1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Petrilli AS, Carneiro Jr. JL, Cypriano M, Angel A, Toledo S. Diferenças clínicas, epidemiológicas e biológicas entre o câncer na criança e no adulto. Rev Bras Cancerol 2022. [DOI: 10.32635/2176-9745.rbc.1997v43n3.2853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
O câncer representa hoje a primeira causa de morte por doença entre a população de faixa etária compreendida entre 1 e 21 anos nos Estados Unidos e em outros países economicamente desenvolvidos. No Brasil, esta doença figura como a terceira causa de morte por doença entre a população de faixa etária compreendida entre 1 e 14 anos, sendo já a primeira causa de óbito no município e no estado de São Paulo no grupo etário compreendido entre 5 e 14 anos, excluindo-se acidentes e causas externas. O objetivo deste artigo é informar a classe médica, principalmente a pediátrica, das particularidades do câncer infantil e de suas diferenças com as formas dos adultos, mais conhecidas e frequentes. Graças à moderna abordagem multidisciplinar, o câncer infantil pode atingir índices de cura de 60% a 70%, mas, para tal, é imprescindível o diagnóstico precoce. Portanto, é importante que toda a comunidade pediátrica mostre-se motivada e informada sobre os sinais e sintomas das neoplasias pediátricas, já que não dispomos de métodos de “screening” tão úteis e eficazes como para o controle do câncer do adulto.
Collapse
|
3
|
Aguiar T, Teixeira A, Scliar MO, Sobral de Barros J, Lemes RB, Souza S, Tolezano G, Santos F, Tojal I, Cypriano M, Caminada de Toledo SR, Valadares E, Borges Pinto R, Pinto Artigalas OA, Caetano de Aguirre Neto J, Novak E, Cristofani LM, Miura Sugayama SM, Odone V, Cunha IW, Lima da Costa CM, Rosenberg C, Krepischi A. Unraveling the Genetic Architecture of Hepatoblastoma Risk: Birth Defects and Increased Burden of Germline Damaging Variants in Gastrointestinal/Renal Cancer Predisposition and DNA Repair Genes. Front Genet 2022; 13:858396. [PMID: 35495172 PMCID: PMC9039399 DOI: 10.3389/fgene.2022.858396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/08/2022] [Indexed: 12/21/2022] Open
Abstract
The ultrarare hepatoblastoma (HB) is the most common pediatric liver cancer. HB risk is related to a few rare syndromes, and the molecular bases remain elusive for most cases. We investigated the burden of rare damaging germline variants in 30 Brazilian patients with HB and the presence of additional clinical signs. A high frequency of prematurity (20%) and birth defects (37%), especially craniofacial (17%, including craniosynostosis) and kidney (7%) anomalies, was observed. Putative pathogenic or likely pathogenic monoallelic germline variants mapped to 10 cancer predisposition genes (CPGs: APC, CHEK2, DROSHA, ERCC5, FAH, MSH2, MUTYH, RPS19, TGFBR2 and VHL) were detected in 33% of the patients, only 40% of them with a family history of cancer. These findings showed a predominance of CPGs with a known link to gastrointestinal/colorectal and renal cancer risk. A remarkable feature was an enrichment of rare damaging variants affecting different classes of DNA repair genes, particularly those known as Fanconi anemia genes. Moreover, several potentially deleterious variants mapped to genes impacting liver functions were disclosed. To our knowledge, this is the largest assessment of rare germline variants in HB patients to date, contributing to elucidate the genetic architecture of HB risk.
