These data demonstrate ATM and TP53 are important for the maintenance of telomere homeostasis and the surveillance of telomere dysfunction during neurogenesis.
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Affiliation(s)
- Jusik Kim
- Genomic Instability Research Center, School of Medicine, Ajou University, Suwon, 16499, Republic of Korea
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, 16499, Republic of Korea
| | - Inseo Choi
- Genomic Instability Research Center, School of Medicine, Ajou University, Suwon, 16499, Republic of Korea
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, 16499, Republic of Korea
| | - Youngsoo Lee
- Genomic Instability Research Center, School of Medicine, Ajou University, Suwon, 16499, Republic of Korea.
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, 16499, Republic of Korea.
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44
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Rong H, Gu S, Zhang G, Kang L, Yang M, Zhang J, Shen X, Guan H. MiR-2964a-5p binding site SNP regulates ATM expression contributing to age-related cataract risk. Oncotarget 2017; 8:84945-84957. [PMID: 29156695 PMCID: PMC5689585 DOI: 10.18632/oncotarget.17600] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/11/2017] [Indexed: 01/12/2023] Open
Abstract
This study was to explore the involvement of DNA repair genes in the pathogenesis of age-related cataract (ARC). We genotyped nine single nucleotide polymorphisms (SNPs) of genes responsible to DNA double strand breaks (DSBs) in 804 ARC cases and 804 controls in a cohort of eye diseases in Chinese population and found that the ataxia telangiectasia mutated (ATM) gene-rs4585:G>T was significantly associated with ARC risk. An in vitro functional test found that miR-2964a-5p specifically down-regulated luciferase reporter expression and ATM expression in the cell lines transfected with rs4585 T allele compared to rs4585 G allele. The molecular assay on human tissue samples discovered that ATM expression was down-regulated in majority of ARC tissues and correlated with ATM genotypes. In addition, the Comet assay of cellular DNA damage of peripheral lymphocytes indicated that individuals carrying the G allele (GG/GT) of ATM-rs4585 had lower DNA breaks compared to individuals with TT genotype. These findings suggested that the SNP rs4585 in ATM might affect ARC risk through modulating the regulatory affinity of miR-2964a-5p. The reduced DSBs repair might be involved in ARC pathogenesis.
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Affiliation(s)
- Han Rong
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Eye Department, The Affiliated Huai'an Hospital of Xuzhou Medical University and The Second People's Hospital of Huai'an, Huai'an, Jiangsu, China
| | - Shanshan Gu
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Guowei Zhang
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Lihua Kang
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Mei Yang
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Junfang Zhang
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Xinyue Shen
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Huaijin Guan
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
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45
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Khoronenkova SV. Mechanisms of Non-canonical Activation of Ataxia Telangiectasia Mutated. BIOCHEMISTRY (MOSCOW) 2017; 81:1669-1675. [PMID: 28260489 DOI: 10.1134/s0006297916130058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
ATM is a master regulator of the cellular response to DNA damage. The classical mechanism of ATM activation involves its monomerization in response to DNA double-strand breaks, resulting in ATM-dependent phosphorylation of more than a thousand substrates required for cell cycle progression, DNA repair, and apoptosis. Here, new experimental evidence for non-canonical mechanisms of ATM activation in response to stimuli distinct from DNA double-strand breaks is discussed. It includes cytoskeletal changes, chromatin modifications, RNA-DNA hybrids, and DNA single-strand breaks. Noncanonical ATM activation may be important for the pathology of the multisystemic disease Ataxia Telangiectasia.
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Affiliation(s)
- S V Khoronenkova
- University of Cambridge, Department of Biochemistry, Cambridge, CB2 1GA, UK.
