1
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Gericke GS. A Unifying Hypothesis for the Genome Dynamics Proposed to Underlie Neuropsychiatric Phenotypes. Genes (Basel) 2024; 15:471. [PMID: 38674405 PMCID: PMC11049865 DOI: 10.3390/genes15040471] [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: 03/17/2024] [Revised: 04/04/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
The sheer number of gene variants and the extent of the observed clinical and molecular heterogeneity recorded in neuropsychiatric disorders (NPDs) could be due to the magnified downstream effects initiated by a smaller group of genomic higher-order alterations in response to endogenous or environmental stress. Chromosomal common fragile sites (CFS) are functionally linked with microRNAs, gene copy number variants (CNVs), sub-microscopic deletions and duplications of DNA, rare single-nucleotide variants (SNVs/SNPs), and small insertions/deletions (indels), as well as chromosomal translocations, gene duplications, altered methylation, microRNA and L1 transposon activity, and 3-D chromosomal topology characteristics. These genomic structural features have been linked with various NPDs in mostly isolated reports and have usually only been viewed as areas harboring potential candidate genes of interest. The suggestion to use a higher level entry point (the 'fragilome' and associated features) activated by a central mechanism ('stress') for studying NPD genetics has the potential to unify the existing vast number of different observations in this field. This approach may explain the continuum of gene findings distributed between affected and unaffected individuals, the clustering of NPD phenotypes and overlapping comorbidities, the extensive clinical and molecular heterogeneity, and the association with certain other medical disorders.
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2
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Filipović J, Joksić G, Vujić D, Joksić I, Mrasek K, Weise A, Liehr T. First molecular-cytogenetic characterization of Fanconi anemia fragile sites in primary lymphocytes of FA-D2 patients in different stages of the disease. Mol Cytogenet 2016; 9:70. [PMID: 27625703 PMCID: PMC5020439 DOI: 10.1186/s13039-016-0280-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 08/26/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fanconi anemia (FA) is a chromosomal instability syndrome characterized by increased frequency of chromosomal breakages, chromosomal radial figures and accelerated telomere shortening. In this work we performed detailed molecular-cytogenetic characterization of breakpoints in primary lymphocytes of FA-D2 patients in different stages of the disease using fluorescent in situ hybridization. RESULTS We found that chromosomal breakpoints co-localize on the molecular level with common fragile sites, whereas their distribution pattern depends on the severity of the disease. Telomere quantitative fluorescent in situ hybridization revealed that telomere fusions and radial figures, especially radials which involve telomere sequences are the consequence of critically shortened telomeres that increase with the disease progression and could be considered as a predictive parameter during the course of the disease. Sex chromosomes in FA cells are also involved in radial formation indicating that specific X chromosome regions share homology with autosomes and also could serve as repair templates in resolving DNA damage. CONCLUSIONS FA-D2 chromosomal breakpoints co-localize with common fragile sites, but their distribution pattern depends on the disease stage. Telomere fusions and radials figures which involve telomere sequences are the consequence of shortened telomeres, increase with disease progression and could be of predictive value.
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Affiliation(s)
- Jelena Filipović
- Vinca Institute of Nuclear Sciences, University of Belgrade, Mike Petrovica Alasa 12-14, Belgrade, 11001 Serbia
| | - Gordana Joksić
- Vinca Institute of Nuclear Sciences, University of Belgrade, Mike Petrovica Alasa 12-14, Belgrade, 11001 Serbia
| | - Dragana Vujić
- Mother and Child Health Care Institute of Serbia, "Dr Vukan Cupic", Radoja Dakica 6, Belgrade, 11070 Serbia
| | - Ivana Joksić
- Vinca Institute of Nuclear Sciences, University of Belgrade, Mike Petrovica Alasa 12-14, Belgrade, 11001 Serbia
| | - Kristin Mrasek
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena, D-07743 Germany
| | - Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena, D-07743 Germany
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena, D-07743 Germany
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3
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Gericke GS. Common chromosomal fragile sites (CFS) may be involved in normal and traumatic cognitive stress memory consolidation and altered nervous system immunity. Med Hypotheses 2010; 74:911-8. [PMID: 20138440 DOI: 10.1016/j.mehy.2009.05.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 05/22/2009] [Accepted: 05/26/2009] [Indexed: 11/18/2022]
Abstract
Previous reports of specific patterns of increased fragility at common chromosomal fragile sites (CFS) found in association with certain neurobehavioural disorders did not attract attention at the time due to a shift towards molecular approaches to delineate neuropsychiatric disorder candidate genes. Links with miRNA, altered methylation and the origin of copy number variation indicate that CFS region characteristics may be part of chromatinomic mechanisms that are increasingly linked with neuroplasticity and memory. Current reports of large-scale double-stranded DNA breaks in differentiating neurons and evidence of ongoing DNA demethylation of specific gene promoters in adult hippocampus may shed new light on the dynamic epigenetic changes that are increasingly appreciated as contributing to long-term memory consolidation. The expression of immune recombination activating genes in key stress-induced memory regions suggests the adoption by the brain of this ancient pattern recognition and memory system to establish a structural basis for long-term memory through controlled chromosomal breakage at highly specific genomic regions. It is furthermore considered that these mechanisms for management of epigenetic information related to stress memory could be linked, in some instances, with the transfer of the somatically acquired information to the germline. Here, rearranged sequences can be subjected to further selection and possible eventual retrotranscription to become part of the more stable coding machinery if proven to be crucial for survival and reproduction. While linkage of cognitive memory with stress and fear circuitry and memory establishment through structural DNA modification is proposed as a normal process, inappropriate activation of immune-like genomic rearrangement processes through traumatic stress memory may have the potential to lead to undesirable activation of neuro-inflammatory processes. These theories could have a significant impact on the interpretation of risks posed by heredity and the environment and the search for neuropsychiatric candidate genes.
