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Guilherme RS, Moysés-Oliveira M, Dantas AG, Meloni VA, Colovati ME, Kulikowski LD, Melaragno MI. Position effect modifying gene expression in a patient with ring chromosome 14. J Appl Genet 2015; 57:183-7. [PMID: 26315457 DOI: 10.1007/s13353-015-0311-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/29/2015] [Accepted: 08/12/2015] [Indexed: 10/23/2022]
Abstract
The clinical phenotype of patients with ring chromosomes usually reflects the loss of genomic material during ring formation. However, phenotypic alterations can also be found in the presence of complete ring chromosomes, in which the breakage and rejoining in terminal regions of both chromosome arms result in no gene loss. Here, we present a patient with a ring chromosome 14 that lost nothing but the telomeres. Since he and other patients with a similar chromosome abnormality present certain abnormal characteristics, we investigated the gene expression of eight chromosome 14 genes to find out whether the configuration of the ring had changed it, possibly producing some of these clinical features. The expression of these eight genes was studied by quantitative real-time polymerase chain reaction (qPCR) in the patient and in seven controls matched for gender and age. Two of them were found to be downregulated in the patient compared to the controls, indicating that his phenotype might be related to alterations in the expression of genes located in the abnormal chromosome, even when the copy number is normal. Thus, the phenotypic alterations found in the presence of complete ring chromosomes may be related to changes in the chromatin architecture, bringing about a change of expression by position effect. These results may explain some of the characteristics presented by our patient.
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Affiliation(s)
- Roberta Santos Guilherme
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu, 740, 04023-900, São Paulo, Brazil
| | - Mariana Moysés-Oliveira
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu, 740, 04023-900, São Paulo, Brazil
| | - Anelisa Gollo Dantas
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu, 740, 04023-900, São Paulo, Brazil
| | - Vera Ayres Meloni
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu, 740, 04023-900, São Paulo, Brazil
| | - Mileny Esbravatti Colovati
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu, 740, 04023-900, São Paulo, Brazil
| | - Leslie Domenici Kulikowski
- Department of Pathology, Laboratório de Citogenômica, Universidade de São Paulo, Avenida Dr. Eneas Carvalho de Aguiar 647, 05403-000, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu, 740, 04023-900, São Paulo, Brazil.
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Alosi D, Klitten LL, Bak M, Hjalgrim H, Møller RS, Tommerup N. Dysregulation of FOXG1 by ring chromosome 14. Mol Cytogenet 2015; 8:24. [PMID: 25901181 PMCID: PMC4404611 DOI: 10.1186/s13039-015-0129-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/19/2015] [Indexed: 02/03/2023] Open
Abstract
In this study we performed molecular characterization of a patient with an extra ring chromosome derived from chromosome 14, with severe intellectual disability, epilepsy, cerebral paresis, tetraplegia, osteoporosis and severe thoraco-lumbal scoliosis. Array CGH analysis did not show any genomic imbalance but conventional karyotyping and FISH analysis revealed the presence of an interstitial 14q12q24.3 deletion and an extra ring chromosome derived from the deleted material. The deletion and ring chromosome breakpoints were identified at base-pair level by mate-pair and Sanger sequencing. Both breakpoints disrupted putative long non-coding RNA genes (TCONS00022561;RP11-148E17.1) of unknown function. However, the proximal breakpoint was 225 kb downstream of the forkhead box G1 gene (FOXG1), within the known regulatory landscape of FOXG1. The patient represents the first case of a r(14) arising from an interstitial excision where the phenotype is compatible with dysregulation of FOXG1. In turn, the phenotypic overlap between the present case, the FOXG1 syndrome and the r(14) syndrome supports that dysregulation of FOXG1 may contribute to the classical r(14)-syndrome, likely mediated by dynamic mosaicism.