Collapse
Affiliation(s)
- Talita Aguiar
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Columbia University Irving Medical Center, New York, NY, United States
| | - Anne Teixeira
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Marília O. Scliar
- 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, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Renan B. Lemes
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Silvia Souza
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Giovanna Tolezano
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Fernanda Santos
- Department of Pediatric Oncology, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Israel Tojal
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Monica Cypriano
- GRAACC—Grupo de Apoio Ao Adolescente e Criança Com Câncer, Federal University of São Paulo, São Paulo, Brazil
| | | | - Eugênia Valadares
- Benjamim Guimarães Foundation - Department of Pediatrics Hospital da Baleia, Belo Horizonte, Brazil
| | - Raquel Borges Pinto
- Department of Genetics, Hospital da Criança Conceição, Hospitalar Conceição Group, Porto Alegre, Brazil
| | | | | | - Estela Novak
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
- Molecular Genetics—Foundation Pro Sangue Blood Center of São Paulo, São Paulo, Brazil
| | - Lilian Maria Cristofani
- Pediatric Cancer Institute (ITACI) at the Pediatric Department, São Paulo University Medical School, São Paulo, Brazil
| | - Sofia M. Miura Sugayama
- Department of Pediatric, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Vicente Odone
- 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
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- *Correspondence: Ana Krepischi,
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Rivas M, Aguiar T, Fernandes G, Lemes R, Caires-Júnior L, Goulart E, Telles-Silva K, Maschietto M, Cypriano M, de Toledo S, Carraro D, da Cunha I, da Costa C, Rosenberg C, Krepischi A. DNA methylation as a key epigenetic player for hepatoblastoma characterization. Clin Res Hepatol Gastroenterol 2021; 45:101684. [PMID: 33852955 DOI: 10.1016/j.clinre.2021.101684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Received: 06/29/2020] [Revised: 03/04/2021] [Accepted: 03/18/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND Hepatoblastoma (HB) is a rare embryonal liver tumor of children. Although intrinsic biological differences between tumors can affect prognosis, few groups have studied these differences. Given the recent increased attention to epigenetic mechanisms in the genesis and progression of these tumors, we aimed to classify HB samples according to the stages of liver development and DNA methylation machinery. BASIC PROCEDURES We evaluated the expression of 24 genes associated with DNA methylation and stages of hepatocyte differentiation and global DNA methylation. Using bioinformatics tools and expression data, we propose a stratification model for HB. MAIN FINDINGS Tumors clustered into three groups that presented specific gene expression profiles of the panel of DNA methylation enzymes and hepatocyte differentiation markers. In addition to reinforcing these embryonal tumors' molecular heterogeneity, we propose that a panel of 13 genes can stratify HBs (TET1, TET2, TET3, DNMT1, DNMT3A, UHRF1, ALB, CYP3A4, TDO2, UGT1A1, AFP, HNF4A, and FOXA2). DNA methylation machinery participates in the characterization of HBs, directly reflected in diverse DNA methylation content. The data suggested that a subset of HBs were similar to differentiated livers, with upregulation of mature hepatocyte markers, decreased expression of DNA methylation enzymes, and higher global methylation levels; these findings might predict worse outcomes. CONCLUSIONS HBs are heterogeneous tumors. Despite using a small cohort of 21 HB samples, our findings reinforce that DNA methylation is a robust biomarker for this tumor type.