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Affiliation(s)
- G S Gericke
- Department of Biomedical Sciences, Tshwane University of Technology, Brooklyn Square, Pretoria, Gauteng, South Africa.
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4
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Helmrich A, Stout-Weider K, Matthaei A, Hermann K, Heiden T, Schrock E. Identification of the human/mouse syntenic common fragile site FRA7K/Fra12C1--relation of FRA7K and other human common fragile sites on chromosome 7 to evolutionary breakpoints. Int J Cancer 2007; 120:48-54. [PMID: 17039484 DOI: 10.1002/ijc.22049] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Common fragile sites (CFSs) are expressed as chromosome gaps in cells of different species including human and mouse as a result of the inhibition of DNA replication. They may serve as hot spots for DNA breakage in processes such as tumorigenesis and chromosome evolution. Using multicolor fluorescence in situ hybridization mapping, the authors describe here human CFS FRA7K on chromosome band 7q31.1 and its murine homolog Fra12C1. Within the syntenic FRA7K/Fra12C1 region lies the IMMP2L/Immp2l gene with a size of 899/983 kb. The authors further mapped 2 amplification breakpoints of the breast cancer cell line SKBR3 to the CFSs FRA7G and FRA7H. The 5 molecularly defined CFSs on chromosome 7 do not preferentially colocalize with synteny breaks between the human and mouse genomes and with intragenomic duplications that have occurred during chromosome evolution. In addition, in contrast to all currently reported data, CFSs in chromosome band 7q31 do not show increased DNA helix flexibility in comparison with control regions without CFS expression.
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Affiliation(s)
- Anne Helmrich
- Institute of Clinical Genetics, Medical Faculty "Carl Gustav Carus," University of Technology, 01307 Dresden, Germany.
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5
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Helmrich A, Stout-Weider K, Hermann K, Schrock E, Heiden T. Common fragile sites are conserved features of human and mouse chromosomes and relate to large active genes. Genome Res 2006; 16:1222-30. [PMID: 16954539 PMCID: PMC1581431 DOI: 10.1101/gr.5335506] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Common fragile sites (CFSs) are seen as chromosomal gaps and breaks brought about by inhibition of replication, and it is thought that they cluster with tumor breakpoints. This study presents a comprehensive analysis using conventional and molecular cytogenetic mapping of CFSs and their expression frequencies in two mouse strains, BALB/c and C57BL/6, and in human probands. Here we show that induced mouse CFSs relate to sites of spontaneous gaps and breaks and that CFS expression levels in chromosome bands are conserved between the two mouse strains and between syntenic mouse and human DNA segments. Furthermore, four additional mouse CFSs were found to be homologous to human CFSs on the molecular cytogenetic level (Fra2D-FRA2G, Fra4C2-FRA9E, Fra6A3.1-FRA7G, and Fra6B1-FRA7H), increasing the number of such CFSs already described in the literature to eight. Contrary to previous reports, DNA helix flexibility is not increased in the 15 human and eight mouse CFSs molecularly defined so far, compared to large nonfragile control regions. Our findings suggest that the mechanisms that provoke instability at CFSs are evolutionarily conserved. The role that large transcriptionally active genes may play in CFS expression is discussed.
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Affiliation(s)
- Anne Helmrich
- Institute of Clinical Genetics, Medical Faculty Carl Gustav Carus, University of Technology, 01307 Dresden, Germany.