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Affiliation(s)
- Daniela Alosi
- Department of Cellular and Molecular Medicine, Wilhelm Johannsen Centre for Functional Genome Research, University of Copenhagen, Copenhagen, Denmark
| | - Laura Line Klitten
- Department of Cellular and Molecular Medicine, Wilhelm Johannsen Centre for Functional Genome Research, University of Copenhagen, Copenhagen, Denmark ; Danish Epilepsy Centre, Dianalund, Denmark
| | - Mads Bak
- Department of Cellular and Molecular Medicine, Wilhelm Johannsen Centre for Functional Genome Research, University of Copenhagen, Copenhagen, Denmark
| | - Helle Hjalgrim
- Danish Epilepsy Centre, Dianalund, Denmark ; Institute of Regional Health Services Research, University of Southern Denmark, Odense, Denmark
| | - Rikke Steensbjerre Møller
- Danish Epilepsy Centre, Dianalund, Denmark ; Institute of Regional Health Services Research, University of Southern Denmark, Odense, Denmark
| | - Niels Tommerup
- Department of Cellular and Molecular Medicine, Wilhelm Johannsen Centre for Functional Genome Research, University of Copenhagen, Copenhagen, Denmark
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Guilherme RS, Soares KC, Simioni M, Vieira TP, Gil-da-Silva-Lopes VL, Kim CA, Brunoni D, Spinner NB, Conlin LK, Christofolini DM, Kulikowski LD, Steiner CE, Melaragno MI. Clinical, cytogenetic, and molecular characterization of six patients with ring chromosomes 22, including one with concomitant 22q11.2 deletion. Am J Med Genet A 2014; 164A:1659-65. [PMID: 24700634 DOI: 10.1002/ajmg.a.36512] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 01/31/2014] [Indexed: 11/06/2022]
Abstract
We report here on six patients with a ring chromosome 22 and the range of cytogenetic and phenotypic features presented by them. Genomic analysis was carried out using classical and molecular cytogenetics, MLPA (Multiplex Ligation-dependent Probe Amplification) and genome-wide SNP-array analysis. The ring was found in all patients, but Patient 6 displayed constitutional mosaicism with a normal cell line. Five patients had deletions in the ring chromosome 22, and in four of them the breakpoints--unique for each patient--could be identified by genome-wide SNP-array analysis. One patient presented with a 22q11.2 deletion concomitant with the deletion caused by the ring formation. Common phenotypic features included autism, speech delay and seizures, as previously reported for individuals with r(22) and/or 22q13.3 deletions. Investigation of the genes within the deletions revealed multiple genes related to development of the central nervous system, psychomotor delay, severe language impairment, hypotonia, and autistic symptoms. There was no clear correlation between the severity of clinical features and the size of the deleted segment. This study underscores the variability in ring structure and clinical presentation of the r(22) and adds information to the limited literature on this rare disorder.
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Affiliation(s)
- Roberta Santos Guilherme
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
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Salas-Labadía C, Cervantes-Barragán DE, Cruz-Alcívar R, Daber RD, Conlin LK, Leonard LD, Spinner NB, Durán-McKinster C, Dávila-Ortíz de Montellano DJ, Del Castillo-Ruiz V, Pérez-Vera P. Cytogenomic and phenotypic analysis in low-level monosomy 7 mosaicism with non-supernumerary ring chromosome 7. Am J Med Genet A 2014; 164A:1765-9. [DOI: 10.1002/ajmg.a.36503] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 01/26/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Consuelo Salas-Labadía
- Laboratorio de Cultivo de Tejidos; Departamento de Genética Humana; Instituto Nacional de Pediatría; México DF Mexico
| | - David E. Cervantes-Barragán
- Laboratorio de Cultivo de Tejidos; Departamento de Genética Humana; Instituto Nacional de Pediatría; México DF Mexico
- Current affiliation: Servicio de Genética; Hospital Central Sur de Alta Especialidad; PEMEX Picacho; México DF Mexico
| | - Roberto Cruz-Alcívar
- Laboratorio de Cultivo de Tejidos; Departamento de Genética Humana; Instituto Nacional de Pediatría; México DF Mexico
| | - Robert D. Daber
- Department of Pathology and Laboratory Medicine; Children's Hospital of Philadelphia; Pennsylvania
| | - Laura K. Conlin
- Department of Pathology and Laboratory Medicine; Children's Hospital of Philadelphia; Pennsylvania
| | - Laura D. Leonard
- Department of Pathology and Laboratory Medicine; Children's Hospital of Philadelphia; Pennsylvania
| | - Nancy B. Spinner
- Department of Pathology and Laboratory Medicine; Children's Hospital of Philadelphia; Pennsylvania
| | | | | | | | - Patricia Pérez-Vera
- Laboratorio de Cultivo de Tejidos; Departamento de Genética Humana; Instituto Nacional de Pediatría; México DF Mexico
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Guilherme RS, Dutra ARN, Perez ABA, Takeno SS, Oliveira MM, Kulikowski LD, Klein E, Hamid AB, Liehr T, Melaragno MI. First report of a small supernumerary der(8;14) marker chromosome. Cytogenet Genome Res 2013; 139:284-8. [PMID: 23548553 DOI: 10.1159/000348743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2012] [Indexed: 11/19/2022] Open
Abstract
Small supernumerary marker chromosomes (sSMC) are structurally abnormal chromosomes, generally equal in size or smaller than a chromosome 20 of the same metaphase spread. Most of them are unexpectedly detected in routine karyotype analyses, and it is usually not easy to correlate them with a specific clinical picture. A small group of sSMCs is derived from more than one chromosome, called complex sSMCs. Here, we report on a patient with a de novo complex sSMC, derived from chromosomes 8 and 14. Banding karyotype analysis, multiplex ligation-dependent probe amplification (MLPA), single nucleotide polymorphism (SNP)-based array, and fluorescence in situ hybridization (FISH) were performed to investigate its origin. Array and FISH analyses revealed a der(14)t(8;14)(p23.2;q22.1)dn. The propositus presents some clinical features commonly found in patients with partial duplication or triplication of 8p and 14q. This is the first report describing a patient with a congenital der(14)t(8;14)(p23.2;q22.1)dn sSMC.
