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Kimura TDC, Scarini JF, Lavareze L, Kowalski LP, Coutinho-Camillo CM, Krepischi ACV, Egal ESA, Altemani A, Mariano FV. MicroRNA copy number alterations in the malignant transformation of pleomorphic adenoma to carcinoma ex pleomorphic adenoma. Head Neck 2024; 46:985-1000. [PMID: 38482546 DOI: 10.1002/hed.27717] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 04/10/2024] Open
Abstract
OBJECTIVE This study used array comparative genomic hybridization to assess copy number alterations (CNAs) involving miRNA genes in pleomorphic adenoma (PA), recurrent pleomorphic adenoma (RPA), residual PA, and carcinoma ex pleomorphic adenoma (CXPA). MATERIALS AND METHODS We analyzed 13 PA, 4 RPA, 29 CXPA, and 14 residual PA using Nexus Copy Number Discovery software. The miRNAs genes affected by CNAs were evaluated based on their expression patterns and subjected to pathway enrichment analysis. RESULTS Across the groups, we found 216 CNAs affecting 2261 miRNA genes, with 117 in PA, 59 in RPA, 846 in residual PA, and 2555 in CXPA. The chromosome 8 showed higher involvement in altered miRNAs in PAs and CXPA patients. Six miRNA genes were shared among all groups. Additionally, miR-21, miR-455-3p, miR-140, miR-320a, miR-383, miR-598, and miR-486 were prominent CNAs found and is implicated in carcinogenesis of several malignant tumors. These miRNAs regulate critical signaling pathways such as aerobic glycolysis, fatty acid biosynthesis, and cancer-related pathways. CONCLUSION This study was the first to explore CNAs in miRNA-encoding genes in the PA-CXPA sequence. The findings suggest the involvement of numerous miRNA genes in CXPA development and progression by regulating oncogenic signaling pathways.
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Affiliation(s)
- Talita de Carvalho Kimura
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas (UNICAMP), Piracicaba, São Paulo, Brazil
- Department of Pathology, School of Medical Sciences, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - João Figueira Scarini
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas (UNICAMP), Piracicaba, São Paulo, Brazil
- Department of Pathology, School of Medical Sciences, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Luccas Lavareze
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas (UNICAMP), Piracicaba, São Paulo, Brazil
- Department of Pathology, School of Medical Sciences, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C. Camargo Cancer Center, São Paulo, Brazil
| | | | | | - Erika Said Abu Egal
- Department of Pathology, School of Medical Sciences, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Biorepository and Molecular Pathology, University of Utah (UU), Salt Lake City, Utah, USA
| | - Albina Altemani
- Department of Pathology, School of Medical Sciences, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Fernanda Viviane Mariano
- Department of Pathology, School of Medical Sciences, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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Aguiar TFM, Rivas MP, de Andrade Silva EM, Pires SF, Dangoni GD, Macedo TC, Defelicibus A, Barros BDDF, Novak E, Cristofani LM, Odone V, Cypriano M, de Toledo SRC, da Cunha IW, da Costa CML, Carraro DM, Tojal I, de Oliveira Mendes TA, Krepischi ACV. First Transcriptome Analysis of Hepatoblastoma in Brazil: Unraveling the Pivotal Role of Noncoding RNAs and Metabolic Pathways. Biochem Genet 2024:10.1007/s10528-024-10764-y. [PMID: 38649558 DOI: 10.1007/s10528-024-10764-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/27/2024] [Indexed: 04/25/2024]
Abstract
Hepatoblastoma stands as the most prevalent liver cancer in the pediatric population. Characterized by a low mutational burden, chromosomal and epigenetic alterations are key drivers of its tumorigenesis. Transcriptome analysis is a powerful tool for unraveling the molecular intricacies of hepatoblastoma, shedding light on the effects of genetic and epigenetic changes on gene expression. In this study conducted in Brazilian patients, an in-depth whole transcriptome analysis was performed on 14 primary hepatoblastomas, compared to control liver tissues. The analysis unveiled 1,492 differentially expressed genes (1,031 upregulated and 461 downregulated), including 920 protein-coding genes (62%). Upregulated biological processes were linked to cell differentiation, signaling, morphogenesis, and development, involving known hepatoblastoma-associated genes (DLK1, MEG3, HDAC2, TET1, HMGA2, DKK1, DKK4), alongside with novel findings (GYNG4, CDH3, and TNFRSF19). Downregulated processes predominantly centered around oxidation and metabolism, affecting amines, nicotinamides, and lipids, featuring novel discoveries like the repression of SYT7, TTC36, THRSP, CCND1, GCK and CAMK2B. Two genes, which displayed a concordant pattern of DNA methylation alteration in their promoter regions and dysregulation in the transcriptome, were further validated by RT-qPCR: the upregulated TNFRSF19, a key gene in the embryonic development, and the repressed THRSP, connected to lipid metabolism. Furthermore, based on protein-protein interaction analysis, we identified genes holding central positions in the network, such as HDAC2, CCND1, GCK, and CAMK2B, among others, that emerged as prime candidates warranting functional validation in future studies. Notably, a significant dysregulation of non-coding RNAs (ncRNAs), predominantly upregulated transcripts, was observed, with 42% of the top 50 highly expressed genes being ncRNAs. An integrative miRNA-mRNA analysis revealed crucial biological processes associated with metabolism, oxidation reactions of lipids and carbohydrates, and methylation-dependent chromatin silencing. In particular, four upregulated miRNAs (miR-186, miR-214, miR-377, and miR-494) played a pivotal role in the network, potentially targeting multiple protein-coding transcripts, including CCND1 and CAMK2B. In summary, our transcriptome analysis highlighted disrupted embryonic development as well as metabolic pathways, particularly those involving lipids, emphasizing the emerging role of ncRNAs as epigenetic regulators in hepatoblastomas. These findings provide insights into the complexity of the hepatoblastoma transcriptome and identify potential targets for future therapeutic interventions.
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Affiliation(s)
- Talita Ferreira Marques Aguiar
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
- Columbia University Irving Medical Center, New York, NY, USA
| | - Maria Prates Rivas
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Edson Mario de Andrade Silva
- Department of Biochemistry and Molecular Biology, Federal University of Viçosa, Minas Gerais, Brazil
- Horticultural Sciences Department, University of Florida, Gainesville, USA
| | - Sara Ferreira Pires
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Gustavo Dib Dangoni
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Taiany Curdulino Macedo
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil
| | | | | | - Estela Novak
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Lilian Maria Cristofani
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Vicente Odone
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Monica Cypriano
- Department of Pediatrics, Adolescent and Child With Cancer Support Group (GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | - Silvia Regina Caminada de Toledo
- Department of Pediatrics, Adolescent and Child With Cancer Support Group (GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | | | | | - Dirce Maria Carraro
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Israel Tojal
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | | | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, São Paulo, Brazil.
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da Costa SS, Fishman V, Pinheiro M, Rodrigueiro A, Sanseverino MT, Zielinsky P, Carvalho CMB, Rosenberg C, Krepischi ACV. A germline chimeric KANK1-DMRT1 transcript derived from a complex structural variant is associated with a congenital heart defect segregating across five generations. Chromosome Res 2024; 32:6. [PMID: 38504027 DOI: 10.1007/s10577-024-09750-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/21/2024]
Abstract
Structural variants (SVs) pose a challenge to detect and interpret, but their study provides novel biological insights and molecular diagnosis underlying rare diseases. The aim of this study was to resolve a 9p24 rearrangement segregating in a family through five generations with a congenital heart defect (congenital pulmonary and aortic valvular stenosis and pulmonary artery stenosis), by applying a combined genomic analysis. The analysis involved multiple techniques, including karyotype, chromosomal microarray analysis (CMA), FISH, genome sequencing (GS), RNA-seq, and optical genome mapping (OGM). A complex 9p24 SV was hinted at by CMA results, showing three interspersed duplicated segments. Combined GS and OGM analyses revealed that the 9p24 duplications constitute a complex SV, on which a set of breakpoints matches the boundaries of the CMA duplicated sequences. The proposed structure for this complex rearrangement implies three duplications associated with an inversion of ~ 2 Mb region on chromosome 9 and a SINE element insertion at the more distal breakpoint. Interestingly, this genomic structure of rearrangement forms a chimeric transcript of the KANK1/DMRT1 loci, which was confirmed by both RNA-seq and Sanger sequencing on blood samples from 9p24 rearrangement carriers. Altogether with breakpoint amplification and FISH analysis, this combined approach allowed a deep characterization of this complex rearrangement. Although the genotype-phenotype correlation remains elusive from the molecular mechanism point of view, this study identified a large genomic rearrangement at 9p24 segregating with a familial congenital heart defect, revealing a genetic biomarker that was successfully applied for embryo selection, changing the reproductive perspective of affected individuals.
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Affiliation(s)
- Silvia Souza da Costa
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Veniamin Fishman
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Mara Pinheiro
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | - Maria Teresa Sanseverino
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- School of Medicine, Pontifícia Universidade Catolica do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Paulo Zielinsky
- Department of Pediatrics and Childcare, Federal University of the Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Carla Rosenberg
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.
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Fellows BJ, Tolezano GC, Pires SF, Ruegg MSG, Knapp KM, Krepischi ACV, Bicknell LS. A novel KNL1 intronic splicing variant likely destabilizes the KMN complex, causing primary microcephaly. Am J Med Genet A 2024; 194:e63468. [PMID: 37937525 DOI: 10.1002/ajmg.a.63468] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023]
Abstract
Primary microcephaly (MCPH) is an autosomal recessive disorder characterized by head circumference of at least two standard deviations below the mean. Biallelic variants in the kinetochore gene KNL1 is a known cause of MCPH4. KNL1 is the central component of the KNL1-MIS12-NSL1 (KMN) network, which acts as the signaling hub of the kinetochore and is required for correct chromosomal segregation during mitosis. We identified biallelic KNL1 variants in two siblings from a non-consanguineous family with microcephaly and intellectual disability. The two siblings carry a frameshift variant predicted to prematurely truncate the transcript and undergo nonsense mediated decay, and an intronic single nucleotide variant (SNV) predicted to disrupt splicing. An in vitro splicing assay and qPCR from blood-derived RNA confirmed that the intronic variant skips exon 23, significantly reducing levels of the canonical transcript. Protein modeling confirmed that absence of exon 23, an inframe exon, would disrupt a key interaction within the KMN network and likely destabilize the kinetochore signaling hub, disrupting mitosis. Therefore, this splicing variant is pathogenic and, in trans with a frameshift variant, causes the MCPH phenotype associated with KLN1. This finding furthers the association of splicing variants as a common pathogenic variant class for KNL1.
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Affiliation(s)
- Bridget J Fellows
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Giovanna Cantini Tolezano
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Sara Ferreira Pires
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Mischa S G Ruegg
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Karen M Knapp
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Louise S Bicknell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Tolezano GC, Bastos GC, da Costa SS, Freire BL, Homma TK, Honjo RS, Yamamoto GL, Passos-Bueno MR, Koiffmann CP, Kim CA, Vianna-Morgante AM, de Lima Jorge AA, Bertola DR, Rosenberg C, Krepischi ACV. Burden of Rare Copy Number Variants in Microcephaly: A Brazilian Cohort of 185 Microcephalic Patients and Review of the Literature. J Autism Dev Disord 2024; 54:1181-1212. [PMID: 36502452 DOI: 10.1007/s10803-022-05853-z] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2022] [Indexed: 12/14/2022]
Abstract
Microcephaly presents heterogeneous genetic etiology linked to several neurodevelopmental disorders (NDD). Copy number variants (CNVs) are a causal mechanism of microcephaly whose investigation is a crucial step for unraveling its molecular basis. Our purpose was to investigate the burden of rare CNVs in microcephalic individuals and to review genes and CNV syndromes associated with microcephaly. We performed chromosomal microarray analysis (CMA) in 185 Brazilian patients with microcephaly and evaluated microcephalic patients carrying < 200 kb CNVs documented in the DECIPHER database. Additionally, we reviewed known genes and CNV syndromes causally linked to microcephaly through the PubMed, OMIM, DECIPHER, and ClinGen databases. Rare clinically relevant CNVs were detected in 39 out of the 185 Brazilian patients investigated by CMA (21%). In 31 among the 60 DECIPHER patients carrying < 200 kb CNVs, at least one known microcephaly gene was observed. Overall, four gene sets implicated in microcephaly were disclosed: known microcephaly genes; genes with supporting evidence of association with microcephaly; known macrocephaly genes; and novel candidates, including OTUD7A, BBC3, CNTN6, and NAA15. In the review, we compiled 957 known microcephaly genes and 58 genomic CNV loci, comprising 13 duplications and 50 deletions, which have already been associated with clinical findings including microcephaly. We reviewed genes and CNV syndromes previously associated with microcephaly, reinforced the high CMA diagnostic yield for this condition, pinpointed novel candidate loci linked to microcephaly deserving further evaluation, and provided a useful resource for future research on the field of neurodevelopment.
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Affiliation(s)
- Giovanna Cantini Tolezano
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Giovanna Civitate Bastos
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Bruna Lucheze Freire
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Thais Kataoka Homma
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Rachel Sayuri Honjo
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Guilherme Lopes Yamamoto
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Maria Rita Passos-Bueno
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Celia Priszkulnik Koiffmann
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Chong Ae Kim
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Angela Maria Vianna-Morgante
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Alexander Augusto de Lima Jorge
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Débora Romeo Bertola
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
- Institute of Biosciences, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
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Rezende RC, Menezes de Andrade NL, Branco Dantas NC, de Polli Cellin L, Victorino Krepischi AC, Lerario AM, de Lima Jorge AA. Exome Sequencing Identifies Multiple Genetic Diagnoses in Children with Syndromic Growth Disorders. J Pediatr 2024; 265:113841. [PMID: 37995928 DOI: 10.1016/j.jpeds.2023.113841] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/25/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
OBJECTIVE To evaluate the presence of multiple genetic diagnoses in syndromic growth disorders. STUDY DESIGN We carried out a cross-sectional study to evaluate 115 patients with syndromic tall (n = 24) or short stature (n = 91) of unknown cause from a tertiary referral center for growth disorders. Exome sequencing was performed to assess germline single nucleotide, InDel, and copy number variants. All variants were classified according to ACMG/AMP guidelines. The main outcome measured was the frequency of multiple genetic diagnoses in a cohort of children with syndromic growth disorders. RESULTS The total diagnostic yield of the cohort was 54.8% (63/115). Six patients had multiple genetic diagnoses (tall stature group = 2; short stature group = 4). The proportion of multiple diagnoses within total cases was 5.2% (6/115), and within solved cases was 9.5% (6/63). No characteristics were significantly more frequent when compared with patients with single or multiple genetic findings. Among patients with multiple diagnoses, 3 had syndromes with overlapping clinical features, and the others had syndromes with distinct phenotypes. CONCLUSION Recognition of multiple genetic diagnoses as a possibility in complex cases of syndromic growth disorders opens a new perspective on treatment and genetic counseling for affected patients, defying the medical common sense of trying to fit all findings into one diagnosis.
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Affiliation(s)
- Raissa Carneiro Rezende
- Laboratorio de Endocrinologia Celular e Molecular LIM25, Unidade de Endocrinologia Genetica/Faculdade de Medicina da Universidade de Sao Paulo (FMUSP)/Hospital das Clinicas da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Nathalia Liberatoscioli Menezes de Andrade
- Laboratorio de Endocrinologia Celular e Molecular LIM25, Unidade de Endocrinologia Genetica/Faculdade de Medicina da Universidade de Sao Paulo (FMUSP)/Hospital das Clinicas da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Naiara Castelo Branco Dantas
- Laboratorio de Endocrinologia Celular e Molecular LIM25, Unidade de Endocrinologia Genetica/Faculdade de Medicina da Universidade de Sao Paulo (FMUSP)/Hospital das Clinicas da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Laurana de Polli Cellin
- Laboratorio de Endocrinologia Celular e Molecular LIM25, Unidade de Endocrinologia Genetica/Faculdade de Medicina da Universidade de Sao Paulo (FMUSP)/Hospital das Clinicas da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | | | - Antonio Marcondes Lerario
- Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Alexander Augusto de Lima Jorge
- Laboratorio de Endocrinologia Celular e Molecular LIM25, Unidade de Endocrinologia Genetica/Faculdade de Medicina da Universidade de Sao Paulo (FMUSP)/Hospital das Clinicas da Universidade de Sao Paulo, Sao Paulo, SP, Brazil.