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6
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Schwartz M, Zlotorynski E, Kerem B. The molecular basis of common and rare fragile sites. Cancer Lett 2006; 232:13-26. [PMID: 16236432 DOI: 10.1016/j.canlet.2005.07.039] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2005] [Accepted: 07/30/2005] [Indexed: 11/30/2022]
Abstract
Fragile sites are specific loci that form gaps and constrictions on chromosomes exposed to partial replication stress. Fragile sites are classified as rare or common, depending on their induction and frequency within the population. These loci are known to be involved in chromosomal rearrangements in tumors and are associated with human diseases. Therefore, the understanding of the molecular basis of fragile sites is of high significance. Here we discuss the works performed in recent years that investigated the characteristics of fragile sites which underlie their inherent instability.
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Affiliation(s)
- Michal Schwartz
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem 91904, Israel
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7
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Valladares A, Palma-Padilla V, Mejía-Aranguré JM, Guevara-Yánez R, Lerma-Reyes A, Salamanca-Gómez F. Cytogenetic studies in children with Down syndrome and acute leukemia. Leuk Res 2005; 29:1241-6. [PMID: 16164980 DOI: 10.1016/j.leukres.2005.03.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Accepted: 03/11/2005] [Indexed: 11/16/2022]
Abstract
The frequency of chromosomal alterations was compared among four children groups: those with Down syndrome and acute leukemia (DS/AL), those with acute leukemia (AL), those with only Down syndrome (DS) and healthy children (NC). The frequency of acquired chromosome abnormalities was larger in the AL group, followed by the DS/AL. The gaps and isogaps were more frequent in children with only DS. The polymorphisms of the constitutive heterochromatin were larger in the DS/AL group. These findings appear to imply that more genetic changes are necessary to develop AL in the case of healthy children compared to children with DS.
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Affiliation(s)
- Adán Valladares
- Unit of Medical Research in Human Genetics, National Medical Center, IMSS, CMN siglo XXI, Av. Cuauhtémoc 330, Col. Doctores, CP 06725 Mexico City, Mexico
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8
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Zlotorynski E, Rahat A, Skaug J, Ben-Porat N, Ozeri E, Hershberg R, Levi A, Scherer SW, Margalit H, Kerem B. Molecular basis for expression of common and rare fragile sites. Mol Cell Biol 2003; 23:7143-51. [PMID: 14517285 PMCID: PMC230307 DOI: 10.1128/mcb.23.20.7143-7151.2003] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fragile sites are specific loci that form gaps, constrictions, and breaks on chromosomes exposed to partial replication stress and are rearranged in tumors. Fragile sites are classified as rare or common, depending on their induction and frequency within the population. The molecular basis of rare fragile sites is associated with expanded repeats capable of adopting unusual non-B DNA structures that can perturb DNA replication. The molecular basis of common fragile sites was unknown. Fragile sites from R-bands are enriched in flexible sequences relative to nonfragile regions from the same chromosomal bands. Here we cloned FRA7E, a common fragile site mapped to a G-band, and revealed a significant difference between its flexibility and that of nonfragile regions mapped to G-bands, similar to the pattern found in R-bands. Thus, in the entire genome, flexible sequences might play a role in the mechanism of fragility. The flexible sequences are composed of interrupted runs of AT-dinucleotides, which have the potential to form secondary structures and hence can affect replication. These sequences show similarity to the AT-rich minisatellite repeats that underlie the fragility of the rare fragile sites FRA16B and FRA10B. We further demonstrate that the normal alleles of FRA16B and FRA10B span the same genomic regions as the common fragile sites FRA16C and FRA10E. Our results suggest that a shared molecular basis, conferred by sequences with a potential to form secondary structures that can perturb replication, may underlie the fragility of rare fragile sites harboring AT-rich minisatellite repeats and aphidicolin-induced common fragile sites.
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Affiliation(s)
- Eitan Zlotorynski
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel 91904
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9
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Dhillon VS, Husain SA, Ray GN. Expression of aphidicolin-induced fragile sites and their relationship between genetic susceptibility in breast cancer, ovarian cancer, and non-small-cell lung cancer patients. TERATOGENESIS, CARCINOGENESIS, AND MUTAGENESIS 2003; Suppl 1:35-45. [PMID: 12616595 DOI: 10.1002/tcm.10068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Fragile sites are nonrandomly located gaps and/or breaks and their expres-sion can be induced by specific culture conditions. There are many reports in the literature that indicate that these sites can act as factors that predispose to specific chromosome aberrations and other complex rearrangement in the chromosome and their association with cancers. In the present study, the expression of the fragile sites induced by aphidicolin was evaluated on prometaphase chromosomes from peripheral blood lymphocytes of 55 patients with breast cancer patients belonging to different stages of the cancer, 25 patients with epithelial ovarian cancer, and 13 with non-small-cell lung cancer, 100 of their first-degree clinically healthy female relatives, and 100 normal age-matched healthy persons without a familial history of cancer. The frequency of expression of the fragile sites in cancer patients and their first-degree relatives was found to be statistically significant (P<0.05) than those of the controls. In different stages of breast cancer patients, 6q26 is the best-defined fragile site whereas 13q13 is confined to stage II and stage III patients only. The chromosomal aberration rate/cell in breast cancer patients was found to be 0.29+/-0.13, in epithelial ovarian cancer patients 0.38+/-0.14, and in non-small-cell lung cancer 0.29+/-0.11 as compared to 0.07+/-0.03 in controls, and was found to be statistically significant. Therefore, our results indicate that these fragile sites may be the unstable sites in the genome and, hence, can be used as suitable and reliable markers for genetic predisposition to breast cancer, epithelial ovarian cancer, and in non-small-cell lung cancer.
