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NF1 patient missense variants predict a role for ATM in modifying neurofibroma initiation. Acta Neuropathol 2020; 139:157-174. [PMID: 31664505 DOI: 10.1007/s00401-019-02086-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 01/01/2023]
Abstract
In Neurofibromatosis type 1, NF1 gene mutations in Schwann cells (SC) drive benign plexiform neurofibroma (PNF), and no additional SC changes explain patient-to-patient variability in tumor number. Evidence from twin studies suggests that variable expressivity might be caused by unidentified modifier genes. Whole exome sequencing of SC and fibroblast DNA from the same resected PNFs confirmed biallelic SC NF1 mutations; non-NF1 somatic SC variants were variable and present at low read number. We identified frequent germline variants as possible neurofibroma modifier genes. Genes harboring variants were validated in two additional cohorts of NF1 patients and by variant burden test. Genes including CUBN, CELSR2, COL14A1, ATR and ATM also showed decreased gene expression in some neurofibromas. ATM-relevant DNA repair defects were also present in a subset of neurofibromas with ATM variants, and in some neurofibroma SC. Heterozygous ATM G2023R or homozygous S707P variants reduced ATM protein expression in heterologous cells. In mice, genetic Atm heterozygosity promoted Schwann cell precursor self-renewal and increased tumor formation in vivo, suggesting that ATM variants contribute to neurofibroma initiation. We identify germline variants, rare in the general population, overrepresented in NF1 patients with neurofibromas. ATM and other identified genes are candidate modifiers of PNF pathogenesis.
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Abstract
IMPACT STATEMENT This review provides various genetic and cell line data previously published in a way to explain how cellular stress can lead into genetic instability.
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Affiliation(s)
- Jung Joo Moon
- 1 JS Yoon Memorial Cancer Research Institute LLC, Lutherville, MD 2109, USA
| | - Alexander Lu
- 1 JS Yoon Memorial Cancer Research Institute LLC, Lutherville, MD 2109, USA
| | - Chulso Moon
- 1 JS Yoon Memorial Cancer Research Institute LLC, Lutherville, MD 2109, USA.,2 Department of Otolaryngology-Head and Neck Surgery, The Johns Hopkins Medical Institution, Baltimore, MD 21205, USA
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Capalbo A, Hoffmann ER, Cimadomo D, Maria Ubaldi F, Rienzi L. Human female meiosis revised: new insights into the mechanisms of chromosome segregation and aneuploidies from advanced genomics and time-lapse imaging. Hum Reprod Update 2017; 23:706-722. [DOI: 10.1093/humupd/dmx026] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 08/11/2017] [Indexed: 12/14/2022] Open
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Santaguida S, Richardson A, Iyer DR, M'Saad O, Zasadil L, Knouse KA, Wong YL, Rhind N, Desai A, Amon A. Chromosome Mis-segregation Generates Cell-Cycle-Arrested Cells with Complex Karyotypes that Are Eliminated by the Immune System. Dev Cell 2017; 41:638-651.e5. [PMID: 28633018 PMCID: PMC5536848 DOI: 10.1016/j.devcel.2017.05.022] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 03/07/2017] [Accepted: 05/23/2017] [Indexed: 01/14/2023]
Abstract
Aneuploidy, a state of karyotype imbalance, is a hallmark of cancer. Changes in chromosome copy number have been proposed to drive disease by modulating the dosage of cancer driver genes and by promoting cancer genome evolution. Given the potential of cells with abnormal karyotypes to become cancerous, do pathways that limit the prevalence of such cells exist? By investigating the immediate consequences of aneuploidy on cell physiology, we identified mechanisms that eliminate aneuploid cells. We find that chromosome mis-segregation leads to further genomic instability that ultimately causes cell-cycle arrest. We further show that cells with complex karyotypes exhibit features of senescence and produce pro-inflammatory signals that promote their clearance by the immune system. We propose that cells with abnormal karyotypes generate a signal for their own elimination that may serve as a means for cancer cell immunosurveillance.
