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Capela de Matos RR, Othman M, Ferreira GM, Monteso K, de Souza MT, Rouxinol M, Melo JB, Carreira IM, Abdelhay E, Liehr T, Ribeiro RC, Silva M. Somatic homozygous loss of SH2B3, and a non-Robertsonian translocation t(15;21)(q25.3;q22.1) with NTRK3 rearrangement, in an adolescent with progenitor B-cell acute lymphoblastic leukemia with the iAMP21. Cancer Genet 2021; 262-263:16-22. [PMID: 34974289 DOI: 10.1016/j.cancergen.2021.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 11/04/2021] [Accepted: 12/20/2021] [Indexed: 11/18/2022]
Abstract
Intrachromosomal amplification of chromosome 21 (iAMP21) occurs in ∼2% of B-cell acute lymphoblastic leukemia (ALL) and is considered to confer a poor prognosis. The relapse risk is associated with therapy intensity, suggesting that other somatic mutations may influence iAMP21-ALL prognosis. This abnormality is characterized by multiple copies of the RUNX1 gene in chromosome 21 and appears to arise through multiple breakage-fusion bridge cycles and chromothripsis. Rob(15;21) or a ring chromosome 21 have been associated with an increased risk for iAMP21-ALL, suggesting that constitutional genetic abnormalities may also drive leukemogenesis. Here we describe homozygous deletion of the SH2B3 gene, chromothripsis of chromosome 21, and a non-Robertsonian somatic t(15;21)(q25.3;q22.1) with NTRK3 gene rearrangement in an adolescent with iAMP21-B-ALL. Molecular cytogenetic studies detected iAMP21 with aCGH analysis revealing further genomic imbalances. The RT-qPCR analysis detected elevated expression levels of RUNX1 (68-fold) and reduced expression of CDK6 (0.057-fold). Studies with constitutive cells collected from mouth swabs showed that SH2B3 biallelic deletion was a somatic alteration occurring during clonal evolution. The identification of novel secondary genetic changes was valuable to discuss sporadic iAMP21 leukemogenic mechanisms. For the first time, we show a t(15;21)(q25.3;q22.1) with NTRK3 rearrangement in an adolescent with iAMP21-ALL.
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Affiliation(s)
- R R Capela de Matos
- Cytogenetics Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil; Post-Graduate Programme in Oncology, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - Mak Othman
- Jena University Hospital, Institute of Human Genetics, Jena, Germany
| | - G M Ferreira
- Stem Cells Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - Kca Monteso
- Cytogenetics Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil; Post-Graduate Programme in Oncology, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - M T de Souza
- Cytogenetics Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - M Rouxinol
- Lagoa Federal Hospital, Rio de Janeiro, Brazil
| | - J B Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal; Centre of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - I M Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal; Centre of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - E Abdelhay
- Stem Cells Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil; Post-Graduate Programme in Oncology, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil
| | - T Liehr
- Jena University Hospital, Institute of Human Genetics, Jena, Germany
| | - R C Ribeiro
- Departments of Oncology and Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mlm Silva
- Cytogenetics Department, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil; Post-Graduate Programme in Oncology, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA-RJ), Rio de Janeiro, Brazil.
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Ribeiro IP, Carreira IM, Esteves L, Caramelo F, Liehr T, Melo JB. Chromosomal breakpoints in a cohort of head and neck squamous cell carcinoma patients. Genomics 2019; 112:297-303. [PMID: 30802597 DOI: 10.1016/j.ygeno.2019.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 10/27/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) presents complex chromosomal rearrangements, however, the molecular mechanisms behind HNSCC development remain elusive. The identification of the recurrent chromosomal breakpoints could help to understand these mechanisms. Array-CGH was performed in HNSCC patients and the chromosomal breakpoints involved in gene amplification/loss were analyzed. Frequent breakpoints were clustered in chromosomes 12p, 8p, 3q, 14q, 6p, 4q, Xq and 8q. Chromosomes 6, 14, 3, 8 and X exhibited higher susceptibility to have breaks than other chromosomes. We observed that low copy repeat DNA sequences are localized at or flanking breakpoint sites, ranging from 0 to 200 bp. LINES, SINES and Simple Repeats were the most frequent repeat elements identified in these regions. We conclude that in our cohort specific peri-centromeric and telomeric regions were frequently involved in breakpoints, being the presence of low copy repeats elements one of the explanations for the common rearrangement events observed.
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Affiliation(s)
- I P Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal; iCBR-CIMAGO - Center of Investigation on Environment, Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - I M Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal; iCBR-CIMAGO - Center of Investigation on Environment, Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - L Esteves
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - F Caramelo
- Laboratory of Biostatistics and Medical Informatics, IBILI - Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - T Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - J B Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal; iCBR-CIMAGO - Center of Investigation on Environment, Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.