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Affiliation(s)
- Varinderpal S Dhillon
- Department of Molecular and Clinical Genetics, Royal Prince Alfred Hospital, Camperdown, Australia.
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10
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van Duin M, Steenbergen RDM, de Wilde J, Helmerhorst TJM, Verheijen RHM, Risse EKJ, Meijer CJLM, Snijders PJF. Telomerase activity in high-grade cervical lesions is associated with allelic imbalance at 6Q14-22. Int J Cancer 2003; 105:577-82. [PMID: 12740903 DOI: 10.1002/ijc.11145] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Our study attempts to establish the relationship between telomerase activity and allelic imbalance (AI) on chromosomes 3p and 6 in high-risk HPV-containing cervical lesions. These chromosomes were implicated previously in telomerase regulation in HPV containing immortalized cells and cervical cancer cells. Allelotyping and telomerase analysis were carried out on 28 high-grade cervical lesions (CIN III: n = 20; cervical carcinomas: n = 8), using 23 microsatellite markers on 3p, 6p and 6q. Clear telomerase activity was found in 17 of 28 lesions (61%). Allelic imbalance frequency at 6q14-22 was significantly higher in lesions with detectable telomerase activity, compared to lesions without telomerase activity (p = 0.02). No association was found between telomerase activity and AI at any of the remaining regions studied on 3p and chromosome 6. In addition, in telomerase positive passages of the HPV 16 immortalized cell line FK16A, shown recently to be responsive to chromosome 6 mediated telomerase repression, AI was found in the overlapping region of 6q14-27. These data suggest that 6q14-22 may contain 1 or more genes involved in telomerase deregulation and immortalization during cervical carcinogenesis.
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MESH Headings
- Adult
- Allelic Imbalance
- Carcinoma, Squamous Cell/enzymology
- Carcinoma, Squamous Cell/genetics
- Cell Line, Transformed
- Cell Transformation, Viral/genetics
- Chromosomes, Human, Pair 3/genetics
- Chromosomes, Human, Pair 6/genetics
- DNA, Neoplasm/genetics
- DNA-Binding Proteins
- Female
- Genome, Viral
- Humans
- Keratinocytes/cytology
- Male
- Microsatellite Repeats
- Middle Aged
- Neoplasm Proteins/analysis
- Papillomaviridae/physiology
- Papillomavirus Infections/genetics
- Penis
- RNA, Messenger/analysis
- RNA, Neoplasm/analysis
- Telomerase/analysis
- Telomerase/genetics
- Transfection
- Tumor Virus Infections/genetics
- Uterine Cervical Neoplasms/enzymology
- Uterine Cervical Neoplasms/genetics
- Uterine Cervical Dysplasia/enzymology
- Uterine Cervical Dysplasia/genetics
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Affiliation(s)
- Mark van Duin
- Department of Pathology, Vrije Universiteit Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
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11
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Matyakhina L, Pack S, Kirschner LS, Pak E, Mannan P, Jaikumar J, Taymans SE, Sandrini F, Carney JA, Stratakis CA. Chromosome 2 (2p16) abnormalities in Carney complex tumours. J Med Genet 2003; 40:268-77. [PMID: 12676898 PMCID: PMC1735422 DOI: 10.1136/jmg.40.4.268] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Carney complex (CNC) is an autosomal dominant multiple endocrine neoplasia and lentiginosis syndrome characterised by spotty skin pigmentation, cardiac, skin, and breast myxomas, and a variety of endocrine and other tumours. The disease is genetically heterogeneous; two loci have been mapped to chromosomes 17q22-24 (the CNC1 locus) and 2p16 (CNC2). Mutations in the PRKAR1A tumour suppressor gene were recently found in CNC1 mapping kindreds, while the CNC2 and perhaps other genes remain unidentified. Analysis of tumour chromosome rearrangements is a useful tool for uncovering genes with a role in tumorigenesis and/or tumour progression. CGH analysis showed a low level 2p amplification recurrently in four of eight CNC tumours; one tumour showed specific amplification of the 2p16-p23 region only. To define more precisely the 2p amplicon in these and other tumours, we completed the genomic mapping of the CNC2 region, and analysed 46 tumour samples from CNC patients with and without PRKAR1A mutations by fluorescence in situ hybridisation (FISH) using bacterial artificial chromosomes (BACs). Consistent cytogenetic changes of the region were detected in 40 (87%) of the samples analysed. Twenty-four samples (60%) showed amplification of the region represented as homogeneously stained regions (HSRs). The size of the amplicon varied from case to case, and frequently from cell to cell in the same tumour. Three tumours (8%) showed both amplification and deletion of the region in their cells. Thirteen tumours (32%) showed deletions only. These molecular cytogenetic changes included the region that is covered by BACs 400-P-14 and 514-O-11 and, in the genetic map, corresponds to an area flanked by polymorphic markers D2S2251 and D2S2292; other BACs on the centromeric and telomeric end of this region were included in varying degrees. We conclude that cytogenetic changes of the 2p16 chromosomal region that harbours the CNC2 locus are frequently observed in tumours from CNC patients, including those with germline, inactivating PRKAR1A mutations. These changes are mostly amplifications of the 2p16 region, that overlap with a previously identified amplicon in sporadic thyroid cancer, and an area often deleted in sporadic adrenal tumours. Both thyroid and adrenal tumours constitute part of CNC indicating that the responsible gene(s) in this area may indeed be involved in both inherited and sporadic endocrine tumour pathogenesis and/or progression.