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46
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Enriquez-Rios V, Dumitrache LC, Downing SM, Li Y, Brown EJ, Russell HR, McKinnon PJ. DNA-PKcs, ATM, and ATR Interplay Maintains Genome Integrity during Neurogenesis. J Neurosci 2017; 37:893-905. [PMID: 28123024 PMCID: PMC5296783 DOI: 10.1523/jneurosci.4213-15.2016] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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Affiliation(s)
- Vanessa Enriquez-Rios
- Department of Genetics, St Jude Children's Research Hospital, Memphis, Tennessee 38105
- College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, and
| | - Lavinia C Dumitrache
- Department of Genetics, St Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Susanna M Downing
- Department of Genetics, St Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Yang Li
- Department of Genetics, St Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Eric J Brown
- Abramson Family Cancer Research Institute and the Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Helen R Russell
- Department of Genetics, St Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Peter J McKinnon
- Department of Genetics, St Jude Children's Research Hospital, Memphis, Tennessee 38105,
- College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, and
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47
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Liu X, Shao Z, Jiang W, Lee BJ, Zha S. PAXX promotes KU accumulation at DNA breaks and is essential for end-joining in XLF-deficient mice. Nat Commun 2017; 8:13816. [PMID: 28051062 PMCID: PMC5216128 DOI: 10.1038/ncomms13816] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/26/2016] [Indexed: 01/08/2023] Open
Abstract
Non-homologous end-joining (NHEJ) is the most prominent DNA double strand break (DSB) repair pathway in mammalian cells. PAXX is the newest NHEJ factor, which shares structural similarity with known NHEJ factors—XRCC4 and XLF. Here we report that PAXX is dispensable for physiological NHEJ in otherwise wild-type mice. Yet Paxx−/− mice require XLF and Xlf−/− mice require PAXX for end-ligation. As such, Xlf−/−Paxx−/− mice display severe genomic instability and neuronal apoptosis, which eventually lead to embryonic lethality. Despite their structural similarities, only Xlf−/− cells, but not Paxx−/− cells require ATM/DNA-PK kinase activity for end-ligation. Mechanistically, PAXX promotes the accumulation of KU at DSBs, while XLF enhances LIG4 recruitment without affecting KU dynamics at DNA breaks in vivo. Together these findings identify the molecular functions of PAXX in KU accumulation at DNA ends and reveal distinct, yet critically complementary functions of PAXX and XLF during NHEJ. Non-homologous end-joining is the key pathway for repairing double-stranded DNA breaks in mammalian cells. Here the authors show that PAXX promotes the accumulation of KU at DNA breaks and is essential for end-joining in cells lacking XLF.
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Affiliation(s)
- Xiangyu Liu
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Institute for Cancer Genetics, Columbia University, 1130 Saint Nicholas Avenue, Room 501, New York City, New York 10032, USA
| | - Zhengping Shao
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Institute for Cancer Genetics, Columbia University, 1130 Saint Nicholas Avenue, Room 501, New York City, New York 10032, USA
| | - Wenxia Jiang
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Institute for Cancer Genetics, Columbia University, 1130 Saint Nicholas Avenue, Room 501, New York City, New York 10032, USA
| | - Brian J Lee
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Institute for Cancer Genetics, Columbia University, 1130 Saint Nicholas Avenue, Room 501, New York City, New York 10032, USA
| | - Shan Zha
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Institute for Cancer Genetics, Columbia University, 1130 Saint Nicholas Avenue, Room 501, New York City, New York 10032, USA.,Division of Pediatric Oncology, Hematology and Stem Cell Transplantation, Department of Pediatrics, College of Physicians &Surgeons, Columbia University, 1130 Saint Nicholas Avenue, Room 501, New York City, New York 10032, USA
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48
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Gustincich S, Zucchelli S, Mallamaci A. The Yin and Yang of nucleic acid-based therapy in the brain. Prog Neurobiol 2016; 155:194-211. [PMID: 27887908 DOI: 10.1016/j.pneurobio.2016.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 11/16/2016] [Accepted: 11/20/2016] [Indexed: 02/06/2023]
Abstract
The post-genomic era has unveiled the existence of a large repertory of non-coding RNAs and repetitive elements that play a fundamental role in cellular homeostasis and dysfunction. These may represent unprecedented opportunities to modify gene expression at the right time in the correct space in vivo, providing an almost unlimited reservoir of new potential pharmacological agents. Hijacking their mode of actions, the druggable genome can be extended to regulatory RNAs and DNA elements in a scalable fashion. Here, we discuss the state-of-the-art of nucleic acid-based drugs to treat neurodegenerative diseases. Beneficial effects can be obtained by inhibiting (Yin) and increasing (Yang) gene expression, depending on the disease and the drug target. Together with the description of the current use of inhibitory RNAs (small inhibitory RNAs and antisense oligonucleotides) in animal models and clinical trials, we discuss the molecular basis and applications of new classes of activatory RNAs at transcriptional (RNAa) and translational (SINEUP) levels.
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Affiliation(s)
- Stefano Gustincich
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), Genova, Italy; Area of Neuroscience, SISSA, Trieste, Italy.