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Carvalho LML, Jorge AADL, Bertola DR, Krepischi ACV, Rosenberg C. A Comprehensive Review of Syndromic Forms of Obesity: Genetic Etiology, Clinical Features and Molecular Diagnosis. Curr Obes Rep 2024:10.1007/s13679-023-00543-y. [PMID: 38277088 DOI: 10.1007/s13679-023-00543-y] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/08/2023] [Indexed: 01/27/2024]
Abstract
Syndromic obesity refers to obesity occurring with additional clinical findings, such as intellectual disability/developmental delay, dysmorphic features, and congenital malformations. PURPOSE OF REVIEW: To present a narrative review regarding the genetic etiology, clinical description, and molecular diagnosis of syndromic obesity, which is a rare condition with high phenotypic variability and genetic heterogeneity. The following syndromes are presented in this review: Prader-Willi, Bardet-Biedl, Pseudohypoparathyroidism, Alström, Smith-Magenis, Cohen, Temple, 1p36 deletion, 16p11.2 microdeletion, Kleefstra, SIM1-related, Börjeson-Forssman-Lehmann, WAGRO, Carpenter, MORM, and MYT1L-related syndromes. RECENT FINDINGS: There are three main groups of mechanisms for syndromic obesity: imprinting, transcriptional activity regulation, and cellular cilia function. For molecular diagnostic, methods of genome-wide investigation should be prioritized over sequencing of panels of syndromic obesity genes. In addition, we present novel syndromic conditions that need further delineation, but evidences suggest they have a higher frequency of obesity. The etiology of syndromic obesity tends to be linked to disrupted neurodevelopment (central) and is associated with a diversity of genes and biological pathways. In the genetic investigation of individuals with syndromic obesity, the possibility that the etiology of the syndromic condition is independent of obesity should be considered. The accurate genetic diagnosis impacts medical management, treatment, and prognosis, and allows proper genetic counseling.
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Affiliation(s)
- Laura Machado Lara Carvalho
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
| | - Alexander Augusto de Lima Jorge
- Genetic Endocrinology Unit, Cellular and Molecular Endocrinology Laboratory (LIM/25), Faculty of Medicine, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Débora Romeo Bertola
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
- Genetics Unit of Instituto da Criança, Faculty of Medicine, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
| | - Carla Rosenberg
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil.
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8
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Tolezano GC, Bastos GC, da Costa SS, Scliar MDO, de Souza CFM, Van Der Linden H, Fernandes WLM, Otto PA, Vianna-Morgante AM, Haddad LA, Honjo RS, Yamamoto GL, Kim CA, Rosenberg C, Jorge AADL, Bertola DR, Krepischi ACV. Clinical Characterization and Underlying Genetic Findings in Brazilian Patients with Syndromic Microcephaly Associated with Neurodevelopmental Disorders. Mol Neurobiol 2024:10.1007/s12035-023-03894-8. [PMID: 38180615 DOI: 10.1007/s12035-023-03894-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024]
Abstract
Microcephaly is characterized by an occipitofrontal circumference at least two standard deviations below the mean for age and sex. Neurodevelopmental disorders (NDD) are commonly associated with microcephaly, due to perturbations in brain development and functioning. Given the extensive genetic heterogeneity of microcephaly, managing patients is hindered by the broad spectrum of diagnostic possibilities that exist before conducting molecular testing. We investigated the genetic basis of syndromic microcephaly accompanied by NDD in a Brazilian cohort of 45 individuals and characterized associated clinical features, as well as evaluated the effectiveness of whole-exome sequencing (WES) as a diagnostic tool for this condition. Patients previously negative for pathogenic copy number variants underwent WES, which was performed using a trio approach for isolated index cases (n = 31), only the index in isolated cases with parental consanguinity (n = 8) or affected siblings in familial cases (n = 3). Pathogenic/likely pathogenic variants were identified in 19 families (18 genes) with a diagnostic yield of approximately 45%. Nearly 86% of the individuals had global developmental delay/intellectual disability and 51% presented with behavioral disturbances. Additional frequent clinical features included facial dysmorphisms (80%), brain malformations (67%), musculoskeletal (71%) or cardiovascular (47%) defects, and short stature (54%). Our findings unraveled the underlying genetic basis of microcephaly in half of the patients, demonstrating a high diagnostic yield of WES for microcephaly and reinforcing its genetic heterogeneity. We expanded the phenotypic spectrum associated with the condition and identified a potentially novel gene (CCDC17) for congenital microcephaly.
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Affiliation(s)
- Giovanna Cantini Tolezano
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Giovanna Civitate Bastos
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Marília de Oliveira Scliar
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Carolina Fischinger Moura de Souza
- Postgraduate Program in Child and Adolescent Health, Universidade Federal do Rio Grande do Sul, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | | | | | - Paulo Alberto Otto
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Angela M Vianna-Morgante
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Luciana Amaral Haddad
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Rachel Sayuri Honjo
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Guilherme Lopes Yamamoto
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Chong Ae Kim
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Alexander Augusto de Lima Jorge
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Débora Romeo Bertola
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Human Genome and Stem-Cell Research Center, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
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Costa SS, Fishman V, Pinheiro M, Rodrigueiro A, Sanseverino MT, Zielinsky P, Carvalho CMB, Rosenberg C, Krepischi ACV. A germline chimeric KANK1-DMRT1 transcript derived from a complex structural variant is associated with a congenital heart defect segregating across five generations. Res Sq 2023:rs.3.rs-3740005. [PMID: 38168413 PMCID: PMC10760254 DOI: 10.21203/rs.3.rs-3740005/v1] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Structural variants (SVs) pose a challenge to detect and interpret, but their study provides novel biological insights and molecular diagnosis underlying rare diseases. The aim of this study was to resolve a 9p24 rearrangement segregating in a family through five generations with a congenital heart defect (congenital pulmonary and aortic valvular stenosis, and pulmonary artery stenosis), by applying a combined genomic analysis. The analysis involved multiple techniques, including karyotype, chromosomal microarray analysis (CMA), FISH, whole-genome sequencing (WGS), RNA-seq and optical genome mapping (OGM). A complex 9p24 SV was hinted at by CMA results, showing three interspersed duplicated segments. Combined WGS and OGM analyses revealed that the 9p24 duplications constitute a complex SV, on which a set of breakpoints match the boundaries of the CMA duplicated sequences. The proposed structure for this complex rearrangement implies three duplications associated with an inversion of ~ 2Mb region on chromosome 9 with a SINE element insertion at the more distal breakpoint. Interestingly, this hypothesized genomic structure of rearrangement forms a chimeric transcript of the KANK1/DMRT1 loci, which was confirmed by RNA-seq on blood from 9p24 rearrangement carriers. Altogether with breakpoint amplification and FISH analysis, this combined approach allowed a deep characterization of this complex rearrangement. Although the genotype-phenotype correlation remains elusive from the molecular mechanism point of view, this study identified a large genomic rearrangement at 9p segregating with a familial congenital clinical trait, revealing a genetic biomarker that was successfully applied for embryo selection, changing the reproductive perspective of affected individuals.
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Pires SF, Barros JSD, Costa SSD, Carmo GBD, Scliar MDO, Lengert AVH, Boldrini É, Silva SRMD, Vidal DO, Maschietto M, Krepischi ACV. Analysis of the Mutational Landscape of Osteosarcomas Identifies Genes Related to Metastasis and Prognosis and Disrupted Biological Pathways of Immune Response and Bone Development. Int J Mol Sci 2023; 24:10463. [PMID: 37445641 DOI: 10.3390/ijms241310463] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 07/15/2023] Open
Abstract
Osteosarcoma (OS) is the most prevalent type of bone tumor, but slow progress has been achieved in disentangling the full set of genomic events involved in its initiation and progression. We assessed by NGS the mutational spectrum of 28 primary OSs from Brazilian patients, and identified 445 potentially deleterious SNVs/indels and 1176 copy number alterations (CNAs). TP53 was the most recurrently mutated gene, with an overall rate of ~60%, considering SNVs/indels and CNAs. The most frequent CNAs (~60%) were gains at 1q21.2q21.3, 6p21.1, and 8q13.3q24.22, and losses at 10q26 and 13q14.3q21.1. Seven cases presented CNA patterns reminiscent of complex events (chromothripsis and chromoanasynthesis). Putative RB1 and TP53 germline variants were found in five samples associated with metastasis at diagnosis along with complex genomic patterns of CNAs. PTPRQ, KNL1, ZFHX4, and DMD alterations were prevalent in metastatic or deceased patients, being potentially indicative of poor prognosis. TNFRSF11B, involved in skeletal system development and maintenance, emerged as a candidate for osteosarcomagenesis due to its biological function and a high frequency of copy number gains. A protein-protein network enrichment highlighted biological pathways involved in immunity and bone development. Our findings reinforced the high genomic OS instability and heterogeneity, and led to the identification of novel disrupted genes deserving further evaluation as biomarkers due to their association with poor outcomes.
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Affiliation(s)
- Sara Ferreira Pires
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
| | - Juliana Sobral de Barros
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
| | - Silvia Souza da Costa
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
| | - Gabriel Bandeira do Carmo
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
| | - Marília de Oliveira Scliar
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
| | | | - Érica Boldrini
- Barretos Children's Cancer Hospital, Barretos 14784-400, Brazil
| | | | - Daniel Onofre Vidal
- Molecular Oncology Research Center (CPOM), Barretos Cancer Hospital, Barretos 14784-384, Brazil
| | - Mariana Maschietto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-884, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem-Cell Research Center, Institute of Biosciences, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo 05508-090, Brazil
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Machado Lara Carvalho L, Varella Branco E, Delgado Sarafian R, Shigeru Kobayashi G, Tófoli de Araújo F, Santos Souza L, de Paula Moreira D, Shih Ping Hsia G, Maria Goloni Bertollo E, Barbosa Buck C, Souza da Costa S, Mendes Fialho D, Tadeu Galante Rocha de Vasconcelos F, Abreu Brito L, Elena de Souza Fraga Machado L, Cabreira Ramos I, da Veiga Pereira L, Priszkulnik Koiffmann C, Rita Dos Santos E Passos-Bueno M, Antonio de Oliveira Mendes T, Cristina Victorino Krepischi A, Rosenberg C. Establishment of iPSC lines and zebrafish with loss-of-function AHDC1 variants: models for Xia-Gibbs syndrome. Gene 2023; 871:147424. [PMID: 37054903 DOI: 10.1016/j.gene.2023.147424] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/12/2023] [Accepted: 04/06/2023] [Indexed: 04/15/2023]
Abstract
Xia-Gibbs syndrome (XGS) is a syndromic form of intellectual disability caused by heterozygous AHDC1 variants, but the pathophysiological mechanisms underlying this syndrome are still unclear. In this manuscript, we describe the development of two different functional models: three induced pluripotent stem cell (iPSC) lines with different loss-of-function (LoF) AHDC1 variants, derived by reprogramming peripheral blood mononuclear cells from XGS patients, and a zebrafish strain with a LoF variant in the ortholog gene (ahdc1) obtained through CRISPR/Cas9-mediated editing. The three iPSC lines showed expression of pluripotency factors (SOX2, SSEA-4, OCT3/4, and NANOG). To verify the capacity of iPSC to differentiate into the three germ layers, we obtained embryoid bodies (EBs), induced their differentiation, and confirmed the mRNA expression of ectodermal, mesodermal, and endodermal markers using the TaqMan hPSC Scorecard. The iPSC lines were also approved for the following quality tests: chromosomal microarray analysis (CMA), mycoplasma testing, and short tandem repeat (STR) DNA profiling. The zebrafish model has an insertion of four base pairs in the ahdc1 gene, is fertile, and breeding between heterozygous and wild-type (WT) animals generated offspring in a genotypic proportion in agreement with Mendelian law. The established iPSC and zebrafish lines were deposited on the hpscreg.eu and zfin.org platforms, respectively. These biological models are the first for XGS and will be used in future studies that investigate the pathophysiology of this syndrome, unraveling its underlying molecular mechanisms.
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Affiliation(s)
- Laura Machado Lara Carvalho
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Elisa Varella Branco
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Raquel Delgado Sarafian
- National Embryonic Stem Cell Laboratory Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Gerson Shigeru Kobayashi
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Fabiano Tófoli de Araújo
- National Embryonic Stem Cell Laboratory Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Lucas Santos Souza
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Danielle de Paula Moreira
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Gabriella Shih Ping Hsia
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | | | | | - Silvia Souza da Costa
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Davi Mendes Fialho
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | | | - Luciano Abreu Brito
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | | | - Igor Cabreira Ramos
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Lygia da Veiga Pereira
- National Embryonic Stem Cell Laboratory Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Celia Priszkulnik Koiffmann
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | | | | | | | - Carla Rosenberg
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil.
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12
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Pires SF, de Barros JS, da Costa SS, de Oliveira Scliar M, Van Helvoort Lengert A, Boldrini É, da Silva SRM, Tasic L, Vidal DO, Krepischi ACV, Maschietto M. DNA methylation patterns suggest the involvement of DNMT3B and TET1 in osteosarcoma development. Mol Genet Genomics 2023; 298:721-733. [PMID: 37020053 DOI: 10.1007/s00438-023-02010-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/24/2023] [Indexed: 04/07/2023]
Abstract
DNA methylation may be involved in the development of osteosarcomas. Osteosarcomas commonly arise during the bone growth and remodeling in puberty, making it plausible to infer the involvement of epigenetic alterations in their development. As a highly studied epigenetic mechanism, we investigated DNA methylation and related genetic variants in 28 primary osteosarcomas aiming to identify deregulated driver alterations. Methylation and genomic data were obtained using the Illumina HM450K beadchips and the TruSight One sequencing panel, respectively. Aberrant DNA methylation was spread throughout the osteosarcomas genomes. We identified 3146 differentially methylated CpGs comparing osteosarcomas and bone tissue samples, with high methylation heterogeneity, global hypomethylation and focal hypermethylation at CpG islands. Differentially methylated regions (DMR) were detected in 585 loci (319 hypomethylated and 266 hypermethylated), mapped to the promoter regions of 350 genes. These DMR genes were enriched for biological processes related to skeletal system morphogenesis, proliferation, inflammatory response, and signal transduction. Both methylation and expression data were validated in independent groups of cases. Six tumor suppressor genes harbored deletions or promoter hypermethylation (DLEC1, GJB2, HIC1, MIR149, PAX6, and WNT5A), and four oncogenes presented gains or hypomethylation (ASPSCR1, NOTCH4, PRDM16, and RUNX3). Our analysis also revealed hypomethylation at 6p22, a region that contains several histone genes. Copy-number changes in DNMT3B (gain) and TET1 (loss), as well as overexpression of DNMT3B in osteosarcomas provide a possible explanation for the observed phenotype of CpG island hypermethylation. While the detected open-sea hypomethylation likely contributes to the well-known osteosarcoma genomic instability, enriched CpG island hypermethylation suggests an underlying mechanism possibly driven by overexpression of DNMT3B likely resulting in silencing of tumor suppressors and DNA repair genes.
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Affiliation(s)
- Sara Ferreira Pires
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Juliana Sobral de Barros
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Marília de Oliveira Scliar
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | | | | | - Ljubica Tasic
- Laboratory of Biological Chemistry, Institute of Chemistry, University of Campinas, Campinas, Brazil
| | - Daniel Onofre Vidal
- Molecular Oncology Research Center (CPOM), Barretos Cancer Hospital, Barretos, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Mariana Maschietto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.
- Research Center, Boldrini Children's Hospital, Campinas, SP, Brazil.