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Affiliation(s)
- L Matyakhina
- Section on Endocrinology and Genetics, Developmental Endocrinology Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-1862, USA
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12
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Abstract
The organization and replication of DNA render fragile sites (FSs) prone to breakage, recombination as well as becoming preferential targets for mutagens-carcinogens and integration of oncogenic viruses. For many years, attempts to link FSs and cancer generated mostly circumstantial evidence. The discoveries that chromosome translocations, amplification of proto-oncogenes, deletion of tumor suppressor genes, and integration of oncogenic viruses all result from the specific breakage of genomic DNA at FSs, however, have provided compelling support for such a link, further suggesting a causative role for FSs in cancer.
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Affiliation(s)
- Nicholas C Popescu
- Molecular Cytogenetics Section, Laboratory of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814-4958, USA.
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13
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Lebbar A, Viot G, Szpiro-Tapia S, Baverel F, Rabineau D, Dupont JM. Pregnancy outcome following prenatal diagnosis of an isodicentric X chromosome: first case report. Prenat Diagn 2002; 22:973-5. [PMID: 12424758 DOI: 10.1002/pd.444] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
An isodicentric X chromosome, idic (X)(q27) was found in a female fetus during cytogenetic studies performed on amniotic cells due to advanced maternal age. No mosaicism was observed. Although segmental inversion duplications have been described for several other chromosomes, isodicentric chromosomes are reported only for gonosomes. Genetic counselling was based on ultrasound findings, cytogenetic replication studies and published cases of X chromosomes duplications ascertained pre- and postnatally. The pregnancy resulted in the birth of a healthy female infant.
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Affiliation(s)
- A Lebbar
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Cochin-Port Royal, AP/HP-Université Paris 5, Paris, France.
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14
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Morelli C, Karayianni E, Magnanini C, Mungall AJ, Thorland E, Negrini M, Smith DI, Barbanti-Brodano G. Cloning and characterization of the common fragile site FRA6F harboring a replicative senescence gene and frequently deleted in human tumors. Oncogene 2002; 21:7266-76. [PMID: 12370818 DOI: 10.1038/sj.onc.1205573] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2001] [Revised: 03/29/2002] [Accepted: 04/15/2002] [Indexed: 11/08/2022]
Abstract
The common fragile site FRA6F, located at 6q21, is an extended region of about 1200 kb, with two hot spots of breakage each spanning about 200 kb. Transcription mapping of the FRA6F region identified 19 known genes, 10 within the FRA6F interval and nine in a proximal or distal position. The nucleotide sequence of FRA6F is rich in repetitive elements (LINE1 and LINE2, Alu, MIR, MER and endogenous retroviral sequences) as well as in matrix attachment regions (MARs), and shows several DNA segments with increased helix flexibility. We found that tight clusters of stem-loop structures were localized exclusively in the two regions with greater frequency of breakage. Chromosomal instability at FRA6F probably depends on a complex interaction of different factors, involving regions of greater DNA flexibility and MARs. We propose an additional mechanism of fragility at FRA6F, based on stem-loop structures which may cause delay or arrest in DNA replication. A senescence gene likely maps within FRA6F, as suggested by detection of deletion and translocation breakpoints involving this fragile site in immortal human-mouse cell hybrids and in SV40-immortalized human fibroblasts containing a human chromosome 6 deleted at q21. Deletion breakpoints within FRA6F are common in several types of human leukemias and solid tumors, suggesting the presence of a tumor suppressor gene in the region. Moreover, a gene associated to hereditary schizophrenia maps within FRA6F. Therefore, FRA6F may represent a landmark for the identification and cloning of genes involved in senescence, leukemia, cancer and schizophrenia.