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Affiliation(s)
- R S Guilherme
- Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
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Guilherme RS, Meloni VDF, Takeno SS, Pellegrino R, Brunoni D, Kulikowski LD, Melaragno MI. Twenty-year cytogenetic and molecular follow-up of a patient with ring chromosome 15: a case report. J Med Case Rep 2012; 6:283. [PMID: 22958471 PMCID: PMC3459701 DOI: 10.1186/1752-1947-6-283] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 03/09/2012] [Indexed: 11/28/2022] Open
Abstract
Introduction Ring chromosome 15 is a rare disorder, with only a few over 40 cases reported in the literature. There are only two previous reports of cases where patients with ring chromosome 15 have been followed-up. Case presentation We report here on the 20-year clinical and cytogenetic follow-up of a patient with a ring chromosome 15. Our patient, a Caucasoid Asian woman, presented with short stature, microcephaly, minor dysmorphic features, hyperextensible knees, generalized hirsutism, café-au-lait and small hypochromic spots spread over her face and the front of her chest and abdomen, dorsolumbar scoliosis and mild intellectual disability. She was followed-up from the age of eight to 28 years. When she was 27 years old, she was reported by her mother to present with compulsive overeating and an aggressive mood when challenged. Karyotyping revealed that the majority of her cells harbored one normal chromosome and one ring chromosome. Silver staining revealed the presence of the nucleolar organizer region in the ring chromosome. Ring loss and/or secondary aberrations exhibited a slight increase over time, from 4.67% in 1989 to 7.67% in 2009, with the presence of two monocentric rings, cells with interlocked rings, a dicentric ring, and broken or open rings. A genome-wide array technique detected a 5.5Mb deletion in 15q26.2. Conclusions We observed that some phenotypic alterations in our patient can be associated with gene loss and haploinsufficiency. Other features may be related to different factors, including ring instability and epigenetic factors.
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Affiliation(s)
- Roberta S Guilherme
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, São Paulo 04023-900, Brazil.
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Bakhshandeh B, Soleimani M, Hafizi M, Paylakhi SH, Ghaemi N. MicroRNA signature associated with osteogenic lineage commitment. Mol Biol Rep 2012; 39:7569-81. [PMID: 22350160 DOI: 10.1007/s11033-012-1591-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 01/31/2012] [Indexed: 01/22/2023]
Abstract
Cell-based approaches offer a potential therapeutic strategy for appropriate bone manufacturing. Capable of differentiating into multiple cell types especially osteoblasts spontaneously, unrestricted somatic stem cell (USSC) seems to be a suitable candidate. Recent studies have shown the involvement of microRNAs in several biological processes. miRNA microarray profiling was applied in order to identify the osteo-specific miRNA signature. Prior to this analysis, osteogenic commitment of osteoblasts was evaluated by measuring ALPase activity, biomineralization, specific staining and evaluation of some main osteogenic marker genes. To support our findings, various in silico explorations (for both putative targets and signaling pathways) and empirical analyses (miRNA transfections followed by qPCR of osteogenic indicators and ALPase activity measurement) were carried out. The function of GSK-3b inhibitor was also studied to investigate the role of WNT in osteogenesis. Transient modulation of multiple osteo-miRs (such as mir-199b, 1274a, 30b) with common targets (such as BMPR, TCFs, SMADs) as mediators of osteogenic pathways including cell-cell interactions, WNT and TGF-beta pathways, suggests a mechanism for rapid induction of the osteogenesis as an anti-miRNA therapy. The results of this research have identified the miRNA signature which regulates the osteogenesis mechanism in USSC. To conclude, our study reveals more details about the allocation of USSCs into osteogenic lineage through modulatory effect of miRNAs on targets and pathways required for creating a tissue-specific phenotype and may aid in future clinical interventions.