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Dangoni GD, Teixeira ACB, Aguiar TF, Sugayama SMM, Filho VO, Bertola DR, Krepischi ACV. A rare case of hepatoblastoma in a syndromic child with a de novo germline JAG1 mutation. Pediatr Blood Cancer 2023; 70:e30311. [PMID: 36965188 DOI: 10.1002/pbc.30311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/27/2023]
Affiliation(s)
- Gustavo Dib Dangoni
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Anne Caroline Barbosa Teixeira
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
- Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Talita Ferreira Aguiar
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, New York, USA
| | - Sofia Mizuho Miura Sugayama
- Faculty of Medicine, Department of Pediatrics, Instituto de Tratamento do Câncer Infantil (ITACI), University of São Paulo, São Paulo, SP, Brazil
| | - Vicente Odone Filho
- Faculty of Medicine, Department of Pediatrics, Instituto de Tratamento do Câncer Infantil (ITACI), University of São Paulo, São Paulo, SP, Brazil
| | - Débora Romeo Bertola
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
- Genetics Unit, Instituto da Criança, Hospital das Clinicas Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
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Schnöll C, Krepischi ACV, Renck AC, Lima Amato LG, Kulikowski LD, Dantas NCB, Costa EMF, Mendonça BB, Latronico AC, Jorge AADL, Gontijo Silveira LF. SIN3A defects associated with syndromic congenital hypogonadotropic hypogonadism: an overlap with Witteveen-Kolk syndrome. Neuroendocrinology 2023:000529615. [PMID: 36758531 DOI: 10.1159/000529615] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
INTRODUCTION Congenital hypogonadotropic hypogonadism (CHH) is a rare condition caused by GnRH deficiency. More than 40 genes have been associated with the pathogenesis of CHH, but most cases still remain without a molecular diagnosis. Mutations involving the same gene (e.g. FGFR1, PROK2/PROKR2, CHD7) were found to cause normosmic CHH and Kallmann syndrome, with and without associated phenotypes, illustrating the coexistence of CHH with signs of other complex syndromes. The Witteveen-Kolk syndrome (WITKOS), caused by defects of the SIN3A gene, is a heterogeneous disorder characterized by distinctive facial features, microcephaly, short stature, delayed cognitive and motor development. Although micropenis and cryptorchidism have been reported in this syndrome, WITKOS has not been formally associated with CHH so far. PATIENTS AND METHODS A man with Kallmann syndrome (KS) associated with mild syndromic features (S1) and a boy with global developmental delay, syndromic short stature, micropenis and cryptorchidism (S2), in whom common genetic defects associated with CHH and short stature had been previously excluded, were studied by either chromosomal microarray analysis (CMA) or whole exome sequencing (WES). RESULTS Rare SIN3A pathogenic variants were identified in these two unrelated patients with CHH phenotypic features. A 550 kb deletion at 15q24.1, including the whole SIN3A gene, was identified in S1, and a SIN3A nonsense rare variant (p.Arg471*) was detected in S2. CONCLUSION These findings lead us to propose a link between SIN3A defects and CHH, especially in syndromic cases, based on these two patients with overlapping phenotypes of WITKOS and CHH.
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Carvalho LML, Pinto CF, de Oliveira Scliar M, Otto PA, Krepischi ACV, Rosenberg C. SCAF4-related syndromic intellectual disability. Am J Med Genet A 2023; 191:570-574. [PMID: 36333968 DOI: 10.1002/ajmg.a.63032] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/13/2022] [Accepted: 10/13/2022] [Indexed: 11/07/2022]
Abstract
The causal link between variants in the SCAF4 gene and a syndromic form of intellectual disability (ID) was established in 2020 by Fliedner et al. Since then, no additional cases have been reported. We performed exome sequencing in a 16-year-old Brazilian male presenting with ID, epilepsy, behavioral problems, speech impairment, facial dysmorphisms, heart malformations, and obesity. A de novo pathogenic variant [SCAF4(NM_020706.2):c.374_375dup(p.Glu126LeufsTer20)] was identified. This is the second study reporting the involvement of SCAF4 in syndromic ID, and the description of the patient's clinical features contributes to defining the phenotypic spectrum of this recently described Mendelian disorder.
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Affiliation(s)
- Laura Machado Lara Carvalho
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo (USP), Sao Paulo, Sao Paulo, Brazil
| | - Carla Franchi Pinto
- Department of Pathological Sciences, Faculty of Medical Sciences of Santa Casa de São Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Marília de Oliveira Scliar
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo (USP), Sao Paulo, Sao Paulo, Brazil
| | - Paulo A Otto
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo (USP), Sao Paulo, Sao Paulo, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo (USP), Sao Paulo, Sao Paulo, Brazil
| | - Carla Rosenberg
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo (USP), Sao Paulo, Sao Paulo, Brazil
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Machado RA, de Andrade RS, Pêgo SPB, Krepischi ACV, Coletta RD, Martelli-Júnior H. New evidence of genetic heterogeneity causing hereditary gingival fibromatosis and ALK and CD36 as new candidate genes. J Periodontol 2023; 94:108-118. [PMID: 35665929 DOI: 10.1002/jper.22-0219] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 04/04/2022] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 02/02/2023]
Abstract
BACKGROUND Hereditary gingival fibromatosis (HGF) is an uncommon genetic condition characterized by slow but progressive fibrous, non-hemorrhagic, and painless growth of the gingival tissues due to the increased deposition of collagen and other macromolecules of the extracellular matrix. HGF occurs in approximately 1:750,000 individuals and can exhibit dominant or recessive inheritance. To date, five loci (2p21-p22, 2p22.3-p23.3, 4q12, 5q13-q22, and 11p15) and three genes [REST (RE1-silencing transcription factor), SOS1 (Son-of-Sevenless-1), and ZNF862 (zinc finger protein 862 gene)] have been associated with HGF. Here, our study aimed to identify genetic variants associated with HGF by applying whole-exome sequencing (WES) and bioinformatics analyses. METHODS Thirteen Brazilian individuals with HGF and nine relatives without HGF from four unrelated families were chosen for our investigation. Blood collected from the patients and their relatives were used for WES. Five Web-available tools, namely, CADD, PolyPhen, SIFT, Mutation Taster, and Franklin's algorithms, were used to predict protein damage. RESULTS WES revealed pathogenic variants affecting the known HGF genes REST (c.1491_1492delAG) and SOS1 (c.3265_3266insTAAC) in two families. Additionally, potentially pathogenic variants segregating in the other two families were mapped to ALK receptor tyrosine kinase gene (ALK) (c.361C > T) and to collagen type I receptor and thrombospondin receptor gene (CD36) (c.1133G > T). CONCLUSION Our findings reinforce the high genetic heterogeneity of HGF, identifying new variants in HGF known genes (REST and SOS1) and ALK and CD36 as new genes that cause HGF.
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Affiliation(s)
- Renato Assis Machado
- Department of Oral Diagnosis, School of Dentistry, University of Campinas (FOP/UNICAMP), Piracicaba, São Paulo, Brazil.,Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Rodrigo Soares de Andrade
- Department of Oral Diagnosis, School of Dentistry, University of Campinas (FOP/UNICAMP), Piracicaba, São Paulo, Brazil
| | - Sabina Pena Borges Pêgo
- Stomatology Clinic, Dental School, State University of Montes Claros (Unimontes), Montes Claros, Minas Gerais, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo (IB/USP), São Paulo, Brazil
| | - Ricardo D Coletta
- Department of Oral Diagnosis, School of Dentistry, University of Campinas (FOP/UNICAMP), Piracicaba, São Paulo, Brazil.,Graduate Program in Oral Biology, School of Dentistry, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Hercílio Martelli-Júnior
- Stomatology Clinic, Dental School, State University of Montes Claros (Unimontes), Montes Claros, Minas Gerais, Brazil.,Center for Rehabilitation of Craniofacial Anomalies, Dental School, University of José Rosario Vellano (Unifenas), Alfenas, Minas Gerais, Brazil
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17
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Bastos GC, Tolezano GC, Krepischi ACV. Rare CNVs and Known Genes Linked to Macrocephaly: Review of Genomic Loci and Promising Candidate Genes. Genes (Basel) 2022; 13:genes13122285. [PMID: 36553552 PMCID: PMC9778424 DOI: 10.3390/genes13122285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Macrocephaly frequently occurs in single-gene disorders affecting the PI3K-AKT-MTOR pathway; however, epigenetic mutations, mosaicism, and copy number variations (CNVs) are emerging relevant causative factors, revealing a higher genetic heterogeneity than previously expected. The aim of this study was to investigate the role of rare CNVs in patients with macrocephaly and review genomic loci and known genes. We retrieved from the DECIPHER database de novo <500 kb CNVs reported on patients with macrocephaly; in four cases, a candidate gene for macrocephaly could be pinpointed: a known microcephaly gene-TRAPPC9, and three genes based on their functional roles-RALGAPB, RBMS3, and ZDHHC14. From the literature review, 28 pathogenic CNV genomic loci and over 300 known genes linked to macrocephaly were gathered. Among the genomic regions, 17 CNV loci (~61%) exhibited mirror phenotypes, that is, deletions and duplications having opposite effects on head size. Identifying structural variants affecting head size can be a preeminent source of information about pathways underlying brain development. In this study, we reviewed these genes and recurrent CNV loci associated with macrocephaly, as well as suggested novel potential candidate genes deserving further studies to endorse their involvement with this phenotype.
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18
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Freire BL, Homma TK, Lerario AM, Seo GH, Han H, de Assis Funari MF, Gomes NL, Rosemberg C, Krepischi ACV, de Andrade Vasques G, Malaquias AC, de Lima Jorge AA. High frequency of genetic/epigenetic disorders in short stature children born with very low birth weight. Am J Med Genet A 2022; 188:2599-2604. [PMID: 35792504 DOI: 10.1002/ajmg.a.62892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 02/04/2022] [Revised: 04/27/2022] [Accepted: 06/21/2022] [Indexed: 01/24/2023]
Abstract
Most infants born with very low birth weight (VLBW, birth weight < 1500 g) show spontaneous catch-up growth in postnatal life. The reasons for the absence of catch-up growth are not entirely understood. We performed a comprehensive investigation of 52 children born with VLBW. Ten children had a history of an external cause that explained the VLBW and five refused genetic evaluation. Twenty-three cases were initially evaluated by a candidate gene approach. Patients with a negative result in the candidate gene approach (n = 14) or without clinical suspicion (n = 14) were assessed by chromosome microarray analysis (CMA) and/or whole-exome sequencing (WES). A genetic condition was identified in 19 of 37 (51.4%) patients without an external cause, nine by candidate gene approach, and 10 by a genomic approach (CMA/WES). Silver-Russell syndrome was the most frequent diagnosis (n = 5) and the remaining patients were diagnosed with other rare monogenic conditions. Almost all patients with a positive genetic diagnosis exhibited syndromic features (94.4%). However, microcephaly, neurodevelopmental disorders, major malformation, or facial dysmorphism were also frequently observed in children with an external cause. In conclusion, a significant proportion of children born with VLBW with persistent short stature have a genetic/epigenetic condition.
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Affiliation(s)
- Bruna Lucheze Freire
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil.,Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil
| | - Thais Kataoka Homma
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil.,Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil
| | - Antônio Marcondes Lerario
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan, USA
| | - Go Hun Seo
- Division of Medical Genetics, 3billion Inc., Seoul, South Korea
| | - Heonjong Han
- Division of Medical Genetics, 3billion Inc., Seoul, South Korea
| | - Mariana Ferreira de Assis Funari
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil.,Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil
| | - Nathalia Lisboa Gomes
- Unidade de Endocrinologia, Santa Casa de Belo Horizonte, Belo Horizonte, Minas Gerais, Brazil
| | - Carla Rosemberg
- Department of Genetics & Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Consolacao, Brazil
| | | | - Gabriela de Andrade Vasques
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil.,Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil
| | - Alexsandra Christianne Malaquias
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil.,Unidade de Endocrinologia Pediátrica, Departamento de Pediatria, Irmandade da Santa Casa de Misericórdia de São Paulo, Faculdade de Ciências Médicas da Santa Casa de São Paulo, São Paulo, Consolacao, Brazil
| | - Alexander Augusto de Lima Jorge
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil.,Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Consolacao, Brazil
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19
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Fidalgo F, Torrezan GT, de Sá BCS, Barros BDDF, Moredo LF, Valieris R, de Souza SJ, Duprat JP, Krepischi ACV, Carraro DM. Family-based whole-exome sequencing identifies rare variants potentially related to cutaneous melanoma predisposition in Brazilian melanoma-prone families. PLoS One 2022; 17:e0262419. [PMID: 35085295 PMCID: PMC8794197 DOI: 10.1371/journal.pone.0262419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 12/25/2021] [Indexed: 11/19/2022] Open
Abstract
Genetic predisposition accounts for nearly 10% of all melanoma cases and has been associated with a dozen moderate- to high-penetrance genes, including CDKN2A, CDK4, POT1 and BAP1. However, in most melanoma-prone families, the genetic etiology of cancer predisposition remains undetermined. The goal of this study was to identify rare genomic variants associated with cutaneous melanoma susceptibility in melanoma-prone families. Whole-exome sequencing was performed in 2 affected individuals of 5 melanoma-prone families negative for mutations in CDKN2A and CDK4, the major cutaneous melanoma risk genes. A total of 288 rare coding variants shared by the affected relatives of each family were identified, including 7 loss-of-function variants. By performing in silico analyses of gene function, biological pathways, and variant pathogenicity prediction, we underscored the putative role of several genes for melanoma risk, including previously described genes such as MYO7A and WRN, as well as new putative candidates, such as SERPINB4, HRNR, and NOP10. In conclusion, our data revealed rare germline variants in melanoma-prone families contributing with a novel set of potential candidate genes to be further investigated in future studies.
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Affiliation(s)
- Felipe Fidalgo
- Genomics and Molecular Biology Group, International Research Center/CIPE, A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Giovana Tardin Torrezan
- Genomics and Molecular Biology Group, International Research Center/CIPE, A.C.Camargo Cancer Center, São Paulo, Brazil
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation (INCITO), São Paulo, Brazil
| | | | | | | | - Renan Valieris
- Laboratory of Bioinformatics and Computational Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Sandro J. de Souza
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation (INCITO), São Paulo, Brazil
- Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil
- Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | | | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Dirce Maria Carraro
- Genomics and Molecular Biology Group, International Research Center/CIPE, A.C.Camargo Cancer Center, São Paulo, Brazil
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation (INCITO), São Paulo, Brazil
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20
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Barros JS, Aguiar TFM, Costa SS, Rivas MP, Cypriano M, Toledo SRC, Novak EM, Odone V, Cristofani LM, Carraro DM, Werneck da Cunha I, Costa CML, Vianna-Morgante AM, Rosenberg C, Krepischi ACV. Copy Number Alterations in Hepatoblastoma: Literature Review and a Brazilian Cohort Analysis Highlight New Biological Pathways. Front Oncol 2021; 11:741526. [PMID: 34956867 PMCID: PMC8692715 DOI: 10.3389/fonc.2021.741526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/10/2021] [Indexed: 12/19/2022] Open
Abstract
Hepatoblastoma (HB) is a rare embryonal tumor, although it is the most common pediatric liver cancer. The aim of this study was to provide an accurate cytogenomic profile of this type of cancer, for which information in cancer databases is lacking. We performed an extensive literature review of cytogenetic studies on HBs disclosing that the most frequent copy number alterations (CNAs) are gains of 1q, 2/2q, 8/8q, and 20; and losses at 1p and 4q. Furthermore, the CNA profile of a Brazilian cohort of 26 HBs was obtained by array-CGH; the most recurrent CNAs were the same as shown in the literature review. Importantly, HBs from female patients, high-risk stratification tumors, tumors who developed in older patients (> 3 years at diagnosis) or from patients with metastasis and/or deceased carried a higher diversity of chromosomal alterations, specifically chromosomal losses at 1p, 4, 11q and 18q. In addition, we distinguished three major CNA profiles: no detectable CNA, few CNAs and tumors with complex genomes. Tumors with simpler genomes exhibited a significant association with the epithelial fetal subtype of HBs; in contrast, the complex genome group included three cases with epithelial embryonal histology, as well as the only HB with HCC features. A significant association of complex HB genomes was observed with older patients who developed high-risk tumors, metastasis, and deceased. Moreover, two patients with HBs exhibiting complex genomes were born with congenital anomalies. Together, these findings suggest that a high load of CNAs, mainly chromosomal losses, particularly losses at 1p and 18, increases the tendency to HB aggressiveness. Additionally, we identified six hot-spot chromosome regions most frequently affected in the entire group: 1q31.3q42.3, 2q23.3q37.3, and 20p13p11.1 gains, besides a 5,3 Mb amplification at 2q24.2q24.3, and losses at 1p36.33p35.1, 4p14 and 4q21.22q25. An in-silico analysis using the genes mapped to these six regions revealed several enriched biological pathways such as ERK Signaling, MicroRNAs in Cancer, and the PI3K-Akt Signaling, in addition to the WNT Signaling pathway; further investigation is required to evaluate if disturbances of these pathways can contribute to HB tumorigenesis. The analyzed gene set was found to be associated with neoplasms, abnormalities of metabolism/homeostasis and liver morphology, as well as abnormal embryonic development and cytokine secretion. In conclusion, we have provided a comprehensive characterization of the spectrum of chromosomal alterations reported in HBs and identified specific genomic regions recurrently altered in a Brazilian HB group, pointing to new biological pathways, and relevant clinical associations.