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Affiliation(s)
- Cristina Morelli
- Department of Experimental and Diagnostic Medicine, Section of Microbiology and Center for Biotechnology, University of Ferrara, I-44100 Ferrara, Italy
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15
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Gümüş G, Sunguroğlu A, Tükün A, Sayin DB, Bökesoy I. Common fragile sites associated with the breakpoints of chromosomal aberrations in hematologic neoplasms. CANCER GENETICS AND CYTOGENETICS 2002; 133:168-71. [PMID: 11943347 DOI: 10.1016/s0165-4608(01)00569-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Fragile sites are specific regions of chromosomes prone to breakage when cells are cultured under specific conditions. These sites are divided into two classes: common and rare. Common fragile sites are expressed in all individuals at different frequencies, whereas rare ones are found only in certain individuals. Common and rare fragile sites have been shown to display a number of characteristics of instability being preferential sites for chromosomal deletions, duplications, and rearrangements. Moreover, a majority of mapped oncogenes are located at or near these fragile sites. These observations have led to the suggestion that both classes of fragile sites may play a significant role in chromosomal rearrangements involved in oncogene activation or tumor supressor gene inactivation. For these reasons, involvement of common and rare fragile sites and their relevance to specific chromosome breakpoints in cancer have received much attention. In this study, which reports on the cytogenetic findings obtained from 256 patients with chronic myelocytic leukemia, 103 with acute myelocytic leukemia, 40 with acute lymphocytic leukemia, 33 with myelodysplastic syndrome, we documented the fragile sites involved in chromosomal aberrations involving oncogenes, tumor supressor genes, and other known genes important in cell cycle regulation localized at these sites.
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MESH Headings
- Bone Marrow/pathology
- Chromosome Aberrations
- Chromosome Fragile Sites
- Chromosome Fragility/genetics
- Genes, Tumor Suppressor/physiology
- Genes, cdc/physiology
- Humans
- Karyotyping
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/pathology
- Oncogenes/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology
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Affiliation(s)
- Güvem Gümüş
- Ankara University, Faculty of Medicine, Medical Biology Department, Ankara, Turkey.
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Aboura A, Coulomb-L'Herminé A, Audibert F, Capron F, Frydman R, Tachdjian G. De novo interstitial direct duplication 1(q23.1q31.1) in a fetus with Pierre Robin sequence and camptodactyly. AMERICAN JOURNAL OF MEDICAL GENETICS 2002; 108:153-9. [PMID: 11857566 DOI: 10.1002/ajmg.10219] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Interstitial duplications of chromosomal region 1q are rarely seen. We report the first prenatal diagnosis of pure partial trisomy 1q. The fetus was karyotyped for polyhydramnios, micrognathia, and flexion of fingers of both hands. Conventional and molecular cytogenetics showed a de novo direct duplication of the chromosomal region 1q23.1q31.1 leading to a partial trisomy 1q. At autopsy, the fetus showed Pierre Robin sequence (PRS) and camptodactyly. The main histological finding was a decreased number of motoneurons with apoptotic features in the anterior horn of the spinal cord. A literature review and our observations suggest that genetic material mapping to chromosome 1q25 could be responsible for PRS with distal arthrogryposis when this is in triple dose.
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Affiliation(s)
- A Aboura
- Cytogénétique, Hôpital Antoine Béclère, Clamart, France
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17
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Kotzot D, Martinez MJ, Bagci G, Basaran S, Baumer A, Binkert F, Brecevic L, Castellan C, Chrzanowska K, Dutly F, Gutkowska A, Karaüzüm SB, Krajewska-Walasek M, Luleci G, Miny P, Riegel M, Schuffenhauer S, Seidel H, Schinzel A. Parental origin and mechanisms of formation of cytogenetically recognisable de novo direct and inverted duplications. J Med Genet 2000; 37:281-6. [PMID: 10745046 PMCID: PMC1734569 DOI: 10.1136/jmg.37.4.281] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Cytogenetic, FISH, and molecular results of 20 cases with de novo tandem duplications of 18 different autosomal chromosome segments are reported. There were 12 cases with direct duplications, three cases with inverted duplications, and five in whom determination of direction was not possible. In seven cases a rearrangement between non-sister chromatids (N-SCR) was found, whereas in the remaining 13 cases sister chromatids (SCR) were involved. Paternal and maternal origin (7:7) was found almost equally in cases with SCR (3:4) and N-SCR (4:3). In the cases with proven inversion, there was maternal and paternal origin in one case each. Twenty three out of 43 cytogenetically determined breakpoints correlated with common or rare fragile sites. In five cases, including all those with proven inverse orientation, all breakpoints corresponded to common or rare fragile sites. In at least two cases, one with an interstitial duplication (dup(19)(q11q13)) and one with a terminal duplication (dup(8) (p10p23)), concomitant deletions (del(8) (p23p23.3) and del(19)(q13q13)) were found.