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Affiliation(s)
- Stefano Santaguida
- Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-543, Cambridge, MA 02138, USA.
| | - Amelia Richardson
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Divya Ramalingam Iyer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Ons M'Saad
- Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-543, Cambridge, MA 02138, USA
| | - Lauren Zasadil
- Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-543, Cambridge, MA 02138, USA
| | - Kristin A Knouse
- Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-543, Cambridge, MA 02138, USA; Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Yao Liang Wong
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nicholas Rhind
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Arshad Desai
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Angelika Amon
- Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Massachusetts Institute of Technology, 76-543, Cambridge, MA 02138, USA.
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Badoer C, Garrec C, Goossens D, Ellison G, Mills J, Dzial M, Housni HE, Berwouts S, Concolino P, Guevellou VGL, Delnatte C, Favero JD, Capoluongo E, Bézieau S. Performance of multiplicom's BRCA MASTR Dx kit on the detection of BRCA1 and BRCA2 mutations in fresh frozen ovarian and breast tumor samples. Oncotarget 2016; 7:81357-81366. [PMID: 27793035 PMCID: PMC5348397 DOI: 10.18632/oncotarget.12877] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 09/08/2016] [Indexed: 12/25/2022] Open
Abstract
Next-generation sequencing (NGS) has enabled new approaches for detection of mutations in the BRCA1 and BRCA2 genes responsible for hereditary breast and ovarian cancer (HBOC). The search for germline mutations in the BRCA1 and BRCA2 genes is of importance with respect to oncogenetic and surgical (bilateral mastectomy, ovariectomy) counselling. Testing tumor material for BRCA mutations is of increasing importance for therapeutic decision making as the poly ADP ribose polymerase (PARP) inhibitor, olaparib, is now available to treat patients with specific forms of ovarian cancer and BRCA mutations. Molecular genetics laboratories should develop reliable and sensitive techniques for the complete analysis of the BRCA1 and BRCA2 genes. This is a challenge due to the size of the coding sequence of the BRCA1/2 genes, the absence of hot spot mutations, and particularly by the lower DNA quality obtained from Formalin-Fixed Paraffin-Embedded (FFPE) tissue. As a result, a number of analyses are uninterpretable and do not always provide a result to the clinician, limiting the optimal therapeutic management of patients. The availability of Fresh Frozen Tissue (FFT) for some laboratories and the excellent quality of the DNA extracted from it offers an alternative. For this reason, we evaluated Multiplicom's BRCA MASTR Dx assay on a set of 97 FFT derived DNA samples, in combination with the MID for Illumina MiSeq for BRCA1 and BRCA2 mutation detection. We obtained interpretable NGS results for all tested samples and showed > 99,7% sensitivity, specificity and accuracy.
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Affiliation(s)
- Cindy Badoer
- Laboratoire de Génétique Moléculaire, Clinique Universitaire de Bruxelles-Hôpital Erasme-Université Libre de Bruxelles (CUB-Erasme-ULB), Brussels, Belgium
| | - Céline Garrec
- Institut de Biologie, Laboratoire de Génétique Moléculaire, Service de Génétique Médicale, CHU Nantes, Nantes, France
| | | | - Gillian Ellison
- AstraZeneca, Personalised Healthcare and Biomarkers, Alderley Park, Macclesfield, UK
| | - John Mills
- AstraZeneca, Personalised Healthcare and Biomarkers, Alderley Park, Macclesfield, UK
| | - Mélina Dzial
- Laboratoire de Génétique Moléculaire, Clinique Universitaire de Bruxelles-Hôpital Erasme-Université Libre de Bruxelles (CUB-Erasme-ULB), Brussels, Belgium
| | - Hakim El Housni
- Laboratoire de Génétique Moléculaire, Clinique Universitaire de Bruxelles-Hôpital Erasme-Université Libre de Bruxelles (CUB-Erasme-ULB), Brussels, Belgium
| | | | - Paola Concolino
- Laboratory of Clinical Molecular and Personalized Diagnostics, Foundation Policlinico Gemelli and Catholic University of Rome, Italy
| | - Virginie Guibert-Le Guevellou
- Institut de Biologie, Laboratoire de Génétique Moléculaire, Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Capucine Delnatte