Collapse
Affiliation(s)
- Maria Rivas
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Talita Aguiar
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil; Department of Urology - NYU Grossman School of Medicine, New York City, NY, USA
| | - Gustavo Fernandes
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Renan Lemes
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Luiz Caires-Júnior
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, 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, SP, Brazil
| | - Kayque Telles-Silva
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | | | - Monica Cypriano
- Department of Pediatrics, Adolescent and Child with Cancer Support Group (GRAACC), Federal University of São Paulo, SP, Brazil
| | - Silvia de Toledo
- Department of Pediatrics, Adolescent and Child with Cancer Support Group (GRAACC), Federal University of São Paulo, SP, Brazil
| | - Dirce Carraro
- International Center for Research, A. C. Camargo Cancer Center, SP, Brazil
| | | | - Cecilia da Costa
- Department of Pediatric Oncology, A. C. Camargo Cancer Center, 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
| | - Ana 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.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Aguiar TF, Rodrigues T, Prates M, Santos FAD, Fernandes G, Costa CMLD, Cunha IWD, Cypriano M, Toledo SRCD, Souza JESD, Valadares E, Borges R, Odone V, Tojal I, Carraro D, Rosenberg C, Krepischi AC. Abstract 2072: Genomic studies of Brazilian patients with hepatoblastoma: Insight into somatic mutations using whole-exome sequencing. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2072] [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
Hepatoblastomas (HB) are embryonal tumors of the liver with histological features that resemble different stages of liver differentiation. The identification of molecular pathways involved in HB development can expand the understanding of the connections between disruption of normal differentiation and cancer. Exome sequencing (244K Agilent SureSelect Target Enrichment) analysis was performed for 6 HBs matched with their non tumoral liver tissues (fresh frozen tissues). Bioinformatic analysis of exome data identified somatic variants in 69 genes which were chosen for validation using a target sequencing panel (SureSelectXT Target Enrichment System for Illumina Paired-End Sequencing Library). The gene panel was composed of the detected 69 genes and other 48 genes related with HB or cancer, and it was used to investigated additional 13 HB samples as a validation group. 60% of the patients were male, and the mean age at diagnosis was 36 months. 13% of this cohort presented pulmonary metastasis. All patients received pre-surgery chemotherapy (SIOPEL and COG protocol).
Results: A total of 71 somatic rare coding mutations (missense and loss-of-function) were validated in 53 genes considering the entire HB group. The somatic analysis reveals pathogenic mutations in the CTNNB1 gene and a recurrent missense mutation in the CX3CL1 gene; the role of these mutations was explored by IHQ studies of their proteins as well as by gene expression analysis by RT-PCR. We also used results from Illumina 450k to evaluated the methylation levels of CX3CL1 and CX3CR1 genes. Methylation values for CpG sites in each sample were measured as β-and CpG sites were grouped into categories, promoter (1stExon; 5'UTR; TSS1500; TSS200) or gene body, information provided by Illumina, based on UCSC data (GRhC 37). The methylation level of each category was obtained by averaging the β-values of all CpGs mapped in the category for each gene, followed by Wilcoxon test correction by calculating the false discovery rate (FDR).
Conclusion: Most investigated HBs carry few potentially pathogenic genetic mutations (≤ 5 mutations). This observed low frequency of somatic mutations is a result similar to previous studies. The proposed explanation is based on the fact that pediatric tumors would originate from precursor cells with pluripotent characteristics; therefore, such tumors may require fewer mutations than adult solid tumors to develop. The congenital HB case of our cohort is discrepant from this scenario since a relatively high number of somatic mutations were found compared to the HB group. To our knowledge, this is the first comprehensive genomic characterization of Brazilian HBs. Next steps include expanding the casuistry of exome sequenced tumors, including two cases of HB associated with Hirschprung disease.
Grants: FAPESP (2016/04785-0; 2017/11212-0), FAPESP (2013/08028-1), CNPq (141625/2016-3).
Citation Format: Talita F. Aguiar, Tatiane Rodrigues, Maria Prates, Fernanda Aparecida dos Santos, Gustavo Fernandes, Cecília Maria Lima da Costa, Isabela Werneck da Cunha, Monica Cypriano, Silvia Regina Caminada de Toledo, Jorge Estefano S. de Souza, Eugênia Valadares, Raquel Borges, Vicente Odone, Israel Tojal, Dirce Carraro, Carla Rosenberg, Ana C.V. Krepischi. Genomic studies of Brazilian patients with hepatoblastoma: Insight into somatic mutations using whole-exome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2072.
Collapse
|
10
|
Rivas M, Costa CD, Toledo S, Cypriano M, Caires L, Goulart E, Carraro D, Werneck I, Rosenberg C, Zatz M, Krepischi A. Abstract A10: Epigenetic mechanisms in liver tumors: Gene expression analysis of epigenetic machinery in hepatoblastomas. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.tcm17-a10] [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
Liver tumors in children are rare and account for only 1-4% of all pediatric solid tumors. While hepatocellular carcinoma is predominant in adults, the most common liver cancer in children is hepatoblastoma, an embryonal tumor. The prognosis of patients with advanced tumor stages remains poor as well as surviving children often face severe effects following aggressive chemotherapy.