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Affiliation(s)
- D Kotzot
- Institute for Medical Genetics, University of Zürich, Zürich, Switzerland.
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18
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Pineau P, Nagai H, Prigent S, Wei Y, Gyapay G, Weissenbach J, Tiollais P, Buendia MA, Dejean A. Identification of three distinct regions of allelic deletions on the short arm of chromosome 8 in hepatocellular carcinoma. Oncogene 1999; 18:3127-34. [PMID: 10340384 DOI: 10.1038/sj.onc.1202648] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The chromosome 8p is associated with a large number of allelic imbalances in epithelial tumors including hepatocellular carcinoma (HCC). However, no tumor suppressor gene has been identified so far in this particular region of the genome. To further clarify the pattern of allelic deletions on chromosome 8p in HCC, we have undertaken high-density polymorphic marker analysis of 109 paired normal and primary tumor samples using 40 microsatellites positioned every 2 cm in average throughout 8p. We found that 60% of the tumors exhibited loss of heterozygosity (LOH) at one or more loci at 8p with three distinct minimal deleted areas: a 13 cm region in the distal part of 8p21, a 9 cm area in the more proximal portion of 8p22 and a 5 cm area in 8p23. These data strongly suggest the presence of at least three novel tumor suppressor loci on 8p in hepatocellular carcinoma.
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Affiliation(s)
- P Pineau
- Unité de Recombinaison & Expression Génétique, INSERM U163, Institut Pasteur, Paris, France
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19
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Abstract
Deletions and translocations at 5q13 point out a locus involved in the development of acute myeloblastic leukemia (AML) and myelodysplastic syndromes (MDS) as well as other neoplasms. The chromosomal rearrangements of 5q13 are well documented, but have not been a primary focus of research. In this report, we provide evidence for a novel critical locus at 5q13.3, encoding gene(s) which may be disrupted by chromosomal translocations or deletions. Rare cases of myeloid neoplasms with t(5q13) as the sole chromosomal anomaly argue for a gene which gives rise to fusion proteins. Our preliminary studies have localized one of the critical genes to a <3 Mb. interval between the polymorphic markers AFMB347yf9 and GATAP18104 at the band 5q13.3. Other results also suggest that the 5q 13.3 locus may span a fragile site which undergoes unbalanced translocations and interstitial deletions accompanied by loss of significant segments of chromosome 5. Molecular reagents generated by the human genome mapping and sequencing initiative will allow us to characterize the critical genes at 5q13.3 and facilitate genotypic analysis of AML and MDS.
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Affiliation(s)
- P D Castro
- Department of Molecular Hematology and Therapy, The University of Texas M.D. Anderson Cancer Center, Houston 77030, USA
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20
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Gericke GS. Chromosomal fragility may be indicative of altered higher-order DNA organization as the underlying genetic diathesis in complex neurobehavioral disorders. Med Hypotheses 1998; 50:319-26. [PMID: 9690767 DOI: 10.1016/s0306-9877(98)90004-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Preliminary observations concerning increased chromosomal fragility in association with behavioural disorders in humans allow an opportunity to suggest a cohesive theory regarding the possible importance of higher-order DNA modifications in the coordination of gene function in brain evolution and during development. Visible or submicroscopic acentric chromosomal fragments are formed as an accompaniment to chromosomal breakage and are associated with sequence amplification. During genomic reintegration of extrachromosomally amplified repeat sequence elements, functional consequences could include unequal crossing over with gain-of-function, and/or deletion with loss-of-function. This process could result in regulatory changes in gene function in association with normal coding regions, since fragile sites appear to be located at or near upstream DNaseI-hypersensitive areas. Earlier research on chromosomal breakage in relation to transposon behaviour in maize has set a precedent by which many elements in a network could be coordinately controlled, a principle which may allow transcriptional control over multiple areas in the genome simultaneously. The hypothesis proposed in this paper implies that a small number of fundamental higher-order changes may be responsible for influencing a wide range of genetic alterations leading to complex phenotypes, sometimes segregating as distinct entities within pedigrees, or alternatively, and perhaps more commonly, presenting with several overlapping phenotypes in some other families. Studying only pure multiplex families in psychiatric genetics may not be sufficient for an understanding of the underlying genetic diathesis in this group of disorders. Validation of the fragile site hypothesis for complex neurobehavioural disorders may offer additional avenues for gene therapy based either on preferential integration of exogenous DNA at fragile sites, or utilizing the acentric fragments to modify sequence amplification extrachromosomally.