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Affiliation(s)
- Behnaz Bakhshandeh
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
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Colovati ME, da Silva LR, Takeno SS, Mancini TI, N Dutra AR, Guilherme RS, de Mello CB, Melaragno MI, A Perez AB. Marfan syndrome with a complex chromosomal rearrangement including deletion of the FBN1 gene. Mol Cytogenet 2012; 5:5. [PMID: 22260333 PMCID: PMC3339390 DOI: 10.1186/1755-8166-5-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 01/19/2012] [Indexed: 11/10/2022] Open
Abstract
Background The majority of Marfan syndrome (MFS) cases is caused by mutations in the fibrillin-1 gene (FBN1), mapped to chromosome 15q21.1. Only few reports on deletions including the whole FBN1 gene, detected by molecular cytogenetic techniques, were found in literature. Results We report here on a female patient with clinical symptoms of the MFS spectrum plus craniostenosis, hypothyroidism and intellectual deficiency who presents a 1.9 Mb deletion, including the FBN1 gene and a complex rearrangement with eight breakpoints involving chromosomes 6, 12 and 15. Discussion This is the first report of MFS with a complex chromosome rearrangement involving a deletion of FBN1 and contiguous genes. In addition to the typical clinical findings of the Marfan syndrome due to FBN1 gene haploinsufficiency, the patient presents features which may be due to the other gene deletions and possibly to the complex chromosome rearrangement.
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Affiliation(s)
- Mileny Es Colovati
- Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, SP, Brasil.
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Guilherme RS, Meloni VFA, Kim CA, Pellegrino R, Takeno SS, Spinner NB, Conlin LK, Christofolini DM, Kulikowski LD, Melaragno MI. Mechanisms of ring chromosome formation, ring instability and clinical consequences. BMC MEDICAL GENETICS 2011; 12:171. [PMID: 22188645 PMCID: PMC3309960 DOI: 10.1186/1471-2350-12-171] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 12/21/2011] [Indexed: 11/15/2022]
Abstract
Background The breakpoints and mechanisms of ring chromosome formation were studied and mapped in 14 patients. Methods Several techniques were performed such as genome-wide array, MLPA (Multiplex Ligation-Dependent Probe Amplification) and FISH (Fluorescent in situ Hybridization). Results The ring chromosomes of patients I to XIV were determined to be, respectively: r(3)(p26.1q29), r(4)(p16.3q35.2), r(10)(p15.3q26.2), r(10)(p15.3q26.13), r(13)(p13q31.1), r(13)(p13q34), r(14)(p13q32.33), r(15)(p13q26.2), r(18)(p11.32q22.2), r(18)(p11.32q21.33), r(18)(p11.21q23), r(22)(p13q13.33), r(22)(p13q13.2), and r(22)(p13q13.2). These rings were found to have been formed by different mechanisms, such as: breaks in both chromosome arms followed by end-to-end reunion (patients IV, VIII, IX, XI, XIII and XIV); a break in one chromosome arm followed by fusion with the subtelomeric region of the other (patients I and II); a break in one chromosome arm followed by fusion with the opposite telomeric region (patients III and X); fusion of two subtelomeric regions (patient VII); and telomere-telomere fusion (patient XII). Thus, the r(14) and one r(22) can be considered complete rings, since there was no loss of relevant genetic material. Two patients (V and VI) with r(13) showed duplication along with terminal deletion of 13q, one of them proved to be inverted, a mechanism known as inv-dup-del. Ring instability was detected by ring loss and secondary aberrations in all but three patients, who presented stable ring chromosomes (II, XIII and XIV). Conclusions We concluded that the clinical phenotype of patients with ring chromosomes may be related with different factors, including gene haploinsufficiency, gene duplications and ring instability. Epigenetic factors due to the circular architecture of ring chromosomes must also be considered, since even complete ring chromosomes can result in phenotypic alterations, as observed in our patients with complete r(14) and r(22).
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Affiliation(s)
- Roberta S Guilherme
- Genetics Division, Department of Morphology and Genetics, Federal University of São Paulo, Botucatu Street 740, Zip Code 04023-900, São Paulo, Brazil.
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