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Affiliation(s)
- Juliana Sobral Barros
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Talita Ferreira Marques Aguiar
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.,Department of Urology, New York University (NYU) Grossman School of Medicine, New York, NY, United States
| | - Silvia Souza Costa
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Maria Prates Rivas
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Monica Cypriano
- Department of Pediatrics, Institute of Pediatric Oncology, Support Group for Children and Adolescents with Cancer (IOP-GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | - Silvia Regina Caminada Toledo
- Department of Pediatrics, Institute of Pediatric Oncology, Support Group for Children and Adolescents with Cancer (IOP-GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | - Estela Maria Novak
- Department of Pediatrics, Institute of Childhood Cancer Treatment (ITACI), Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Vicente Odone
- Department of Pediatrics, Institute of Childhood Cancer Treatment (ITACI), Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Lilian Maria Cristofani
- Department of Pediatrics, Institute of Childhood Cancer Treatment (ITACI), Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Dirce Maria Carraro
- International Research Center, AC Camargo Cancer Center (ACCCC), São Paulo, Brazil
| | | | | | - Angela M Vianna-Morgante
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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21
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Carvalho LML, da Costa SS, Campagnari F, Kaufman A, Bertola DR, da Silva IT, Krepischi ACV, Koiffmann CP, Rosenberg C. Two novel pathogenic variants in MED13L: one familial and one isolated case. J Intellect Disabil Res 2021; 65:1049-1057. [PMID: 34713510 DOI: 10.1111/jir.12891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 08/12/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Genetic variants involving the MED13L gene can lead to an autosomal dominant syndrome characterised by intellectual disability/developmental delay and facial dysmorphism. METHODS We investigated two cases (one familial and one isolated) of intellectual disability with speech delay and dysmorphic facial features by whole-exome sequencing analyses. Further, we performed a literature review about clinical and molecular aspects of MED13L gene and syndrome. RESULTS Two MED13L variants have been identified [MED13L(NM_015335.5):c.4417C>T and MED13L(NM_015335.5):c.2318delC] and were classified as pathogenic according to the ACMG (American College of Medical Genetics and Genomics) guidelines. One of the variants was present in sibs. CONCLUSIONS The two pathogenic variants identified have not been previously reported. Importantly, this is the first report of a familial case of MED13L nonsense mutation. Although the parents of the affected children were no longer available for analysis, their apparently normal phenotypes were surmised from familial verbal descriptions corresponding to normal mental behaviour and phenotype. In this situation, the familial component of mutation transmission might be caused by gonadal mosaicism of a MED13L mutation in a gonad from either the father or the mother. The case reports and the literature review presented in this manuscript can be useful for genetic counselling.
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Affiliation(s)
- L M L Carvalho
- Human Genome and Stem Cell Research Centre, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - S S da Costa
- Human Genome and Stem Cell Research Centre, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | | | - A Kaufman
- Department of Psychiatry, Faculty of Medicine, University of São Paulo (USP), São Paulo, SP, Brazil
| | - D R Bertola
- Human Genome and Stem Cell Research Centre, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - I T da Silva
- International Centre for Research, A. C. Camargo Cancer Centre, São Paulo, SP, Brazil
| | - A C V Krepischi
- Human Genome and Stem Cell Research Centre, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - C P Koiffmann
- Human Genome and Stem Cell Research Centre, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - C Rosenberg
- Human Genome and Stem Cell Research Centre, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (USP), São Paulo, SP, Brazil
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22
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Abdala BB, Gonçalves AP, Dos Santos JM, Boy R, de Carvalho CMB, Grochowski CM, Krepischi ACV, Rosenberg C, Gusmão L, Pehlivan D, Pimentel MMG, Santos-Rebouças CB. Molecular and clinical insights into complex genomic rearrangements related to MECP2 duplication syndrome. Eur J Med Genet 2021; 64:104367. [PMID: 34678473 DOI: 10.1016/j.ejmg.2021.104367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 03/11/2021] [Revised: 10/04/2021] [Accepted: 10/16/2021] [Indexed: 10/20/2022]
Abstract
MECP2 duplication syndrome (MDS) is caused by copy number variation (CNV) spanning the MECP2 gene at Xq28 and is a major cause of intellectual disability (ID) in males. Herein, we describe two unrelated males harboring non-recurrent complex Xq28 rearrangements associated with MDS. Copy number gains were initially detected by quantitative real-time polymerase chain reaction and further delineated by high-resolution array comparative genomic hybridization, familial segregation, expression analysis and X-chromosome inactivation (XCI) evaluation in a carrier mother. SNVs within the rearrangements and/or fluorescent in situ hybridization (FISH) were used to assess the parental origin of the rearrangements. Patient 1 exhibited an intrachromosomal rearrangement, whose structure is consistent with a triplicated segment presumably embedded in an inverted orientation between two duplicated sequences (DUP-TRP/INV-DUP). The rearrangement was inherited from the carrier mother, who exhibits extreme XCI skewing and subtle psychiatric symptoms. Patient 2 presented a de novo (X;Y) unbalanced translocation resulting in duplication of Xq28 and deletion of Yp, originated in the paternal gametogenesis. Neurodevelopmental trajectory and non-neurological symptoms were consistent with previous reports, with the exception of cerebellar vermis hypoplasia in patient 2. Although both patients share the core MDS phenotype, patient 1 showed MECP2 transcript levels in blood similar to controls. Understanding the molecular mechanisms related to MDS is essential for designing targeted therapeutic strategies.
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Affiliation(s)
- Bianca Barbosa Abdala
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andressa Pereira Gonçalves
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jussara Mendonça Dos Santos
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Boy
- Pedro Ernesto University Hospital, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Texas, USA; Section of Neurology, Department of Pediatrics, Baylor College of Medicine, Texas, USA
| | - Márcia Mattos Gonçalves Pimentel
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cíntia Barros Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil.
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23
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Costa CIS, da Silva Montenegro EM, Zarrei M, de Sá Moreira E, Silva IMW, de Oliveira Scliar M, Wang JYT, Zachi EC, Branco EV, da Costa SS, Lourenço NCV, Vianna-Morgante AM, Rosenberg C, Krepischi ACV, Scherer SW, Passos-Bueno MR. Copy number variations in a Brazilian cohort with autism spectrum disorders highlight the contribution of cell adhesion genes. Clin Genet 2021; 101:134-141. [PMID: 34664255 DOI: 10.1111/cge.14072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/16/2021] [Revised: 10/01/2021] [Accepted: 10/12/2021] [Indexed: 11/28/2022]
Abstract
Prediction of pathogenicity of rare copy number variations (CNVs), a genomic alteration known to contribute to the etiology of autism spectrum disorder (ASD), represents a serious limitation to interpreting genetic tests, particularly for genetic counseling purposes. Chromosomal microarray analysis (CMA) was conducted in a unique collection of 144 Brazilian individuals with ASD of strong European and African ancestries. Rare CNVs were detected in 39 patients: 41 of unknown significance (VUS), four pathogenic and one likely pathogenic CNVs (clinical yield of 4.1%; 5/122). Based on gene content and recurrence in three large cohorts [a Brazilian neurodevelopmental disorder cohort, the autism MSSNG cohort, and the Canadian-based Centre for Applied Genomics microarray database], this work strengthened the pathogenicity of 14 genes (FAT1, CAMK4, BIRC6, DPP6, CSMD1, CTNNA3, CDH8/CDH11, CDH13, OR1C1, CNTN6, CNTNAP4, FGF2 and PTPRN2) within 14 CNVs. Notably, enrichment of cell adhesion proteins to ASD etiology was identified (p < 0.05), highlighting the importance of these gene families in the etiology of ASD.
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Affiliation(s)
- Claudia Ismania Samogy Costa
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Eduarda Morgana da Silva Montenegro
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Mehdi Zarrei
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Eloísa de Sá Moreira
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Isabela Maya Wahys Silva
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Marília de Oliveira Scliar
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jaqueline Yu Ting Wang
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Elaine Cristina Zachi
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Elisa Varella Branco
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Silvia Souza da Costa
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Naila Cristina Vilaça Lourenço
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Angela Maria Vianna-Morgante
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Carla Rosenberg
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana Cristina Victorino Krepischi
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Stephen W Scherer
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Maria Rita Passos-Bueno
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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24
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Nishi MY, Faria Júnior JAD, Krepischi ACV, de Moraes DR, da Costa SS, Silva ESDN, Costa EMF, Mendonca BB, Domenice S. A Small Supernumerary Xp Marker Chromosome Including Genes NR0B1 and MAGEB Causing Partial Gonadal Dysgenesis and Gonadoblastoma. Sex Dev 2021; 16:55-63. [PMID: 34510040 DOI: 10.1159/000517085] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 05/06/2021] [Indexed: 11/19/2022] Open
Abstract
Copy number variations of several genes involved in the process of gonadal determination have been identified as a cause of 46,XY differences of sex development. We report a non-syndromic 14-year-old female patient who was referred with primary amenorrhea, absence of breast development, and atypical genitalia. Her karyotype was 47,XY,+mar/46,XY, and FISH analysis revealed the X chromosome origin of the marker chromosome. Array-CGH data identified a pathogenic 2.0-Mb gain of an Xp21.2 segment containing NR0B1/DAX1 and a 1.9-Mb variant of unknown significance from the Xp11.21p11.1 region. This is the first report of a chromosomal microarray analysis to reveal the genetic content of a small supernumerary marker chromosome detected in a 47,XY,+der(X)/46,XY karyotype in a non-syndromic girl with partial gonadal dysgenesis and gonadoblastoma. Our findings indicate that the mosaic presence of the small supernumerary Xp marker, encompassing the NR0B1/DAX1 gene, may have been the main cause of dysgenetic testes development, although the role of MAGEB and other genes mapped to the Xp21 segment could not be completely ruled out.
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Affiliation(s)
- Mirian Yumie Nishi
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - José Antônia Diniz Faria Júnior
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil,
| | | | - Daniela Rodrigues de Moraes
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Silvia Souza da Costa
- Departamento de Genética e Biologia Evolutiva do Instituto de Biociências da Universidade de São Paulo, São Paulo, Brazil
| | - Elinaelma Suelane do Nascimento Silva
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Elaine Maria Frade Costa
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Berenice Bilharinho Mendonca
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Sorahia Domenice
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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25
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da Rocha LA, Pires LVL, Yamamoto GL, Magliocco Ceroni JR, Honjo RS, de Novaes França Bisneto E, Oliveira LAN, Rosenberg C, Krepischi ACV, Passos-Bueno MR, Kim CA, Bertola DR. Congenital limb deficiency: Genetic investigation of 44 individuals presenting mainly longitudinal defects in isolated or syndromic forms. Clin Genet 2021; 100:615-623. [PMID: 34341987 DOI: 10.1111/cge.14041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 05/10/2021] [Revised: 06/29/2021] [Accepted: 07/29/2021] [Indexed: 11/30/2022]
Abstract
Congenital limb deficiency (CLD), one of the most common congenital anomalies, is characterized by hypoplasia/aplasia of one or more limb bones and can be isolated or syndromic. The etiology in CLD is heterogeneous, including environmental and genetic factors. A fraction remains with no etiological factor identified. We report the study of 44 Brazilian individuals presenting isolated or syndromic CLD, mainly with longitudinal defects. Genetic investigation included particularly next-generation sequencing (NGS) and/or chromosomal microarray. The overall diagnostic yield was 45.7%, ranging from 60.9% in the syndromic to 16.7% in the non-syndromic group. In TAR syndrome, a common variant in 3´UTR of RBM8A, in trans with 1q21.1 microdeletion, was detected, corroborating the importance of this recently reported variant in individuals of African ancestry. NGS established a diagnosis in three individuals in syndromes recently reported or still under delineation (an acrofacial dysostosis, Coats plus and Verheij syndromes), suggesting a broader phenotypic spectrum in these disorders. Although a low rate of molecular detection in non-syndromic forms was observed, it is still possible that variants in non-coding regions and small CNVs, not detected by the techniques applied in this study, could play a role in the etiology of CLD.