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Affiliation(s)
- G S Gericke
- MRC Neurogenetics Research Laboratory, Pretoria, South Africa.
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21
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Abstract
Fragile sites have been interesting for mapping chromosomal regions involved in disease and ageing. The chromosomal fragile site expression from 38 Down's syndrome (DS) individuals aged 0-48 years was investigated in blood peripheral lymphocytes. Fragile sites were statistically characterized as the minimum expected number of lesions per band based on a Poisson distribution. The results showed that the fragile site 2q11 was associated with the DS condition and fragile sites 5q31, 6p21 and 9q12 with ageing in DS subjects. Fragility in 6p21 has also been associated with Alzheimer's disease patients.
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Affiliation(s)
- M A Smith
- Departamento de Morfologia, Disciplina de Genética, UNIFESP Escola Paulista de Medicina, São Paulo, Brazil.
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22
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Bergthorsson JT, Johannsdottir J, Jonasdottir A, Eiriksdottir G, Egilsson V, Ingvarsson S, Barkardottir RB, Arason A. Chromosome imbalance at the 3p14 region in human breast tumours: high frequency in patients with inherited predisposition due to BRCA2. Eur J Cancer 1998; 34:142-7. [PMID: 9624249 DOI: 10.1016/s0959-8049(97)00339-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Our previous studies have indicated that genetic aberrations in the 3p14 region are more frequent in malignant tumours from hereditary breast cancer patients than sporadic breast cancers. The main purpose of this study was to test if BRCA2 susceptibility alleles contribute to imbalance in the 3p14 region. We mapped allelic imbalance at 3p14 in tumours from Icelandic sisters affected with breast cancer using a set of 10 microsatellite markers (tel-D3S1295-D3S1234-D3S1300-D3S1600-D3S1233+ ++-D3S1217-D3S1261-D3S1296-D3S1210- D3S1284-cen). The patients were of known carrier status with respect to the 999del5 mutation in BRCA2 which is the most common cause of hereditary breast cancer in Iceland. Of 103 patients, 32 in the group were mutation carriers. A high degree of imbalance was observed in tumours from BRCA2 mutation carriers, ranging from 44 to 88% for individual markers. This was significantly higher than the percentage of imbalance in tumours from non-carriers, where the frequency ranged from 25 to 43%. In both groups, we noted elevated 3p14 imbalance in patients with bilateral disease. Allelic imbalance was most commonly observed near the marker D3S1210 (3p14.1-p12) and the FHIT gene (3p21.1-p14.2) for both groups. We conclude that genomic aberrations in 3p14 are especially frequent in tumours with BRCA2 gene defects, and suggest that this is caused by regional loss of chromosome stability rather than selection.
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Affiliation(s)
- J T Bergthorsson
- Department of Pathology, University Hospital of Iceland, Reykjavik, Iceland
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24
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Musio A, Sbrana I. Aphidicolin-sensitive specific common fragile sites: a biomarker of exposure to pesticides. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 1997; 29:250-255. [PMID: 9142167 DOI: 10.1002/(sici)1098-2280(1997)29:3<250::aid-em4>3.0.co;2-g] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In this work, we analyzed the aphidicolin-sensitive common fragile sites in seven females and four males occupationally exposed to pesticides and in ten controls. The same males had been monitored one year earlier in a previous study by the same authors. Results showed enhanced expression in exposed subjects at eight bands, namely, 6q25, 7p22, 7q22, 7q32, 13q14, 14q24, 16q22, and 16q23. Most of these bonds were fragile sites and breakpoints involved in chromosome rearrangements found in hematopoietic tumors. Moreover, six of these bands were already detected, with enhanced expression, in the first monitoring carried out on male subjects. These results indicated that fragile sites analysis is a reproducible cell response to human exposure to pesticides.
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Affiliation(s)
- A Musio
- Dipartimento di Scienze dell' Ambiente e del Territorio, Università degli Studi di Pisa, Italy
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25
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Abstract
A relationship between telomere shortening and ageing has been established. A series of young and elderly healthy donors. Alzheimer disease patients, young and old Down's syndrome individuals were cytogenetically analyzed. No preferential damage in distal bands was seen in age-related chromosome instability.
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