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Pires DAF, Coelho EGA, Melo JB, Oliveira DAA, Ribeiro MN, Gus Cothran E, Juras R. Genetic relationship between the Nordestino horse and national and international horse breeds. Genet Mol Res 2016; 15:gmr7881. [PMID: 27173248 DOI: 10.4238/gmr.15027881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Knowledge of genetic diversity and relationships between breeds is very important for conservation programs. Hair samples were collected from 393 individual Nordestino horses and genotyped using 14 microsatellite markers in order to investigate the genetic relationship between this breed and 66 international horse breeds. There was high allelic diversity and inbreeding coefficient within population values were not significant, which was probably due to crossbreeding. Despite the Nordestino horse population being in Hardy-Weinberg equilibrium, a global deficit of heterozygotes was observed. This may represent evidence of repeated use of the same stallions for breeding, which is consistent with the high number of castrated males found. Campolina, Mangalarga Marchador, and Mangalarga were the Brazilian horse breeds most closely related to the Nordestino horse, which is a reflection of recent introgressions. Among Iberian horse breeds, the Sorraia breed appears to have had an important influence on the genetics of the Nordestino horse. Those results provide important information that can guide future conservation programs.
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Affiliation(s)
- D A F Pires
- Instituto Federal de Educação, Ciência e Tecnologia de Pernambuco, Campus Barreiros, Barreiros, PE, Brasil
| | - E G A Coelho
- Laboratório de Genética da Escola de Veterinária, Departamento de Zootecnia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - J B Melo
- Departamento de Estudos Básicos e Instrumentais, Universidade Estadual do Sudoeste da Bahia, Itapetinga, BA, Brasil
| | - D A A Oliveira
- Laboratório de Genética da Escola de Veterinária, Departamento de Zootecnia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - M N Ribeiro
- Departamento de Zootecnia, Universidade Federal Rural de Pernambuco, Recife, PE, Brasil
| | - E Gus Cothran
- Department of Veterinary Integrative Biosciences, Texas A & M University, College Station, TX, USA
| | - R Juras
- Department of Veterinary Integrative Biosciences, Texas A & M University, College Station, TX, USA
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Duarte IF, Ladeirinha AF, Lamego I, Gil AM, Carvalho L, Carreira IM, Melo JB. Potential Markers of Cisplatin Treatment Response Unveiled by NMR Metabolomics of Human Lung Cells. Mol Pharm 2013; 10:4242-51. [DOI: 10.1021/mp400335k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- I. F. Duarte
- CICECO,
Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - A. F. Ladeirinha
- Laboratory
of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, 3000 Coimbra, Portugal
| | - I. Lamego
- CICECO,
Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - A. M. Gil
- CICECO,
Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - L. Carvalho
- University Hospitals of Coimbra, 3000-075 Coimbra, Portugal
- Institute
of Pathological Anatomy, Faculty of Medicine, University of Coimbra, 3000 Coimbra, Portugal
- CIMAGO,
Faculty of Medicine, University of Coimbra, 3000 Coimbra, Portugal
| | - I. M. Carreira
- Laboratory
of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, 3000 Coimbra, Portugal
- CIMAGO,
Faculty of Medicine, University of Coimbra, 3000 Coimbra, Portugal
| | - J. B. Melo
- Laboratory
of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, 3000 Coimbra, Portugal
- CIMAGO,
Faculty of Medicine, University of Coimbra, 3000 Coimbra, Portugal
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Pires DAF, Coelho EGA, Melo JB, Oliveira DAA, Ribeiro MN, Gus Cothran E, Juras R, Khanshour A. Diversidade genética e estrutura populacional de subpopulações remanescentes da raça equina nordestino. ARCH ZOOTEC 2013. [DOI: 10.21071/az.v63i242.551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
O presente trabalho teve como objetivo avaliar a estrutura e diversidade genética de quatro subpopulações do cavalo Nordestino utilizando 14 marcadores microssatélites. Amostras de bulbo capilar de 393 cavalos foram coletadas, distribuídos em: 61 animais do vale do Salitre (JUAZ-BA) localizado no estado da Bahia, 89 das mesorregiões Norte e Centro-Norte do estado do Piauí, 58 animais da cidade de Agrestina (AGRE-PE) e 185 das mesorregiões Sertão e Sertão do São Francisco localizado no estado de Pernambuco (SERT-PE). A diversidade genética, diferenciação genética e efeito de gargalo genético foram avaliados nas 4 subpopulações do cavalo Nordestino. Observou-se elevada diversidade genética e valores de Fis que não evidenciaram níveis de consanguinidade significativa, prova-velmente isso se deve à acasalamentos entre as subpopulações. Efeito de gargalo genético recente não foi detectado para as quatro subpopulações, porém os modelos IAM e TPM sugeriram um efeito de gargalo genético não recente. Isso pode ser reflexo da redução no número de reprodutores decorrente da castração de machos, processo de mecanização e mudanças no estilo de vida das populações da zona rural. Eventos mais antigos do efeito de gargalo genético não foram suficientes para evidenciar uma diferenciação genética entre as 4 subpopulações, portanto elas formam um só grupo genético.