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Affiliation(s)
- Letícia Alves da Rocha
- Genetics Unit, Instituto da Criança, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Lucas Vieira Lacerda Pires
- Genetics Unit, Instituto da Criança, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Guilherme Lopes Yamamoto
- Genetics Unit, Instituto da Criança, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.,Human Genome and Stem-Cell Research Center, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - José Ricardo Magliocco Ceroni
- Genetics Unit, Instituto da Criança, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Rachel Sayuri Honjo
- Genetics Unit, Instituto da Criança, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Edgard de Novaes França Bisneto
- Orthopedics and Traumatology Institute, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Luiz Antônio Nunes Oliveira
- Radiology, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- Human Genome and Stem-Cell Research Center, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem-Cell Research Center, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem-Cell Research Center, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Chong Ae Kim
- Genetics Unit, Instituto da Criança, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Débora Romeo Bertola
- Genetics Unit, Instituto da Criança, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.,Human Genome and Stem-Cell Research Center, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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26
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de Castro Fonseca M, de Oliveira JF, Araujo BHS, Canateli C, do Prado PFV, Amorim Neto DP, Bosque BP, Rodrigues PV, de Godoy JVP, Tostes K, Filho HVR, Nascimento AFZ, Saito A, Tonoli CCC, Batista FAH, de Oliveira PSL, Figueira AC, Souza da Costa S, Krepischi ACV, Rosenberg C, Westfahl H, da Silva AJR, Franchini KG. Molecular and cellular basis of hyperassembly and protein aggregation driven by a rare pathogenic mutation in DDX3X. iScience 2021; 24:102841. [PMID: 34381968 PMCID: PMC8335631 DOI: 10.1016/j.isci.2021.102841] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/21/2021] [Accepted: 07/08/2021] [Indexed: 12/30/2022] Open
Abstract
Current studies estimate that 1–3% of females with unexplained intellectual disability (ID) present de novo splice site, nonsense, frameshift, or missense mutations in the DDX3X protein (DEAD-Box Helicase 3 X-Linked). However, the cellular and molecular mechanisms by which DDX3X mutations impair brain development are not fully comprehended. Here, we show that the ID-linked missense mutation L556S renders DDX3X prone to aggregation. By using a combination of biophysical assays and imaging approaches, we demonstrate that this mutant assembles solid-like condensates and amyloid-like fibrils. Although we observed greatly reduced expression of the mutant allele in a patient who exhibits skewed X inactivation, this appears to be enough to sequestrate healthy proteins into solid-like ectopic granules, compromising cell function. Therefore, our data suggest ID-linked DDX3X L556S mutation as a disorder arising from protein misfolding and aggregation. DDX3X mutations skew X-inactivation and are found in 1-3% of unexplained ID in females DDX3X mutant proteins assemble solid-like condensates and amyloid-like fibrils Aberrant granules formed by DDX3X mutants sequestrate healthy DDX3X protein ID-linked DDX3X L556S mutation decreases cell viability and induces apoptosis
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Affiliation(s)
- Matheus de Castro Fonseca
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Juliana Ferreira de Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Bruno Henrique Silva Araujo
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Camila Canateli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Paula Favoretti Vital do Prado
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Dionísio Pedro Amorim Neto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Beatriz Pelegrini Bosque
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Paulla Vieira Rodrigues
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - João Vitor Pereira de Godoy
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Katiane Tostes
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Helder Veras Ribeiro Filho
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Andrey Fabricio Ziem Nascimento
- Brazilian Synchrotron Light National Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Angela Saito
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Celisa Caldana Costa Tonoli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Fernanda Aparecida Heleno Batista
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Paulo Sergio Lopes de Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Ana Carolina Figueira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Harry Westfahl
- Brazilian Synchrotron Light National Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Antônio José Roque da Silva
- Brazilian Synchrotron Light National Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Kleber Gomes Franchini
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Internal Medicine, School of Medicine, University of Campinas, Campinas, Brazil
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27
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Tolezano GC, da Costa SS, Scliar MDO, Fernandes WLM, Otto PA, Bertola DR, Rosenberg C, Vianna-Morgante AM, Krepischi ACV. Investigating Genetic Factors Contributing to Variable Expressivity of Class I 17p13.3 Microduplication. Int J Mol Cell Med 2021; 9:296-306. [PMID: 33688487 PMCID: PMC7936075 DOI: 10.22088/ijmcm.bums.9.4.296] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/02/2021] [Indexed: 11/13/2022]
Abstract
17p13.3 microduplications are rare copy number variations (CNVs) associated with variable phenotypes, including facial dysmorphism, developmental delay, intellectual disability, and autism. Typically, when a recognized pathogenic CNV is identified, other genetic factors are not considered. We investigated via whole-exome sequencing the presence of additional variants in four carriers of class I 17p13.3 microduplications. A 730 kb 17p13.3 microduplication was identified in two half-brothers with intellectual disability, but not in a third affected half-brother or blood cells from their normal mother (Family A), thus leading to the hypothesis of maternal germline mosaicism. No additional pathogenic variants were detected in Family A. Two affected siblings carried maternally inherited 450 kb 17p13.3 microduplication (Family B); the three carriers of the microduplication exhibited microcephaly and learning disability/speech impairment of variable degrees. Exome analysis revealed a variant of uncertain significance in RORA, a gene already linked to autism, in the autistic boy; his sister was heterozygous for a CYP1B1 pathogenic variant that could be related to her congenital glaucoma. Besides, both siblings carried a loss-of-function variant in DIP2B, a candidate gene for intellectual disability, which was inherited from their father, who also exhibited learning disability in childhood. In conclusion, additional pathogenic variants were revealed in two affected carriers of class I 17p13.3 microduplication (Family B), probably adding to their phenotypes. These results provided new evidence regarding the contribution of RORA and DIP2B to neurocognitive deficits, and highlighted the importance of full genetic investigation in carriers of CNV syndromes with variable expressivity. Finally, we suggest that microcephaly may be a rare clinical feature also related to the presence of the class I 17p13.3 microduplication.
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Affiliation(s)
- Giovanna Cantini Tolezano
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Silvia Souza da Costa
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Marília de Oliveira Scliar
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | | | - Paulo Alberto Otto
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Débora Romeo Bertola
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil .,Instituto da Criança, Hospital das Clínicas, University of São Paulo Medical, São Paulo, SP, Brazil
| | - Carla Rosenberg
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Angela Maria Vianna-Morgante
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
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28
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Rivas MP, Aguiar TFM, Maschietto M, Lemes RB, Caires-Júnior LC, Goulart E, Telles-Silva KA, Novak E, Cristofani LM, Odone V, Cypriano M, de Toledo SRC, Carraro DM, Escobar MQ, Lee H, Johnston M, da Costa CML, da Cunha IW, Tasic L, Pearson PL, Rosenberg C, Timchenko N, Krepischi ACV. Hepatoblastomas exhibit marked NNMT downregulation driven by promoter DNA hypermethylation. Tumour Biol 2020; 42:1010428320977124. [PMID: 33256542 DOI: 10.1177/1010428320977124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Hepatoblastomas exhibit the lowest mutational burden among pediatric tumors. We previously showed that epigenetic disruption is crucial for hepatoblastoma carcinogenesis. Our data revealed hypermethylation of nicotinamide N-methyltransferase, a highly expressed gene in adipocytes and hepatocytes. The expression pattern and the role of nicotinamide N-methyltransferase in pediatric liver tumors have not yet been explored, and this study aimed to evaluate the effect of nicotinamide N-methyltransferase hypermethylation in hepatoblastomas. We evaluated 45 hepatoblastomas and 26 non-tumoral liver samples. We examined in hepatoblastomas if the observed nicotinamide N-methyltransferase promoter hypermethylation could lead to dysregulation of expression by measuring mRNA and protein levels by real-time quantitative polymerase chain reaction, immunohistochemistry, and Western blot assays. The potential impact of nicotinamide N-methyltransferase changes was evaluated on the metabolic profile by high-resolution magic angle spinning nuclear magnetic resonance spectroscopy. Significant nicotinamide N-methyltransferase downregulation was revealed in hepatoblastomas, with two orders of magnitude lower nicotinamide N-methyltransferase expression in tumor samples and hepatoblastoma cell lines than in hepatocellular carcinoma cell lines. A specific TSS1500 CpG site (cg02094283) of nicotinamide N-methyltransferase was hypermethylated in tumors, with an inverse correlation between its methylation level and nicotinamide N-methyltransferase expression. A marked global reduction of the nicotinamide N-methyltransferase protein was validated in tumors, with strong correlation between gene and protein expression. Of note, higher nicotinamide N-methyltransferase expression was statistically associated with late hepatoblastoma diagnosis, a known clinical variable of worse prognosis. In addition, untargeted metabolomics analysis detected aberrant lipid metabolism in hepatoblastomas. Data presented here showed the first evidence that nicotinamide N-methyltransferase reduction occurs in hepatoblastomas, providing further support that the nicotinamide N-methyltransferase downregulation is a wide phenomenon in liver cancer. Furthermore, this study unraveled the role of DNA methylation in the regulation of nicotinamide N-methyltransferase expression in hepatoblastomas, in addition to evaluate the potential effect of nicotinamide N-methyltransferase reduction in the metabolism of these tumors. These preliminary findings also suggested that nicotinamide N-methyltransferase level may be a potential prognostic biomarker for hepatoblastoma.
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Affiliation(s)
- Maria Prates Rivas
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Talita Ferreira Marques Aguiar
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | - Renan B Lemes
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Luiz Carlos Caires-Júnior
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ernesto Goulart
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Kayque Alves Telles-Silva
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Estela Novak
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil.,Molecular Genetics-São Paulo's Blood Center, São Paulo, Brazil
| | - Lilian Maria Cristofani
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Vicente Odone
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Monica Cypriano
- Department of Pediatric, Adolescent and Child with Cancer Support Group (GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | - Silvia Regina Caminada de Toledo
- Department of Pediatric, Adolescent and Child with Cancer Support Group (GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | - Dirce Maria Carraro
- International Center for Research, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Melissa Quintero Escobar
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, Campinas, Brazil
| | - Hana Lee
- Department of Surgery, Division of General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michael Johnston
- Department of Surgery, Division of General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Isabela Werneck da Cunha
- Department of Pathology, Rede D'OR São Luiz, São Paulo, Brazil.,Department of Pathology, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Ljubica Tasic
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, Campinas, Brazil
| | - Peter L Pearson
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Nikolai Timchenko
- Department of Surgery, Division of General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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29
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Canton APM, Krepischi ACV, Montenegro LR, Costa S, Rosenberg C, Steunou V, Sobrier ML, Santana L, Honjo RS, Kim CA, de Zegher F, Idkowiak J, Gilligan LC, Arlt W, Funari MFDA, Jorge AADL, Mendonca BB, Netchine I, Brito VN, Latronico AC. Insights from the genetic characterization of central precocious puberty associated with multiple anomalies. Hum Reprod 2020; 36:506-518. [DOI: 10.1093/humrep/deaa306] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/12/2020] [Indexed: 01/08/2023] Open
Abstract
Abstract
STUDY QUESTION
Is there an (epi)genetic basis in patients with central precocious puberty (CPP) associated with multiple anomalies that unmasks underlying mechanisms or reveals novel genetic findings related to human pubertal control?
SUMMARY ANSWER
In a group of 36 patients with CPP associated with multiple phenotypes, pathogenic or likely pathogenic (epi)genetic defects were identified in 12 (33%) patients, providing insights into the genetics of human pubertal control.
WHAT IS KNOWN ALREADY
A few studies have described patients with CPP associated with multiple anomalies, but without making inferences on causalities of CPP. Genetic-molecular studies of syndromic cases may reveal disease genes or mechanisms, as the presentation of such patients likely indicates a genetic disorder.
STUDY DESIGN, SIZE, DURATION
This translational study was based on a genetic-molecular analysis, including genome-wide high throughput methodologies, for searching structural or sequence variants implicated in CPP and DNA methylation analysis of candidate regions.
PARTICIPANTS/MATERIALS, SETTING, METHODS
A cohort of 197 patients (188 girls) with CPP without structural brain lesions was submitted to a detailed clinical evaluation, allowing the selection of 36 unrelated patients (32 girls) with CPP associated with multiple anomalies. Pathogenic allelic variants of genes known to cause monogenic CPP (KISS1R, KISS1, MKRN3 and DLK1) had been excluded in the entire cohort (197 patients). All selected patients with CPP associated with multiple anomalies (n = 36) underwent methylation analysis of candidate regions and chromosomal microarray analysis. A subset (n = 9) underwent whole-exome sequencing, due to presenting familial CPP and/or severe congenital malformations and neurocognitive abnormalities.
MAIN RESULTS AND THE ROLE OF CHANCE
Among the 36 selected patients with CPP, the more prevalent associated anomalies were metabolic, growth and neurocognitive conditions. In 12 (33%) of them, rare genetic abnormalities were identified: six patients presented genetic defects in loci known to be involved with CPP (14q32.2 and 7q11.23), whereas the other six presented defects in candidate genes or regions. In detail, three patients presented hypomethylation of DLK1/MEG3:IG-DMR (14q32.2 disruption or Temple syndrome), resulting from epimutation (n = 1) or maternal uniparental disomy of chromosome 14 (n = 2). Seven patients presented pathogenic copy number variants: three with de novo 7q11.23 deletions (Williams–Beuren syndrome), three with inherited Xp22.33 deletions, and one with de novo 1p31.3 duplication. Exome sequencing revealed potential pathogenic variants in two patients: a sporadic female case with frameshift variants in TNRC6B and AREL1 and a familial male case with a missense substitution in UGT2B4 and a frameshift deletion in MKKS.
LIMITATIONS, REASONS FOR CAUTION
The selection of patients was based on a retrospective clinical characterization, lacking a longitudinal inclusion of consecutive patients. In addition, future studies are needed, showing the long-term (mainly reproductive) outcomes in the included patients, as most of them are not in adult life yet.
WIDER IMPLICATIONS OF THE FINDINGS
The results highlighted the relevance of an integrative clinical-genetic approach in the elucidation of mechanisms and factors involved in pubertal control. Chromosome 14q32.2 disruption indicated the loss of imprinting of DLK1 as a probable mechanism of CPP. Two other chromosomal regions (7q11.23 and Xp22.33) represented new candidate loci potentially involved in this disorder of pubertal timing.
STUDY FUNDING/COMPETING INTEREST(S)
This work was supported by grant number 2018/03198-0 (to A.P.M.C.) and grant number 2013/08028-1 (to A.C.V.K) from the São Paulo Research Foundation (FAPESP), and grant number 403525/2016-0 (to A.C.L.) and grant number 302849/2015-7 (to A.C.L.) and grant number 141625/2016-3 (to A.C.V.K) from the National Council for Scientific and Technological Development (CNPq). The authors have nothing to disclose.
TRIAL REGISTRATION NUMBER
N/A.
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Affiliation(s)
- Ana Pinheiro Machado Canton
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics, LIM42, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | | | - Luciana Ribeiro Montenegro
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics, LIM42, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Silvia Costa
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Virginie Steunou
- University Sorbonne, INSERM, UMR_S 938, Saint-Antoine Research Center, Paris, France
| | - Marie-Laure Sobrier
- University Sorbonne, INSERM, UMR_S 938, Saint-Antoine Research Center, Paris, France
| | - Lucas Santana
- Genetic Endocrinology Unit, LIM25, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Rachel Sayuri Honjo
- Clinical Genetics Unit, Children’s Institute, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Chong Ae Kim
- Clinical Genetics Unit, Children’s Institute, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Francis de Zegher
- Department of Development and Regeneration, University of Leuven, Leuven, Belgium
| | - Jan Idkowiak
- Institute of Metabolism and Systems Research (IMSR), College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Department of Endocrinology and Diabetes, Birmingham Women’s and Children’s Hospital NHS Foundation Trust, Birmingham, UK
| | - Lorna C Gilligan
- Institute of Metabolism and Systems Research (IMSR), College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Wiebke Arlt
- Institute of Metabolism and Systems Research (IMSR), College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Mariana Ferreira de Assis Funari
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics, LIM42, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Alexander Augusto de Lima Jorge
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics, LIM42, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
- Genetic Endocrinology Unit, LIM25, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Berenice Bilharinho Mendonca
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics, LIM42, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Irène Netchine
- University Sorbonne, INSERM, UMR_S 938, Saint-Antoine Research Center, Paris, France
- AP-HP, Armand Trousseau Hospital, Endocrine Functional Exploration Service, Paris, France
| | - Vinicius Nahime Brito
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics, LIM42, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Ana Claudia Latronico
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics, LIM42, Department of Endocrinology and Metabolism, Clinicas Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
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Pires SF, Tolezano GC, da Costa SS, Kawahira RSH, Kim CA, Rosenberg C, Teixeira ACB, Bertola DR, Krepischi ACV. Expanding the role of SETD5 haploinsufficiency in neurodevelopment and neuroblastoma. Pediatr Blood Cancer 2020; 67:e28376. [PMID: 32748512 DOI: 10.1002/pbc.28376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 03/30/2020] [Accepted: 04/14/2020] [Indexed: 11/07/2022]
Affiliation(s)
- Sara Ferreira Pires
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Giovanna Cantini Tolezano
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Silvia Souza da Costa
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Rachel Sayuri Honjo Kawahira
- Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Chong Ae Kim
- Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Anne Caroline Barbosa Teixeira
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Debora Romeo Bertola
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.,Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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Novak EM, Gimenez TM, Neves NH, Vince CSC, Krepischi ACV, Lapa RML, Cristofani LM, Bendit I, Filho VO. Abstract B18: MEG3 and MEG8 aberrant methylation associated with worst prognosis in an infant with neuroblastoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.pedca19-b18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Neuroblastoma (NB) is an extremely rare pediatric cancer accounting for about 12% of childhood cancer-related deaths, due to its dismal prognosis in patients diagnosed over 18 months of age with disseminated disease. However, neonates and infants with neuroblastoma are expected to have a better evolution despite their stage and even unfavorable molecular characteristics. Here, we report an unusual case of low-risk neuroblastoma (stage 2B, nonamplified MYCN) in a 9-month-old girl with unfavorable outcome despite favorable prognostic factors.
Material and Methods: We investigated the coding genes expression (mRNA) and long noncoding RNAs (lncRNAs) in primary and relapse tumors of this patient to look for genomic and epigenetic alterations that could explain the clinical evolution. The cytogenetic profiles of the primary and relapse tumor samples were also obtained. Three primary tumors from patients with neuroblastoma, all classified as stage 1 (INSS) and low-risk (below 18 months of age at diagnosis, nonamplified-MYCN, all alive and free of disease 60 months after diagnosis) were used as controls in RNA sequencing (RNA-Seq. Illumina®) and DNA methylation arrays (Illumina Infinium HumanMethylation450 BeadChip). Somatic copy number alterations were investigated in the primary and relapsed sample using the array-CGH methodology in a 180K platform (Agilent).