- Institut de Biologie, Laboratoire de Génétique Moléculaire, Service de Génétique Médicale, CHU Nantes, Nantes, France
| | | | - Ettore Capoluongo
- Laboratory of Clinical Molecular and Personalized Diagnostics, Foundation Policlinico Gemelli and Catholic University of Rome, Italy
- Molipharma and Giovanni Paolo II Foundation, Campobasso, Italy
| | - Stéphane Bézieau
- Institut de Biologie, Laboratoire de Génétique Moléculaire, Service de Génétique Médicale, CHU Nantes, Nantes, France
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Kar A, Kaur M, Ghosh T, Khan MM, Sharma A, Shekhar R, Varshney A, Saxena S. RPA70 depletion induces hSSB1/2-INTS3 complex to initiate ATR signaling. Nucleic Acids Res 2015; 43:4962-74. [PMID: 25916848 PMCID: PMC4446429 DOI: 10.1093/nar/gkv369] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/08/2015] [Indexed: 01/12/2023] Open
Abstract
The primary eukaryotic single-stranded DNA-binding protein, Replication protein A (RPA), binds to single-stranded DNA at the sites of DNA damage and recruits the apical checkpoint kinase, ATR via its partner protein, ATRIP. It has been demonstrated that absence of RPA incapacitates the ATR-mediated checkpoint response. We report that in the absence of RPA, human single-stranded DNA-binding protein 1 (hSSB1) and its partner protein INTS3 form sub-nuclear foci, associate with the ATR-ATRIP complex and recruit it to the sites of genomic stress. The ATRIP foci formed after RPA depletion are abrogated in the absence of INTS3, establishing that hSSB-INTS3 complex recruits the ATR-ATRIP checkpoint complex to the sites of genomic stress. Depletion of homologs hSSB1/2 and INTS3 in RPA-deficient cells attenuates Chk1 phosphorylation, indicating that the cells are debilitated in responding to stress. We have identified that TopBP1 and the Rad9-Rad1-Hus1 complex are essential for the alternate mode of ATR activation. In summation, we report that the single-stranded DNA-binding protein complex, hSSB1/2-INTS3 can recruit the checkpoint complex to initiate ATR signaling.
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Affiliation(s)
- Ananya Kar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Manpreet Kaur
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Tanushree Ghosh
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Md Muntaz Khan
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Aparna Sharma
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Ritu Shekhar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Akhil Varshney
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Sandeep Saxena
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
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Zhang S, Yuan Y, Hao D. A genomic instability score in discriminating nonequivalent outcomes of BRCA1/2 mutations and in predicting outcomes of ovarian cancer treated with platinum-based chemotherapy. PLoS One 2014; 9:e113169. [PMID: 25437005 PMCID: PMC4249855 DOI: 10.1371/journal.pone.0113169] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 10/24/2014] [Indexed: 12/15/2022] Open
Abstract
Detecting mutation in BRCA1/2 is a generally accepted strategy for screening ovarian cancers that have impaired homologous recombination (HR) ability and improved sensitivity to PARP inhibitor. However, a substantial subset of BRCA-mutant ovarian cancer patients shows less impaired or unimpaired HR ability, resulting in nonequivalent outcome after ovarian cancer development. We hypothesize that genomic instability provides a lifetime record of DNA repair deficiency and predicts ovarian cancer outcome. Based on the multi-dimensional TCGA ovarian cancer data, we developed a biological rationale-driven genomic instability score integrating somatic mutation and copy number change in a tumor genome. The score successfully divided BRCA-mutant ovarian tumors into cases of significantly improved outcome and cases of unimproved outcome. The score was also capable of discriminating HR-deficiency indicated by BRCA1 epigenetically silencing, EMSY amplification and homozygous deletion of core HR genes. We further found that the score was positively correlated with the complete response rate of chemotherapy and the rate of platinum-sensitivity, and predicted improved outcome of ovarian cancer, regardless of BRCA-mutation status. The score may have important value in outcome prediction and clinical trial design.