Hepatoblastomas carry a low mutational burden, and the impairment of epigenetic mechanisms, which are the core of embryogenesis and development, stands out as an alternative route for tumorigenesis.
The main objective of this study was to explore the role of genes associated with methylation and hydroxymethylation in hepatoblastomas. The expression of seven genes of the epigenetic machinery (DNMT1, DNMT3A, DNMT3L, UHRF1, TET1, TET2, and TET3) was analyzed by qPCR (Taqman). The cohort of tumors consisted of 21 hepatoblastomas and a control group of 8 non-tumor differentiated liver tissues. Additionally, a 5hmC quantification assay (Quest 5-hmC DNA ELISA Kit) was applied to assess the level of 5hmC in tumors.
TET1 and TET2 genes, whose proteins are responsible for the active demethylation of 5-methylcytosine (5mC), and consequent production of 5-hydroxymethylcytosine (5hmC), were found to be upregulated. A significant increase in the 5hmC levels was also evident in tumor samples when compared to nontumoral tissues.
We have shown in hepatoblastomas an upregulated profile of TET1 and TET2 enzymes with a resulting elevation of 5hmC level in tumors. Our data suggest that hepatoblastomas could present a pluripotency pattern of gene expression when compared to differentiated livers; to address this issue, the expression levels of three genes associated with pluripotency (POU5F1, SOX2 and NANOG) were evaluated, with no significant alteration.
Therefore, although hepatoblastomas have a more undifferentiated molecular profile than mature hepatocytes, our results indicate that tumor cells are already commited with the differentiation process. Altogether, these data suggest that the development of hepatoblastomas is associated with a blockage in the stages of hepatoblasts.
Citation Format: Maria Rivas, Cecília da Costa, Silvia Toledo, Monica Cypriano, Luiz Caires, Ernesto Goulart, Dirce Carraro, Isabela Werneck, Carla Rosenberg, Mayana Zatz, Ana Krepischi. Epigenetic mechanisms in liver tumors: Gene expression analysis of epigenetic machinery in hepatoblastomas [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 A10.
Collapse
Affiliation(s)
- Maria Rivas
- 1University of São Paulo, São Paulo, SP, Brazil,
| | | | - Silvia Toledo
- 3Grupo de Apoio ao Adolescente e Criança com Câncer - GRAACC, São Paulo, SP, Brazil
| | - Monica Cypriano
- 3Grupo de Apoio ao Adolescente e Criança com Câncer - GRAACC, São Paulo, SP, Brazil
| | - Luiz Caires
- 1University of São Paulo, São Paulo, SP, Brazil,
| | | | | | | | | | - Mayana Zatz
- 1University of São Paulo, São Paulo, SP, Brazil,
| | | |
Collapse
|
11
|
Aguiar T, Rodrigues T, Costa CMLD, Werneck I, Cypriano M, Toledo SRCD, Souza JESD, Tojal I, Carraro DM, Rosenberg C, Krepischi A. Abstract A18: Insights into the somatic mutation burden of hepatoblastomas using whole exome sequencing. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.tcm17-a18] [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
Hepatoblastomas (HB) are embryonal tumors of the liver with histologic features that resemble different stages of liver differentiation. Molecular data on HB tumorigenesis are still scarce because of its rarity. The identification of molecular pathways involved in HB development can expand the understanding of the connections between disruption of normal differentiation and cancer. Exome sequencing is a powerful tool to identify somatic mutations in tumors, possibly related to cancer development.