Results: The cytogenetic profiles of both samples were quite identical, with few copy number alterations. No numerical chromosomal alterations (aneuploidies) were detected; both tumors carry segmental copy number alterations in common, most of them probably present in a nonmosaic state. The differential gene expression analysis based on fold-change (≤ -2 and ≥ 2), p < 0.005, and FDR < 0.05 was used in RNA-seq to identified gene differential expression in primary and relapsed tumors. Interestingly, only two lncRNA, the imprinted maternally expressed genes MEG3 and MEG8, were downregulated in both primary and relapse tumors. MEG3 targets p53 by either directly interacting with p53 or indirectly suppressing the negative regulator MDM2. In the case of MEG8, their functions in cancer remain unknown. Our study then focused on MEG3 and MEG8 methylation analysis. DNA methylation status of the study groups (primary, relapse tumors, and controls) strongly suggested that DMR that covers promoters was responsible for silencing MEG3 and MEG8 genes in primary and relapse tumors, resulting in downregulation of MEG3 and MEG8. Tumor samples from the patient were also used to perform methylation-specific MLPA (MSMLPA) (SALSA® probemix, MRC-Holland). Hypermethylated probes at MEG3 were identified in primary and relapse tumors when compared with controls.
Conclusion: Furthermore, we hypothesized that the methylation gain of the MEG3 and MEG8 locus may be accentuated during cancer progression and therefore, the increased degree of MEG3 and MEG8 suppression was associated with the overall aggressiveness of neuroblastoma.
Citation Format: Estela M. Novak, Thamiris Magalhaes Gimenez, Nathalia Halley Neves, Carolina Sgarioni Camargo Vince, Ana Cristina Victorino Krepischi, Rainer Marco Lopez Lapa, Lilian M. Cristofani, Israel Bendit, Vicente Odone Filho. MEG3 and MEG8 aberrant methylation associated with worst prognosis in an infant with neuroblastoma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B18.
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Affiliation(s)
- Estela M. Novak
- 1Instituto de Tratamento de Câncer Infantil, Universidade de São Paulo, São Paulo, Brazil,
| | | | - Nathalia Halley Neves
- 1Instituto de Tratamento de Câncer Infantil, Universidade de São Paulo, São Paulo, Brazil,
| | | | | | | | - Lilian M. Cristofani
- 1Instituto de Tratamento de Câncer Infantil, Universidade de São Paulo, São Paulo, Brazil,
| | - Israel Bendit
- 4Fundação Pró-Sangue Hemocentro de São Paulo, São Paulo, Brazil
| | - Vicente Odone Filho
- 1Instituto de Tratamento de Câncer Infantil, Universidade de São Paulo, São Paulo, Brazil,
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Aguiar TFM, Rivas MP, Costa S, Maschietto M, Rodrigues T, Sobral de Barros J, Barbosa AC, Valieris R, Fernandes GR, Bertola DR, Cypriano M, Caminada de Toledo SR, Major A, Tojal I, Apezzato MLDP, Carraro DM, Rosenberg C, Lima da Costa CM, Cunha IW, Sarabia SF, Terrada DL, Krepischi ACV. Insights Into the Somatic Mutation Burden of Hepatoblastomas From Brazilian Patients. Front Oncol 2020; 10:556. [PMID: 32432034 PMCID: PMC7214543 DOI: 10.3389/fonc.2020.00556] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/27/2020] [Indexed: 12/23/2022] Open
Abstract
Hepatoblastoma is a very rare embryonal liver cancer supposed to arise from the impairment of hepatocyte differentiation during embryogenesis. In this study, we investigated by exome sequencing the burden of somatic mutations in a cohort of 10 hepatoblastomas, including a congenital case. Our data disclosed a low mutational background and pointed out to a novel set of candidate genes for hepatoblastoma biology, which were shown to impact gene expression levels. Only three recurrently mutated genes were detected: CTNNB1 and two novel candidates, CX3CL1 and CEP164. A relevant finding was the identification of a recurrent mutation (A235G) in two hepatoblastomas at the CX3CL1 gene; evaluation of RNA and protein expression revealed upregulation of CX3CL1 in tumors. The analysis was replicated in two independents cohorts, substantiating that an activation of the CX3CL1/CX3CR1 pathway occurs in hepatoblastomas. In inflammatory regions of hepatoblastomas, CX3CL1/CX3CR1 were not detected in the infiltrated lymphocytes, in which they should be expressed in normal conditions, whereas necrotic regions exhibited negative labeling in tumor cells, but strongly positive infiltrated lymphocytes. Altogether, these data suggested that CX3CL1/CX3CR1 upregulation may be a common feature of hepatoblastomas, potentially related to chemotherapy response and progression. In addition, three mutational signatures were identified in hepatoblastomas, two of them with predominance of either the COSMIC signatures 1 and 6, found in all cancer types, or the COSMIC signature 29, mostly related to tobacco chewing habit; a third novel mutational signature presented an unspecific pattern with an increase of C>A mutations. Overall, we present here novel candidate genes for hepatoblastoma, with evidence that CX3CL1/CX3CR1 chemokine signaling pathway is likely involved with progression, besides reporting specific mutational signatures.
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Affiliation(s)
- Talita Ferreira Marques Aguiar
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil.,Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Maria Prates Rivas
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Silvia Costa
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | - Tatiane Rodrigues
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Juliana Sobral de Barros
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Anne Caroline Barbosa
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Renan Valieris
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Gustavo R Fernandes
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Debora R Bertola
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Monica Cypriano
- Adolescent and Child With Cancer Support Group (GRAACC), Department of Pediatric, Federal University of São Paulo, São Paulo, Brazil
| | - Silvia Regina Caminada de Toledo
- Adolescent and Child With Cancer Support Group (GRAACC), Department of Pediatric, Federal University of São Paulo, São Paulo, Brazil
| | - Angela Major
- Department of Pathology and Immunology, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, United States
| | - Israel Tojal
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | | | - Dirce Maria Carraro
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | - Isabela W Cunha
- Department of Pathology, Rede D'OR-São Luiz, São Paulo, Brazil.,Department of Pathology, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Stephen Frederick Sarabia
- Department of Pathology and Immunology, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, United States
| | - Dolores-López Terrada
- Department of Pathology and Immunology, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, United States.,Department of Pediatrics, Texas Children's Cancer Center, Houston, TX, United States.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, United States
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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Vasco de Albuquerque Albuquerque E, Ferreira de Assis Funari M, Pereira de Souza Quedas E, Sayuri Honjo Kawahira R, Soares Jallad R, Homma TK, Martin RM, Brito VN, Malaquias AC, Lerario AM, Rosenberg C, Victorino Krepischi AC, Ae Kim C, Arnhold IJP, Jorge AADL. Genetic investigation of patients with tall stature. Eur J Endocrinol 2020; 182:139-147. [PMID: 31751304 DOI: 10.1530/eje-19-0785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/15/2019] [Indexed: 11/08/2022]
Abstract
CONTEXT Patients with tall stature often remain undiagnosed after clinical investigation and few studies have genetically assessed this group, most of them without a systematic approach. OBJECTIVE To assess prospectively a group of individuals with tall stature, with and without syndromic features, and to establish a molecular diagnosis for their growth disorder. DESIGN Screening by karyotype (n = 42), chromosome microarray analyses (CMA) (n = 16), MS-MLPA (n = 2) targeted panel (n = 12) and whole-exome sequencing (n = 31). PATIENTS AND METHODS We selected 42 patients with tall stature after exclusion of pathologies in GH/IGF1 axis and divided them into syndromic (n = 30) and non-syndromic (n = 12) subgroups. MAIN OUTCOME MEASURES Frequencies of pathogenic findings. RESULTS We identified two patients with chromosomal abnormalities including SHOX trisomy by karyotype, one 9q22.3 microdeletion syndrome by CMA, two cases of Beckwith-Wiedemann syndrome by targeted MS-MLPA analysis and nine cases with heterozygous pathogenic or likely pathogenic genetic variants by multigene analysis techniques (FBN1 = 3, NSD1 = 2, NFIX = 1, SUZ12 = 1, CHD8 = 1, MC4R = 1). Three of 20 patients analyzed by WES had their diagnosis established. Only one non-syndromic patient had a definitive diagnosis. The sequential genetic assessment diagnosed 14 out of 42 (33.3%) tall patients. CONCLUSION A systematic molecular approach of patients with tall stature was able to identify the etiology in 13 out of 30 (43.3%) syndromic and 1 out of 12 (8.3%) non-syndromic patients, contributing to the genetic counseling and avoiding unfavorable outcomes in the syndromic subgroup.
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Affiliation(s)
- Edoarda Vasco de Albuquerque Albuquerque
- Unidade de Endocrinologia Genética (LIM25), Laboratório de Hormônios e Genética Molecular (LIM42), Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brasil
| | - Mariana Ferreira de Assis Funari
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular (LIM42), Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brasil
| | - Elisângela Pereira de Souza Quedas
- Unidade de Endocrinologia Genética (LIM25), Laboratório de Hormônios e Genética Molecular (LIM42), Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brasil
| | - Rachel Sayuri Honjo Kawahira
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
| | - Raquel Soares Jallad
- Unidade de Neuroendocrinologia, Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brasil
| | - Thaís Kataoka Homma
- Unidade de Endocrinologia Genética (LIM25), Laboratório de Hormônios e Genética Molecular (LIM42), Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brasil
| | - Regina Matsunaga Martin
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular (LIM42), Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brasil
- Unidade de Doenças Osteometabólicas, Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brasil
| | - Vinicius Nahime Brito
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular (LIM42), Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brasil
| | - Alexsandra Christianne Malaquias
- Unidade de Endocrinologia Genética (LIM25), Laboratório de Hormônios e Genética Molecular (LIM42), Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brasil
- Unidade de Endocrinologia Pediátrica, Departamento de Pediatria, Irmandade da Santa Casa de Misericórdia de São Paulo, São Paulo, Brasil
| | - Antonio Marcondes Lerario
- Unidade de Endocrinologia Genética (LIM25), Laboratório de Hormônios e Genética Molecular (LIM42), Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brasil
- Division of Metabolism, Endocrinology and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Carla Rosenberg
- Instituto de Biociências (IB), Universidade de São Paulo (USP), São Paulo, Brasil
| | | | - Chong Ae Kim
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
| | - Ivo Jorge Prado Arnhold
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular (LIM42), Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brasil
| | - Alexander Augusto de Lima Jorge
- Unidade de Endocrinologia Genética (LIM25), Laboratório de Hormônios e Genética Molecular (LIM42), Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brasil
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Mariano FV, Fidalgo F, Casarim ALM, Martins AS, Scarini JF, de Lima Souza RA, Egal ES, Kowalski LP, Krepischi ACV, Altemani A. Somatic copy number alterations in pleomorphic adenoma and recurrent pleomorphic adenoma. Oral Surg Oral Med Oral Pathol Oral Radiol 2019; 129:59-64. [PMID: 31607675 DOI: 10.1016/j.oooo.2019.08.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/07/2019] [Accepted: 08/25/2019] [Indexed: 01/19/2023]
Abstract
OBJECTIVE As the genetic changes in recurrent pleomorphic adenoma (RPA) have not yet been investigated, the aim of this study was to assess the genomic profile of somatic copy number alteration in RPA and pleomorphic adenoma (PA) by using array comparative genomic hybridization (aCGH). STUDY DESIGN Four cases of RPA and 13 cases of PA were evaluated by using aCGH, using a 180 K platform. Data were analyzed by using Nexus Copy Number Discovery. RESULTS The RPA group rarely showed any copy number alteration, except for 1 case that exhibited losses in 5 p15.33 p15.1, 5 q13.1 q35.3 and 12 q12 q13.11. The PA group also showed few copy number alterations, and the most frequent findings involved chromosomes 8: 8p21.3-p12 (gain), 8q12.1 (loss), 8p23.3-q24.3 (gain), and 8q12.1-q21.11 (gain). Genomic amplifications were revealed in the PA group, and the relevant affected genes were MAML2 and LIFR. CONCLUSIONS PA and RPA exhibit few somatic copy number alterations and show a similar genomic profile on aCGH.
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Affiliation(s)
| | - Felipe Fidalgo
- International Research Center, AC Camargo Cancer Center, São Paulo-SP, Brazil
| | | | - Antônio Santos Martins
- Head and Neck Surgery Department, Faculty of Medical Sciences/UNICAMP, Campinas-SP, Brazil
| | | | | | - Erika Said Egal
- Pathology Department, Faculty of Medical Sciences/UNICAMP, Campinas-SP, Brazil
| | - Luiz Paulo Kowalski
- Head and Neck Surgery Department, AC Camargo Cancer Center, São Paulo-SP, Brazil
| | | | - Albina Altemani
- Pathology Department, Faculty of Medical Sciences/UNICAMP, Campinas-SP, Brazil
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35
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Rivas MP, Aguiar TFM, Fernandes GR, Caires-Júnior LC, Goulart E, Telles-Silva KA, Cypriano M, de Toledo SRC, Rosenberg C, Carraro DM, da Costa CML, da Cunha IW, Krepischi ACV. TET Upregulation Leads to 5-Hydroxymethylation Enrichment in Hepatoblastoma. Front Genet 2019; 10:553. [PMID: 31249594 PMCID: PMC6582250 DOI: 10.3389/fgene.2019.00553] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/24/2019] [Indexed: 12/14/2022] Open
Abstract
Hepatoblastoma is an embryonal liver tumor carrying few genetic alterations. We previously disclosed in hepatoblastomas a genome-wide methylation dysfunction, characterized by hypermethylation at specific CpG islands, in addition to a low-level hypomethylation pattern in non-repetitive intergenic sequences, in comparison to non-tumoral liver tissues, shedding light into a crucial role for epigenetic dysregulation in this type of cancer. To explore the underlying mechanisms possibly related to aberrant epigenetic modifications, we evaluated the expression profile of a set of genes engaged in the epigenetic machinery related to DNA methylation (DNMT1, DNMT3A, DNMT3B, DNMT3L, UHRF1, TET1, TET2, and TET3), as well as the 5-hydroxymethylcytosine (5hmC) global level. We observed in hepatoblastomas a general disrupted expression of these genes from the epigenetic machinery, mainly UHRF1, TET1, and TET2 upregulation, in association with an enrichment of 5hmC content. Our findings support a model of active demethylation by TETs in hepatoblastoma, probably during early stages of liver development, which in combination with UHRF1 overexpression would lead to DNA hypomethylation and an increase in overall 5hmC content. Furthermore, our data suggest that decreased 5hmC content might be associated with poor survival rate, highlighting a pivotal role of epigenetics in hepatoblastoma development and progression.