| | - Silvia Zucchelli
- Area of Neuroscience, SISSA, Trieste, Italy; Department of Health Sciences, Universita' del Piemonte Orientale, Novara, Italy
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49
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Lang PY, Nanjangud GJ, Sokolsky-Papkov M, Shaw C, Hwang D, Parker JS, Kabanov AV, Gershon TR. ATR maintains chromosomal integrity during postnatal cerebellar neurogenesis and is required for medulloblastoma formation. Development 2016; 143:4038-4052. [PMID: 27803059 PMCID: PMC5117143 DOI: 10.1242/dev.139022] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 09/16/2016] [Indexed: 02/01/2023]
Abstract
Microcephaly and medulloblastoma may both result from mutations that compromise genomic stability. We report that ATR, which is mutated in the microcephalic disorder Seckel syndrome, sustains cerebellar growth by maintaining chromosomal integrity during postnatal neurogenesis. Atr deletion in cerebellar granule neuron progenitors (CGNPs) induced proliferation-associated DNA damage, p53 activation, apoptosis and cerebellar hypoplasia in mice. Co-deletions of either p53 or Bax and Bak prevented apoptosis in Atr-deleted CGNPs, but failed to fully rescue cerebellar growth. ATR-deficient CGNPs had impaired cell cycle checkpoint function and continued to proliferate, accumulating chromosomal abnormalities. RNA-Seq demonstrated that the transcriptional response to ATR-deficient proliferation was highly p53 dependent and markedly attenuated by p53 co-deletion. Acute ATR inhibition in vivo by nanoparticle-formulated VE-822 reproduced the developmental disruptions seen with Atr deletion. Genetic deletion of Atr blocked tumorigenesis in medulloblastoma-prone SmoM2 mice. Our data show that p53-driven apoptosis and cell cycle arrest - and, in the absence of p53, non-apoptotic cell death - redundantly limit growth in ATR-deficient progenitors. These mechanisms may be exploited for treatment of CGNP-derived medulloblastoma using ATR inhibition.
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Affiliation(s)
- Patrick Y Lang
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Neurology, UNC School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Gouri J Nanjangud
- Molecular Cytogenetics Core Facility, Memorial Sloan Kettering Research Center, New York, NY 10021, USA
| | - Marina Sokolsky-Papkov
- Center for Nanotechnology in Drug Delivery and Division of Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Christine Shaw
- Molecular Cytogenetics Core Facility, Memorial Sloan Kettering Research Center, New York, NY 10021, USA
| | - Duhyeong Hwang
- Center for Nanotechnology in Drug Delivery and Division of Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joel S Parker
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Alexander V Kabanov
- Center for Nanotechnology in Drug Delivery and Division of Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Timothy R Gershon
- Department of Neurology, UNC School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
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50
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Wang H, Dharmalingam P, Vasquez V, Mitra J, Boldogh I, Rao KS, Kent TA, Mitra S, Hegde ML. Chronic oxidative damage together with genome repair deficiency in the neurons is a double whammy for neurodegeneration: Is damage response signaling a potential therapeutic target? Mech Ageing Dev 2016; 161:163-176. [PMID: 27663141 DOI: 10.1016/j.mad.2016.09.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/13/2016] [Accepted: 09/19/2016] [Indexed: 12/14/2022]
Abstract
A foremost challenge for the neurons, which are among the most oxygenated cells, is the genome damage caused by chronic exposure to endogenous reactive oxygen species (ROS), formed as cellular respiratory byproducts. Strong metabolic activity associated with high transcriptional levels in these long lived post-mitotic cells render them vulnerable to oxidative genome damage, including DNA strand breaks and mutagenic base lesions. There is growing evidence for the accumulation of unrepaired DNA lesions in the central nervous system (CNS) during accelerated aging and progressive neurodegeneration. Several germ line mutations in DNA repair or DNA damage response (DDR) signaling genes are uniquely manifested in the phenotype of neuronal dysfunction and are etiologically linked to many neurodegenerative disorders. Studies in our lab and elsewhere revealed that pro-oxidant metals, ROS and misfolded amyloidogenic proteins not only contribute to genome damage in CNS, but also impede their repair/DDR signaling leading to persistent damage accumulation, a common feature in sporadic neurodegeneration. Here, we have reviewed recent advances in our understanding of the etiological implications of DNA damage vs. repair imbalance, abnormal DDR signaling in triggering neurodegeneration and potential of DDR as a target for the amelioration of neurodegenerative diseases.
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Affiliation(s)
- Haibo Wang
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Houston Methodist Neurological Institute, Houston, TX 77030, USA
| | - Prakash Dharmalingam
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Houston Methodist Neurological Institute, Houston, TX 77030, USA
| | - Velmarini Vasquez
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Centre for Neuroscience, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), City of Knowledge, Panama City, Panama; Department of Biotechnology, Acharya Nagarjuna University, Guntur, AP, India; Houston Methodist Neurological Institute, Houston, TX 77030, USA
| | - Joy Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Houston Methodist Neurological Institute, Houston, TX 77030, USA
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - K S Rao
- Centre for Neuroscience, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), City of Knowledge, Panama City, Panama
| | - Thomas A Kent
- Department of Neurology, Baylor College of Medicine and Center for Translational Research on Inflammatory Diseases Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX 77030, USA
| | - Sankar Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Weill Medical College of Cornell University, New York, USA
| | - Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Houston Methodist Neurological Institute, Houston, TX 77030, USA; Weill Medical College of Cornell University, New York, USA.
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