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Melo JB, Pires DAF, Ribeiro MN. Perfil fenotípico do remanescente do cavalo nordestino no nordeste do brasil. ARCH ZOOTEC 2012. [DOI: 10.21071/az.v62i238.659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
O presente trabalho teve como objetivo caracterizar o perfil fenotípico do remanescente do Cavalo Nordestino nos estados de Pernambuco e Piauí, no Nordeste do Brasil. Foram avaliados 238 animais entre machos, fêmeas e machos castrados, através de caracteres morfológicos qualitativos (perfil de chanfro, justaposição dos lábios, forma do pescoço, inclinação de garupa) e fanerópticos (coloração da pelagem, coloração dos cascos anteriores e posteriores e tamanho dos cascos). Foi realizada estatística de distribuição de freqüência para todas as variáveis estudadas. Em relação à coloração da pelagem, para os animais de Pernambuco, houve uma maior predominância da tordilha e castanha, para os animais do Piauí as pelagens tordilha e baia. Para o perfil de chanfro o mais freqüente foi o sub-convexo, depois o retilíneo nos animais avaliados no estado de Pernambuco, o sub-côncavo foi mais presente nos machos do Piauí. A forma do pescoço mais freqüente foi a piramidal, com exceção do tipo cervo para as fêmeas e castrados do Piauí. A coloração dos cascos dos anteriores e posteriores apresentou uma predominância da coloração escura ou preta e depois a rajada. Ocorreu uma maior freqüência dos cascos de tamanho pequenos, com exceção para os machos inteiros e castrados de Pernambuco, com predominância de cascos de tamanho médio. Os animais de Pernambuco apresentaram uma maior freqüência dos lábios firmes e justapostos, para os animais machos e machos castrados do Piauí os lábios justapostos, e com as fêmeas os lábios relaxados, ocorrendo em todas as classes dos animais a presença de lábios relaxado ou belfos. Com relação a inclinação de garupa, observou-se maior freqüência para as formas derreadas e inclinadas, com exceção dos machos inteiros de Pernambuco que apresentaram maior freqüência de garupa ligeiramente inclinada, que atende ao padrão do Cavalo Nordestino.
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Mascarenhas A, Matoso E, Saraiva J, Tönnies H, Gerlach A, Julião MJ, Melo JB, Carreira IM. First prenatally detected small supernumerary neocentromeric derivative chromosome 13 resulting in a non-mosaic partial tetrasomy 13q. Cytogenet Genome Res 2008; 121:293-7. [PMID: 18758175 DOI: 10.1159/000138901] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2008] [Indexed: 11/19/2022] Open
Abstract
Neocentromeres are functional centromeres located in non-centromeric euchromatic regions of chromosomes. The formation of neocentromeres results in conferring mitotic stability to chromosome fragments that do not contain centromeric alpha satellite DNA. We present a report of a prenatal diagnosis referred to cytogenetic studies due to ultrasound malformations such as large cisterna magna, no renal differentiation, hypotelorism and ventriculomegaly. Cytogenetic analysis of GTG-banded chromosomes from amniotic fluid cells and fetal blood cells revealed a de novo small supernumerary marker chromosome. Molecular cytogenetic studies using fluorescence in situ hybridization and comparative genomic hybridization showed this marker to be an inverted duplication of the distal portion of chromosome 13q which did not contain detectable alpha satellite DNA. The neocentromeric constriction was located at band 13q31. The presence of a functional neocentromere on this marker chromosome was confirmed by immunofluorescence with antibodies to centromere protein-C. The anatomopathologic study revealed a female fetus with facial dysmorphisms, low set ears and renal dysplasia. Ten small supernumerary neocentromeric chromosomes originating from the distal region of chromosome 13q have been reported to date. There are only three additional cases described with the location of the neocentromere in band 13q31. This is the first reported case detected prenatally.
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Affiliation(s)
- A Mascarenhas
- Laboratório de Citogenética, Instituto de Biologia Médica e Centro de Neurociências e Biologia Celular, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
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Jardim A, Melo JB, Matoso E, Pires LM, Ramos L, Carreira IM. Two new cases ofde novo small supernumerary marker chromosomes (sSMC) detected at prenatal diagnosis. Prenat Diagn 2007; 27:380-1. [PMID: 17393554 DOI: 10.1002/pd.1650] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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