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Affiliation(s)
- Maria Prates Rivas
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Talita Ferreira Marques Aguiar
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.,International Center of Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | | | - Luiz Carlos Caires-Júnior
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ernesto Goulart
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Kayque Alves Telles-Silva
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Monica Cypriano
- Department of Pediatrics, Support Group for Children and Adolescents With Cancer (GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | - Silvia Regina Caminada de Toledo
- Department of Pediatrics, Support Group for Children and Adolescents With Cancer (GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Dirce Maria Carraro
- International Center of Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | | | | | - Ana Cristina Victorino Krepischi
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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Aguiar TF, Barbosa-Teixeira AC, Costa SS, Ezquina S, Gimenez TM, Novak E, Cristofani LM, Rosenberg C, Odone Filho V, Krepischi ACV. Atypical presentation of a germline APC mutation in a child with supratentorial primitive neuroectodermal tumor. Pediatr Blood Cancer 2019; 66:e27566. [PMID: 30511453 DOI: 10.1002/pbc.27566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 10/23/2018] [Accepted: 10/25/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Talita Ferreira Aguiar
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Anne C Barbosa-Teixeira
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Silvia Souza Costa
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Suzana Ezquina
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Thamiris Magalhães Gimenez
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Estela Novak
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil.,Genética Molecular-Fundação Pró-Sangue, Hemocentro de São Paulo, São Paulo, Brazil
| | - Lilian Maria Cristofani
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Vicente Odone Filho
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
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de Oliveira JF, do Prado PFV, da Costa SS, Sforça ML, Canateli C, Ranzani AT, Maschietto M, de Oliveira PSL, Otto PA, Klevit RE, Krepischi ACV, Rosenberg C, Franchini KG. Mechanistic insights revealed by a UBE2A mutation linked to intellectual disability. Nat Chem Biol 2018; 15:62-70. [PMID: 30531907 DOI: 10.1038/s41589-018-0177-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 10/26/2018] [Indexed: 12/30/2022]
Abstract
Ubiquitin-conjugating enzymes (E2) enable protein ubiquitination by conjugating ubiquitin to their catalytic cysteine for subsequent transfer to a target lysine side chain. Deprotonation of the incoming lysine enables its nucleophilicity, but determinants of lysine activation remain poorly understood. We report a novel pathogenic mutation in the E2 UBE2A, identified in two brothers with mild intellectual disability. The pathogenic Q93E mutation yields UBE2A with impaired aminolysis activity but no loss of the ability to be conjugated with ubiquitin. Importantly, the low intrinsic reactivity of UBE2A Q93E was not overcome by a cognate ubiquitin E3 ligase, RAD18, with the UBE2A target PCNA. However, UBE2A Q93E was reactive at high pH or with a low-pKa amine as the nucleophile, thus providing the first evidence of reversion of a defective UBE2A mutation. We propose that Q93E substitution perturbs the UBE2A catalytic microenvironment essential for lysine deprotonation during ubiquitin transfer, thus generating an enzyme that is disabled but not dead.
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Affiliation(s)
| | | | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Mauricio Luis Sforça
- Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, Brazil
| | - Camila Canateli
- Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, Brazil
| | - Americo Tavares Ranzani
- Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, Brazil
| | - Mariana Maschietto
- Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, Brazil
| | | | - Paulo A Otto
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Kleber Gomes Franchini
- Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, Brazil. .,Department of Internal Medicine, School of Medicine, University of Campinas, Campinas, Brazil.
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Oliveira D, Leal GF, Sertié AL, Caires Jr LC, Goulart E, Musso CM, Oliveira JRMD, Krepischi ACV, Vianna-Morgante AM, Zatz M. 10q23.31 microduplication encompassing PTEN decreases mTOR signalling activity and is associated with autosomal dominant primary microcephaly. J Med Genet 2018; 56:543-547. [DOI: 10.1136/jmedgenet-2018-105471] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/07/2018] [Accepted: 08/29/2018] [Indexed: 01/15/2023]
Abstract
BackgroundHereditary primary microcephaly (MCPH) is mainly characterised by decreased occipitofrontal circumference and variable degree of intellectual disability. MCPH with a dominant pattern of inheritance is a rare condition, so far causally linked to pathogenic variants in the ALFY, DPP6, KIF11 and DYRK1A genes.ObjectiveThis study aimed at identifying the causative variant of the autosomal dominant form of MCPH in a Brazilian family with three affected members.MethodsFollowing clinical evaluation of two sibs and their mother presenting with autosomal dominant MCPH, array comparative genome hybridisation was performed using genomic DNA from peripheral blood of the family members. Gene and protein expression studies were carried out in cultured skin fibroblasts.ResultsA 382 kb microduplication at 10q23.31 was detected, encompassing the entire PTEN, KLLN and ATAD1 genes. PTEN haploinsufficiency has been causally associated with macrocephaly and autism spectrum disorder and, therefore, was considered the most likely candidate gene to be involved in this autosomal dominant form of MCPH. In the patients’ fibroblasts, PTEN mRNA and protein were found to be overexpressed, and the phosphorylation patterns of upstream and downstream components of the mammalian target of rapamycin (mTOR) signalling pathway were dysregulated.ConclusionsTaken together, our results demonstrate that the identified submicroscopic 10q23.31 duplication in a family with MCPH leads to markedly increased expression of PTEN and reduced activity of the mTOR signalling pathway. These results suggest that the most probable pathomechanism underlying the microcephaly phenotype in this family involves downregulation of the mTOR pathway through overexpression of PTEN.
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dos Santos A, Campagnari F, Krepischi ACV, Ribeiro Câmara MDL, de Arruda Brasil RDCE, Vieira L, Vianna-Morgante AM, Otto PA, Pearson PL, Rosenberg C. Insight into the mechanisms and consequences of recurrent telomere capture associated with a sub-telomeric deletion. Chromosome Res 2018; 26:191-198. [DOI: 10.1007/s10577-018-9578-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 11/28/2022]
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Krepischi ACV. Revisitando a origem cromossômica do câncer: aneuploidias promovem ou suprimem o processo tumorigênico? Semin Cienc Biol Saude 2018. [DOI: 10.5433/1679-0367.2017v38n1suplp34] [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] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Alterações citogenéticas que modificam o número de cópias cromossômicas (aneuploidias) são marca do câncer. Entretanto, o papel das aneuploidias no início e na progressão tumoral ainda não é totalmente elucidado. Parte da dificuldade no estudo de seu efeito provém do conjunto complexo e diverso de anormalidades cromossômicas dos diferentes tipos de tumores. Evidências recentes mostram que aneuloidias poderiam agir para antagonizar a tumorigênese em certos contextos genômicos. Ao contrário de mutações de ponto, que afetam poucos genes, ganho ou perda de um cromossomo altera a transcrição de centenas de genes, com potencial de perturbar grande variedade de processos celulares; tal desequilíbrio confere um estresse celular que pode dificultar a sobrevivência e multiplicação de células aneuplóides. Assim, em circunstâncias normais, a aneuploidia age como barreira que suprime a tumorigênese, reduzindo o crescimento de células pré-neoplásicas. No entanto, aneuploidia é uma característica sabidamente comum nos tumores, tendo sido associada à progressão tumoral. Como a aneuploidia poderia promover tumorigênese em certos contextos? Uma hipótese é que a ocorrência da aneuploidia induziria a célula a acumular mutações para superar o efeito negativo do ganho/perda cromossômico, levando assim na célula adaptada à liberação de um potencial oncogênico, que poderia se manter ativo. Estudamos uma coorte de hepatoblastomas (HB), tumores embrionários de fígado, por array-CGH e sequenciamento massivo paralelo (NGS), assim como linhagens celulares de tumores hepáticos. A caracterização citogenômica dos carcinomas hepatocelulares mostrou genomas complexos com muitas alterações cromossômicas, em contraste com o background cromossômico estável dos tumores embrionários, que exibiam principalmente aneuploidias, com prevalência de ganhos. Nossos dados sugerem que alterações cromossômicas desempenham papel limitado na tumorigênese do HB, com efeito mais associado ao processo de aquisição de cromossomos inteiros do que à amplificação de oncogenes ou perda de supressores tumorais. O efeito da aneuploidia ocorreria não por uma combinação particular de cromossomos per se, mas pela interação específica do cariótipo com vários contextos genéticos/epigenéticos.
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Cavalcante de Andrade Silva M, Krepischi ACV, Kulikowski LD, Zanardo EA, Nardinelli L, Leal AM, Costa SS, Muto NH, Rocha V, Velloso EDRP. Deletion of RUNX1 exons 1 and 2 associated with familial platelet disorder with propensity to acute myeloid leukemia. Cancer Genet 2018; 222-223:32-37. [PMID: 29666006 DOI: 10.1016/j.cancergen.2018.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 07/14/2017] [Accepted: 01/16/2018] [Indexed: 01/01/2023]
Abstract
Familial platelet disorder with propensity to acute myeloid leukemia (FPD/AML) associated with RUNX1 mutations is an autosomal dominant disorder included in the group of the myeloid neoplasms with germ line predisposition. We describe two brothers who were diagnosed with hematological malignancies (one with AML and the other with T-cell lymphoblastic lymphoma). There was a history of leukemia in the paternal family and two of their siblings presented with low platelet counts and no history of significant bleeding. A microdeletion encompassing exons 1-2 of RUNX1 (outside the cluster region of the Runt Homology domain and the transactivation domain) was detected in six family members using array-CGH and MLPA validation. A low platelet count was not present in all deletion carriers and, therefore, it should not be used as an indication for screening in suspected families and family members.
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Affiliation(s)
- Marcela Cavalcante de Andrade Silva
- Departamento de Hematologia, Laboratório de Citogenética, Hospital das Clinicas HCFMUSP, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR Av. Dr. Eneas de Carvalho 255, Cerqueira César 01246-000, São Paulo, SP, Brazil.
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP, Brazil Rua do Matão, 321, Butantã, 05508-090, São Paulo, SP, Brazil.
| | - Leslie Domenici Kulikowski
- Departamento de Patologia, Laboratorio de Citogenomica do LIM 03, Hospital das Clinicas HCFMUSP, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR. Av. Dr. Eneas de Carvalho 255, Cerqueira César 01246-000, São Paulo, SP, Brazil.
| | - Evelin Aline Zanardo
- Departamento de Patologia, Laboratorio de Citogenomica do LIM 03, Hospital das Clinicas HCFMUSP, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR. Av. Dr. Eneas de Carvalho 255, Cerqueira César 01246-000, São Paulo, SP, Brazil
| | - Luciana Nardinelli
- Departamento de Hematologia, Laboratório Biologia Tumoral, Hospital das Clinicas HCFMUSP, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR Av. Dr. Eneas de Carvalho 255, Cerqueira César 01246-000, São Paulo, SP, Brazil
| | - Aline Medeiros Leal
- Departamento de Hematologia, Laboratório de Citogenética, Hospital das Clinicas HCFMUSP, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR Av. Dr. Eneas de Carvalho 255, Cerqueira César 01246-000, São Paulo, SP, Brazil
| | - Silvia Souza Costa
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP, Brazil Rua do Matão, 321, Butantã, 05508-090, São Paulo, SP, Brazil
| | - Nair Hideki Muto
- Hospital Israelita Albert Einstein. Av. Albert Einstein, 627/701 Morumbi 05652- 900 - São Paulo, SP, Brazil.
| | - Vanderson Rocha
- Departamento de Hematologia, Laboratório de Citogenética, Hospital das Clinicas HCFMUSP, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR Av. Dr. Eneas de Carvalho 255, Cerqueira César 01246-000, São Paulo, SP, Brazil; Departamento de Hematologia, Laboratório Biologia Tumoral, Hospital das Clinicas HCFMUSP, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR Av. Dr. Eneas de Carvalho 255, Cerqueira César 01246-000, São Paulo, SP, Brazil
| | - Elvira Deolinda Rodrigues Pereira Velloso
- Departamento de Hematologia, Laboratório de Citogenética, Hospital das Clinicas HCFMUSP, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR Av. Dr. Eneas de Carvalho 255, Cerqueira César 01246-000, São Paulo, SP, Brazil; Hospital Israelita Albert Einstein. Av. Albert Einstein, 627/701 Morumbi 05652- 900 - São Paulo, SP, Brazil.
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Mangone FR, Krepischi ACV, Nonogaki S, Carraro DM, Nagai MA. Abstract A02: Potential role of SMC6 downregulation as an indicator of tumor genetic instability in breast cancer. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.tcm17-a02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Genetic instability is a common feature of cancer. Homologous recombination (HR) is involved in one of the major mechanisms of DNA double strand break repair (DSB) and depends on the formation of Holliday junctions (HJ) that should be solved for the maintenance of genomic stability. Deregulation of HR control mechanisms results in DNA damage. Data from the literature has shown that SMC6 complexed with SMC5 is involved in DSB repair. Previous sequencing data from our group showed the occurrence of some SMC6 genetic variants in sporadic breast cancer. In the present study, we sought to investigate a possible association between SMC6 expression level and genomic instability in breast cancer. SMC6 mRNA expression pattern determined by qRT-PCR and Copy Number Variation (CNV) data obtained by using whole-genome comparative genomic hybridization on microarrays, were determined in a cohort of 33 breast cancer samples of women who did not carry BRCA1/BRCA2 mutations. SMC6 protein expression was carried out in a tissue micro-array containing breast cancers samples. Statistical analyses were performed by using SPSS Software 20. Data comparison revealed that tumors with higher SMC6 mRNA expression showed a trend toward lower median numbers of total CNVs per genome, corroborating the role of SMC6 genomic stability maintenance. SMC6 protein expression was tested in a panel of 74 breast cancer tumors, and cases were classified into two groups: SMC6 negative (negative to weak nuclear staining) and SMC6 positive (moderate to strong nuclear staining). No association among SMC6 staining and clinic-pathologic features was observed. However, patients with SMC6 negative tumors had a trend to a shorter disease-free survival (DFS) and overall survival (OS) than those with SMC6 positive tumors (median DFS 29.0 vs. 172.0 months, Log Rank = 0.123 and median OS 30.47 vs. 153.30 months, Log Rank = 0.117). Although preliminary, our findings point to a possible association between SMC6 downregulation and poor outcome of patients, suggesting theatSMC6 may serve as an indicator of tumor genetic instability for patients with breast cancer. Supported by Fapesp and CNPq.
Citation Format: Flavia Rotea Mangone, Ana Cristina Victorino Krepischi, Suely Nonogaki, Dirce Maria Carraro, Maria Aparecida Nagai. Potential role of SMC6 downregulation as an indicator of tumor genetic instability in breast cancer [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A02.
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Affiliation(s)
- Flavia Rotea Mangone
- 1Center for Translational Research in Oncology (CTO), Cancer Institute of São Paulo (ICESP), São Paulo, SP, Brazil,
| | | | - Suely Nonogaki
- 3Anatomic Pathology, A.C. Camargo Cancer Center, Sao Paulo, SP, Brazil,
| | - Dirce Maria Carraro
- 2National Institute of Science and Technology in Oncogenomics, A.C. Camargo Cancer Center, São Paulo, SP, Brazil,
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Ferreira EN, Barros BDF, de Souza JE, Almeida RV, Torrezan GT, Garcia S, Krepischi ACV, Mello CALD, Cunha IWD, Pinto CAL, Soares FA, Dias-Neto E, Lopes A, de Souza SJ, Carraro DM. A genomic case study of desmoplastic small round cell tumor: comprehensive analysis reveals insights into potential therapeutic targets and development of a monitoring tool for a rare and aggressive disease. Hum Genomics 2016; 10:36. [PMID: 27863505 PMCID: PMC5116179 DOI: 10.1186/s40246-016-0092-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/17/2016] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Genome-wide profiling of rare tumors is crucial for improvement of diagnosis, treatment, and, consequently, achieving better outcomes. Desmoplastic small round cell tumor (DSRCT) is a rare type of sarcoma arising from mesenchymal cells of abdominal peritoneum that usually develops in male adolescents and young adults. A specific translocation, t(11;22)(p13;q12), resulting in EWS and WT1 gene fusion is the only recurrent molecular hallmark and no other genetic factor has been associated to this aggressive tumor. Here, we present a comprehensive genomic profiling of one DSRCT affecting a 26-year-old male, who achieved an excellent outcome. METHODS We investigated somatic and germline variants through whole-exome sequencing using a family based approach and, by array CGH, we explored the occurrence of genomic imbalances. Additionally, we performed mate-paired whole-genome sequencing for defining the specific breakpoint of the EWS-WT1 translocation, allowing us to develop a personalized tumor marker for monitoring the patient by liquid biopsy. RESULTS We identified genetic variants leading to protein alterations including 12 somatic and 14 germline events (11 germline compound heterozygous mutations and 3 rare homozygous polymorphisms) affecting genes predominantly involved in mesenchymal cell differentiation pathways. Regarding copy number alterations (CNA) few events were detected, mainly restricted to gains in chromosomes 5 and 18 and losses at 11p, 13q, and 22q. The deletions at 11p and 22q indicated the presence of the classic translocation, t(11;22)(p13;q12). In addition, the mapping of the specific genomic breakpoint of the EWS-WT1 gene fusion allowed the design of a personalized biomarker for assessing circulating tumor DNA (ctDNA) in plasma during patient follow-up. This biomarker has been used in four post-treatment blood samples, 3 years after surgery, and no trace of EWS-WT1 gene fusion was detected, in accordance with imaging tests showing no evidence of disease and with the good general health status of the patient. CONCLUSIONS Overall, our findings revealed genes with potential to be associated with risk assessment and tumorigenesis of this rare type of sarcoma. Additionally, we established a liquid biopsy approach for monitoring patient follow-up based on genomic information that can be similarly adopted for patients diagnosed with a rare tumor.