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Affiliation(s)
- Shaojun Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, P.R. China
| | - Yuan Yuan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, P.R. China; Department of Gynecology and Obstetrics, The Forth Affiliated Hospital of Harbin Medical University, Department of Gynecology and Obstetrics, Harbin 150081, P.R. China
| | - Dapeng Hao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, P.R. China
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Abstract
Within the last decade, multiple novel congenital human disorders have been described with genetic defects in known and/or novel components of several well-known DNA repair and damage response pathways. Examples include disorders of impaired nucleotide excision repair, DNA double-strand and single-strand break repair, as well as compromised DNA damage-induced signal transduction including phosphorylation and ubiquitination. These conditions further reinforce the importance of multiple genome stability pathways for health and development in humans. Furthermore, these conditions inform our knowledge of the biology of the mechanics of genome stability and in some cases provide potential routes to help exploit these pathways therapeutically. Here, I will review a selection of these exciting findings from the perspective of the disorders themselves, describing how they were identified, how genotype informs phenotype, and how these defects contribute to our growing understanding of genome stability pathways.
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Affiliation(s)
- Mark O'Driscoll
- Human DNA Damage Response Disorders Group Genome Damage and Stability Centre, University of Sussex, Brighton, East Sussex BN1 9RQ, United Kingdom
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Balmus G, Zhu M, Mukherjee S, Lyndaker AM, Hume KR, Lee J, Riccio ML, Reeves AP, Sutter NB, Noden DM, Peters RM, Weiss RS. Disease severity in a mouse model of ataxia telangiectasia is modulated by the DNA damage checkpoint gene Hus1. Hum Mol Genet 2012; 21:3408-20. [PMID: 22575700 DOI: 10.1093/hmg/dds173] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The human genomic instability syndrome ataxia telangiectasia (A-T), caused by mutations in the gene encoding the DNA damage checkpoint kinase ATM, is characterized by multisystem defects including neurodegeneration, immunodeficiency and increased cancer predisposition. ATM is central to a pathway that responds to double-strand DNA breaks, whereas the related kinase ATR leads a parallel signaling cascade that is activated by replication stress. To dissect the physiological relationship between the ATM and ATR pathways, we generated mice defective for both. Because complete ATR pathway inactivation causes embryonic lethality, we weakened the ATR mechanism to different degrees by impairing HUS1, a member of the 911 complex that is required for efficient ATR signaling. Notably, simultaneous ATM and HUS1 defects caused synthetic lethality. Atm/Hus1 double-mutant embryos showed widespread apoptosis and died mid-gestationally. Despite the underlying DNA damage checkpoint defects, increased DNA damage signaling was observed, as evidenced by H2AX phosphorylation and p53 accumulation. A less severe Hus1 defect together with Atm loss resulted in partial embryonic lethality, with the surviving double-mutant mice showing synergistic increases in genomic instability and specific developmental defects, including dwarfism, craniofacial abnormalities and brachymesophalangy, phenotypes that are observed in several human genomic instability disorders. In addition to identifying tissue-specific consequences of checkpoint dysfunction, these data highlight a robust, cooperative configuration for the mammalian DNA damage response network and further suggest HUS1 and related genes in the ATR pathway as candidate modifiers of disease severity in A-T patients.