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Affiliation(s)
| | | | | | | | | | - Sheila Garcia
- International Research Center/CIPE, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | | | | | | | | | | | - Emmanuel Dias-Neto
- International Research Center/CIPE, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Ademar Lopes
- Departament of Abdominal Surgery, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | | | - Dirce Maria Carraro
- International Research Center/CIPE, A.C. Camargo Cancer Center, São Paulo, SP, Brazil.
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Mariano FV, Egal ES, Pramio D, Fidalgo F, Sara É, Costa AF, de Oliveira Gondak R, Coletta RD, de Almeida OP, Kowalski LP, Victorino Krepischi AC, Altemani A. Evaluation of a subset of tumor suppressor gene for copy number and epigenitic changes in pleomorphic adenoma and carcinoma ex-pleomorphic adenoma carcinogenesis. Oral Surg Oral Med Oral Pathol Oral Radiol 2016; 122:322-31. [PMID: 27544395 DOI: 10.1016/j.oooo.2016.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 04/19/2016] [Accepted: 05/04/2016] [Indexed: 12/24/2022]
Abstract
OBJECTIVE The progression of pleomorphic adenoma (PA) to carcinoma ex-pleomorphic adenoma (CXPA) encompasses several genomic alterations involving complex pathways. Tumor suppressor genes seem to play important roles in the tumorigenesis of both tumors. The aim of this study was to evaluate copy number and methylation of tumor suppressor genes' status in PA and CXPA samples. STUDY DESIGN Eight cases of PA, 2 cases of residual PA in CXPA, and 5 cases of CXPA were studied; the latter were classified according to invasiveness and histopathological subtype. Changes in 41 tumor suppressor genes were evaluated by multiplex ligation-probe dependent amplification analysis. RESULTS Copy number losses of CASP8, MLH1, and RARB genes were associated with PA and CXPA, while KLK3 and AI69125 copy number losses were exclusive to CXPA. The sarcomatoid carcinoma showed more copy number alterations compared with other subtypes. Hypermethylation of RASSF1 was found mainly in PA and less frequently in malignant tumors. CONCLUSIONS CASP8, MLH1, and RARB tumor suppressor genes were altered by copy number losses during PA progression to CXPA. Lastly, RASSF1 inactivation by methylation was also detected in both tumors.
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Affiliation(s)
| | - Erika Said Egal
- Pathology Department, Faculty of Medical Sciences, UNICAMP, São Paulo, Brazil
| | - Dimitrius Pramio
- Medical Genomics Group, AC Camargo Cancer Center, São Paulo, Brazil
| | - Felipe Fidalgo
- Medical Genomics Group, AC Camargo Cancer Center, São Paulo, Brazil
| | - Érica Sara
- Medical Genomics Group, AC Camargo Cancer Center, São Paulo, Brazil
| | - Ana Flávia Costa
- Medical Genomics Group, AC Camargo Cancer Center, São Paulo, Brazil
| | | | | | | | - Luiz Paulo Kowalski
- Head and Neck and Otorhinolaryngology Surgery Department, AC Camargo Cancer Center, São Paulo, Brazil
| | | | - Albina Altemani
- Pathology Department, Faculty of Medical Sciences, UNICAMP, São Paulo, Brazil
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Fidalgo F, Rodrigues TC, Silva AG, Facure L, de Sá BCS, Duprat JP, Achatz MI, Rosenberg C, Carraro DM, Krepischi ACV. Role of rare germline copy number variation in melanoma-prone patients. Future Oncol 2016; 12:1345-57. [PMID: 27020340 DOI: 10.2217/fon.16.22] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM This work evaluates a possible causative role for germline copy number variants (CNVs) in melanoma predisposition. PATIENTS & METHODS A total of 41 melanoma-prone Brazilian patients were investigated for CNVs using 850K single nucleotide polymorphism arrays. RESULTS Ten rare CNVs were identified in nine patients, comprising 54 known genes, mostly related to cancer. In silico analyses revealed gene enrichment for cellular development and growth, and proliferation, highlighting five genes directly associated with the melanoma phenotype (ANGPT1, IDH1, PDE5A, HIST1H1B and GCNT2). CONCLUSION Patients harboring rare CNVs exhibited a decreased age of disease onset, in addition to an overall higher skin cancer predisposition. Our findings suggest that rare CNVs contribute to melanoma susceptibility, and should be taken into account when investigating cancer risk factors.
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Affiliation(s)
- Felipe Fidalgo
- International Research Center, AC Camargo Cancer Center, São Paulo, Brazil
| | - Tatiane Cristina Rodrigues
- Department of Genetics & Evolutionary Biology, Institute of Biosciences, University of São Paulo, Brazil
| | - Amanda Gonçalves Silva
- Department of Genetics & Evolutionary Biology, Institute of Biosciences, University of São Paulo, Brazil
| | - Luciana Facure
- Department of Skin Cancer, AC Camargo Cancer Center, São Paulo, Brazil
| | | | | | | | - Carla Rosenberg
- Department of Genetics & Evolutionary Biology, Institute of Biosciences, University of São Paulo, Brazil
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Mariano FV, Saccomani LFV, Giovanetti K, Del Negro A, Kowalski LP, Krepischi ACV, Altemani A. Genomic profile of a squamous cell carcinoma ex pleomorphic adenoma compared to a head and neck squamous cell carcinoma. Braz J Otorhinolaryngol 2016; 84:393-397. [PMID: 26971044 PMCID: PMC9449223 DOI: 10.1016/j.bjorl.2015.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/13/2015] [Indexed: 11/20/2022] Open
Affiliation(s)
- Fernanda Viviane Mariano
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patologia, Campinas, SP, Brazil.
| | - Luis Fernando Vidal Saccomani
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patologia, Campinas, SP, Brazil
| | - Karina Giovanetti
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patologia, Campinas, SP, Brazil
| | - André Del Negro
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Cirurgia de Cabeça e Pescoço, Campinas, SP, Brazil
| | - Luiz Paulo Kowalski
- AC Camargo Cancer Center, Departamento de Cirurgia de Cabeça e Pescoço, São Paulo, SP, Brazil
| | - Ana Cristina Victorino Krepischi
- Universidade de São Paulo (UNIFESP), Instituto de Biociências, Departamento de Genética e Biologia Evolucionária, São Paulo, SP, Brazil
| | - Albina Altemani
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patologia, Campinas, SP, Brazil
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Mariano FV, Giovanetti K, Saccomani LFV, Del Negro A, Kowalski LP, Krepischi ACV, Altemani A. Carcinoma ex-pleomorphic adenoma derived from recurrent pleomorphic adenoma shows important difference by array CGH compared to recurrent pleomorphic adenoma without malignant transformation. Braz J Otorhinolaryngol 2016; 82:687-694. [PMID: 26971045 PMCID: PMC9444750 DOI: 10.1016/j.bjorl.2015.12.004] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 12/08/2015] [Indexed: 11/08/2022] Open
Abstract
Introduction A key step of cancer development is the progressive accumulation of genomic changes resulting in disruption of several biological mechanisms. Carcinoma ex-pleomorphic adenoma (CXPA) is an aggressive neoplasm that arises from a pleomorphic adenoma. CXPA derived from a recurrent PA (RPA) has been rarely reported, and the genomic changes associated with these tumors have not yet been studied. Objective We analyzed CXPA from RPAs and RPAs without malignant transformation using array-comparative genomic hybridization (array-CGH) to identify somatic copy number alterations and affected genes. Methods DNA samples extracted from FFPE tumors were submitted to array-CGH investigation, and data was analyzed by Nexus Copy Number Discovery Edition v.7. Results No somatic copy number alterations were found in RPAs without malignant transformation. As for CXPA from RPA, although genomic profiles were unique for each case, we detected some chromosomal regions that appear to be preferentially affected by copy number alterations. The first case of CXPA-RPA (frankly invasive myoepithelial carcinoma) showed copy number alterations affecting 1p36.33p13, 5p and chromosomes 3 and 8. The second case of CXPA-RPA (frankly invasive epithelial-myoepithelial carcinoma) showed several alterations at chromosomes 3, 8, and 16, with two amplifications at 8p12p11.21 and 12q14.3q21.2. The third case of CXPA-RPA (minimally invasive epithelial-myoepithelial carcinoma) exhibited amplifications at 12q13.3q14.1, 12q14.3, and 12q15. Conclusion The occurrence of gains at chromosomes 3 and 8 and genomic amplifications at 8p and 12q, mainly those encompassing the HMGA2, MDM2, WIF1, WHSC1L1, LIRG3, CDK4 in CXAP from RPA can be a significant promotional factor in malignant transformation.
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Affiliation(s)
- Fernanda Viviane Mariano
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patologia, Campinas, SP, Brazil.
| | - Karina Giovanetti
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patologia, Campinas, SP, Brazil
| | - Luis Fernando Vidal Saccomani
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patologia, Campinas, SP, Brazil
| | - André Del Negro
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Cirurgia de Cabeça e Pescoço, Campinas, SP, Brazil
| | - Luiz Paulo Kowalski
- AC Camargo Câncer Center, Departamento de Cirurgia de Cabeça e Pescoço, São Paulo, SP, Brazil
| | | | - Albina Altemani
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Patologia, Campinas, SP, Brazil
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Rodrigues TC, Fidalgo F, da Costa CML, Ferreira EN, da Cunha IW, Carraro DM, Krepischi ACV, Rosenberg C. Upregulated genes at 2q24 gains as candidate oncogenes in hepatoblastomas. Future Oncol 2015; 10:2449-57. [PMID: 25525853 DOI: 10.2217/fon.14.149] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
AIM Cytogenetic data of hepatoblastomas, a rare embryonal tumor of the liver, mostly consist of descriptions of whole-chromosome aneuploidies and large chromosome alterations. High-resolution cytogenetics may provide clues to hepatoblastoma tumorigenesis and indicate markers with clinical significance. PATIENTS & METHODS We used array-CGH (180K) to screen for genomic imbalances in nine hepatoblastomas. Additionally, we investigated the expression pattern of selected genes exhibiting copy number changes. RESULTS Analysis showed mainly whole-chromosome or chromosome-arm aneuploidies, but some focal aberrations were also mapped. Expression analysis of 48 genes mapped at one 10 Mb amplification at 2q24 revealed upregulation of DAPL1, ERMN, GALNT5, SCN1A and SCN3A in the set of tumors compared with differentiated livers. CONCLUSION These genes appear as candidates for hepatoblastoma tumorigenesis.
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Affiliation(s)
- Tatiane Cristina Rodrigues
- Department of Genetics & Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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Fidalgo F, Rodrigues TC, Pinilla M, Silva AG, Maciel MDS, Rosenberg C, de Andrade VP, Carraro DM, Krepischi ACV. Lymphovascular invasion and histologic grade are associated with specific genomic profiles in invasive carcinomas of the breast. Tumour Biol 2015; 36:1835-48. [PMID: 25391423 PMCID: PMC4375298 DOI: 10.1007/s13277-014-2786-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 10/29/2014] [Indexed: 12/28/2022] Open
Abstract
Lymphovascular invasion (LVI) and histologic grade are clinical parameters of high prognostic value in breast cancer and indicate the level of tumor aggressiveness. Many studies have focused on the association of breast cancer subtypes with gene expression and chromosomal profiles, but considerably less genomic information is available regarding traditional prognostic factors such as histologic grade and LVI. We studied by array-CGH a group of 57 invasive ductal carcinomas of the breast to outline the DNA copy number aberration (CNA) profile linked to high histologic grades and LVI. Selected CNAs were validated using real-time quantitative PCR (qPCR). Furthermore, gene expression analysis was performed in a subset of 32 of these tumors, and findings were integrated with array-CGH data. Our findings indicated an accumulation of genomic alterations in high-grade breast tumors compared to low-grade samples. Grade III tumors showed higher number of CNAs and larger aberrations than low-grade tumors and displayed a wide range of chromosomal aberrations, which were mainly 5p, 8q, 10p, 17q12, and 19 gains, and 3p, 4, 5q proximal, 9p, 11p, 18q, and 21 losses. The presence of LVI, a well-established prognostic marker, was not significantly associated with increased genomic instability in comparison to breast tumors negative for LVI, considering the total number of chromosomal alterations. However, a slightly increase in the frequency of specific alterations could be detected in LVI-positive group, such as gains at 5p, 16p, 17q12, and 19, and losses at 8p, 11q, 18q, and 21. Three newly reported small-scale rearrangements were detected in high-risk tumors (LVI-positive grade III) harboring putative breast cancer genes (amplicons at 4q13.3 and 11p11.2, and a deletion at 12p12.3). Furthermore, gene expression analysis uncovered networks highlighting S100A8, MMP1, and MED1 as promising candidate genes involved in high-grade and LVI-positive tumors. In summary, a group of genomic regions could be associated with high-risk tumors, and expression analysis pinpointed candidate genes deserving further investigation. The data has shed some light on the molecular players involved in two highly relevant prognostic factors and may further add to the understanding of the mechanisms of breast cancer aggressiveness.
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Affiliation(s)
- Felipe Fidalgo
- International Research Center, AC Camargo Cancer Center, São Paulo, Brazil
| | - Tatiane Cristina Rodrigues
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Mabel Pinilla
- International Research Center, AC Camargo Cancer Center, São Paulo, Brazil
| | - Amanda Gonçalves Silva
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Victor Piana de Andrade
- Department of Surgical and Investigative Pathology, AC Camargo Cancer Center, São Paulo, Brazil
| | | | - Ana Cristina Victorino Krepischi
- International Research Center, AC Camargo Cancer Center, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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Mariano FV, Gondak RDO, Martins AS, Coletta RD, Paes de Almeida O, Kowalski LP, Krepischi ACV, Altemani A. Genomic copy number alterations of primary and secondary metastasizing pleomorphic adenomas. Histopathology 2015; 67:410-5. [PMID: 25600428 DOI: 10.1111/his.12655] [Citation(s) in RCA: 4] [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: 10/27/2014] [Accepted: 01/13/2015] [Indexed: 12/18/2022]
Abstract
AIMS Metastasizing pleomorphic adenoma (MPA) is a rare tumour, and its mechanism of metastasis still is unknown. To date, there has been no study on MPA genomics. We analysed primary and secondary MPAs with array comparative genomic hybridization to identify somatic copy number alterations and affected genes. METHODS AND RESULTS Tumour DNA samples from primary (parotid salivary gland) and secondary (scalp skin) MPAs were subjected to array comparative genomic hybridization investigation, and the data were analysed with NEXUS COPY NUMBER DISCOVERY. The primary MPA showed copy number losses affecting 3p22.2p14.3 and 19p13.3p123, and a complex pattern of four different deletions at chromosome 6. The 3p deletion encompassed several genes: CTNNB1, SETD2, BAP1, and PBRM1, among others. The secondary MPA showed a genomic profile similar to that of the primary MPA, with acquisition of additional copy number changes affecting 9p24.3p13.1 (loss), 19q11q13.43 (gain), and 22q11.1q13.33 (gain). CONCLUSION Our findings indicated a clonal origin of the secondary MPA, as both tumours shared a common profile of genomic copy number alterations. Furthermore, we were able to detect in the primary tumour a specific pattern of copy number alterations that could explain the metastasizing characteristic, whereas the secondary MPA showed a more unbalanced genome.
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Affiliation(s)
- Fernanda Viviane Mariano
- Pathology Department, Faculty of Medicine, State University of Campinas (UNICAMP), Campinas, Brazil
| | | | | | | | | | - Luiz Paulo Kowalski
- Head and Neck Surgery Department, AC Camargo Cancer Center, São Paulo, Brazil
| | | | - Albina Altemani
- Pathology Department, Faculty of Medicine, State University of Campinas (UNICAMP), Campinas, Brazil
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