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Affiliation(s)
- Gabriel Balmus
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
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Chromosomal instability at the 7q11.23 region impacts on DNA-damage response in lymphocytes from Williams-Beuren syndrome patients. Mutat Res 2011; 724:46-51. [PMID: 21645633 DOI: 10.1016/j.mrgentox.2011.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 04/22/2011] [Accepted: 05/08/2011] [Indexed: 11/21/2022]
Abstract
Williams-Beuren syndrome (WBS) is the chromosomal disorder arising from a hemizygous microdeletion at 7q11.23. The present study was focused on a comparative investigation of genomic integrity in WBS patients by use of cytogenetic methods and the alkaline comet assay. Lymphocytes of whole peripheral blood were cultured and metaphases were examined for frequency and spectrum of chromosome aberrations. A WBS-related microdeletion was detected by means of the FISH (fluorescence in situ hybridization) technique. The blood samples from patients who were carriers of this microdeletion, were tested in the comet assay. For this purpose, freshly collected lymphocytes were exposed to hydrogen peroxide (100μM, 1min, 4°C). The frequencies of endogenous and exogenous DNA damage, and the kinetics and efficiency of DNA repair were measured during three subsequent hours of incubation. Comparison of the two data sets in this group of patients demonstrated a slightly elevated average frequency of chromosome aberrations, significantly increased levels of endogenous and H(2)O(2)-induced DNA damage, and somewhat impaired DNA repair. The relationship between an abnormal DNA-damage response and the 7q11.23 hemizygous microdeletion was confirmed experimentally when comparing the comet assay data in FISH-positive and FISH-negative lymphocytes from WBS-suspected patients. Briefly, our results indicate the impact of chromosomal instability within this region on susceptibility towards DNA damage, which may contribute to pathogenesis of this disease. It was shown also that the comet assay, as well as an experimental design proposed here, seem to be useful tools for estimating genome integrity in WBS patients.
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Abstract
Genomic instability is a characteristic of most cancers. In hereditary cancers, genomic instability results from mutations in DNA repair genes and drives cancer development, as predicted by the mutator hypothesis. In sporadic (non-hereditary) cancers the molecular basis of genomic instability remains unclear, but recent high-throughput sequencing studies suggest that mutations in DNA repair genes are infrequent before therapy, arguing against the mutator hypothesis for these cancers. Instead, the mutation patterns of the tumour suppressor TP53 (which encodes p53), ataxia telangiectasia mutated (ATM) and cyclin-dependent kinase inhibitor 2A (CDKN2A; which encodes p16INK4A and p14ARF) support the oncogene-induced DNA replication stress model, which attributes genomic instability and TP53 and ATM mutations to oncogene-induced DNA damage.
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Crespi B, Summers K, Dorus S. Evolutionary genomics of human intellectual disability. Evol Appl 2010; 3:52-63. [PMID: 25567903 PMCID: PMC3352458 DOI: 10.1111/j.1752-4571.2009.00098.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 07/28/2009] [Indexed: 01/28/2023] Open
Abstract
Previous studies have postulated that X-linked and autosomal genes underlying human intellectual disability may have also mediated the evolution of human cognition. We have conducted the first comprehensive assessment of the extent and patterns of positive Darwinian selection on intellectual disability genes in humans. We report three main findings. First, as noted in some previous reports, intellectual disability genes with primary functions in the central nervous system exhibit a significant concentration to the X chromosome. Second, there was no evidence for a higher incidence of recent positive selection on X-linked than autosomal intellectual disability genes, nor was there a higher incidence of selection on such genes overall, compared to sets of control genes. However, the X-linked intellectual disability genes inferred to be subject to recent positive selection were concentrated in the Rho GTP-ase pathway, a key signaling pathway in neural development and function. Third, among all intellectual disability genes, there was evidence for a higher incidence of recent positive selection on genes involved in DNA repair, but not for genes involved in other functions. These results provide evidence that alterations to genes in the Rho GTP-ase and DNA-repair pathways may play especially-important roles in the evolution of human cognition and vulnerability to genetically-based intellectual disability.
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Affiliation(s)
- Bernard Crespi
- Department of Biosciences, Simon Fraser UniversityBurnaby, BC, Canada
| | - Kyle Summers
- Department of Biology, East Carolina UniversityGreenville, NC, USA
| | - Steve Dorus
- Department of Biology and Biochemistry, University of BathBath, UK
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