We performed a whole-exome sequencing in a discovery cohort of 6 HBs and their paired non-tumoral adjacent liver tissues (capture method 244K Agilent SureSelect Target Enrichment). Bioinformatic analysis of the exome data identified 76 rare somatic variants in coding sequences of 69 genes, which were validated using a target sequencing panel covering the affected genes (SureSelectXT Target Enrichment System for Illumina Paired-End Sequencing Library). These 69 genes and other 48 genes related with HB or cancer were also investigated, in addition to 13 HBs as a validation group. A total of 64 rare somatic mutations in 53 genes were validated in all hepatoblastomas.
Four different pathogenic mutations in the CTNNB1 gene were disclosed in five tumors.
Immunohistochemistry analysis of β-catenin was carried out in eight of the sequenced tumors as well as in a tissue microarray consisting of 19 novel hepatoblastomas cases. The constitutive activity of Wnt-β-catenin pathway, which is caused by the gain-of-function mutations of CTNNB1, was confirmed by the study of protein expression, which shows the accumulation of β-catenin in the nucleus. In addition, CX3CL1 gene was found to be somatically mutated in two different tumors; however, CX3CL1 gene expression was not altered in mutated tumors. We are currently investigating the possible role of CX3CL1 and its receptor (CX3CR1) in hepatoblastomas. Our data highlighted a relatively stable tumoral genome in this type of pediatric liver tumors, which present a small number of potentially pathogenic mutations, a feature that is also a hallmark of adult liver cancer.
Grants: FAPESP (2016/04785-0), FAPESP (2013/08028-1), CNPq (141625/2016-3).
Citation Format: Talita Aguiar, Tatiane Rodrigues, Cecília Maria Lima da Costa, Isabela Werneck, Monica Cypriano, Silvia Regina Caminada de Toledo, Jorge Estefano Santana de Souza, Israel Tojal, Dirce M Carraro, Carla Rosenberg, Ana Krepischi. Insights into the somatic mutation burden of hepatoblastomas using whole exome sequencing [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 A18.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Israel Tojal
- 1A.C. Camargo Cancer Center, São Paulo, SP, Brazil,
| | | | | | | |
Collapse
|
12
|
Maschietto M, Rodrigues TC, Kashiwabara AY, de Araujo ÉSS, Marques Aguiar TF, da Costa CML, da Cunha IW, Dos Reis Vasques L, Cypriano M, Brentani H, de Toledo SRC, Pearson PL, Carraro DM, Rosenberg C, Krepischi ACV. DNA methylation landscape of hepatoblastomas reveals arrest at early stages of liver differentiation and cancer-related alterations. Oncotarget 2016; 8:97871-97889. [PMID: 29228658 PMCID: PMC5716698 DOI: 10.18632/oncotarget.14208] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [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: 03/08/2016] [Accepted: 12/05/2016] [Indexed: 12/18/2022] Open
Abstract
Hepatoblastomas are uncommon embryonal liver tumors accounting for approximately 80% of childhood hepatic cancer. We hypothesized that epigenetic changes, including DNA methylation, could be relevant to hepatoblastoma onset. The methylomes of eight matched hepatoblastomas and non-tumoral liver tissues were characterized, and data were validated in an independent group (11 hepatoblastomas). In comparison to differentiated livers, hepatoblastomas exhibited a widespread and non-stochastic pattern of global low-level hypomethylation. The analysis revealed 1,359 differentially methylated CpG sites (DMSs) between hepatoblastomas and control livers, which are associated with 765 genes. Hypomethylation was detected in hepatoblastomas for ~58% of the DMSs with enrichment at intergenic sites, and most of the hypermethylated CpGs were located in CpG islands. Functional analyses revealed enrichment in signaling pathways involved in metabolism, negative regulation of cell differentiation, liver development, cancer, and Wnt signaling pathway. Strikingly, an important overlap was observed between the 1,359 DMSs and the CpG sites reported to exhibit methylation changes through liver development (p<0.0001), with similar patterns of methylation in both hepatoblastomas and fetal livers compared to adult livers. Overall, our results suggest an arrest at early stages of liver cell differentiation, in line with the hypothesis that hepatoblastoma ontogeny involves the disruption of liver development. This genome-wide methylation dysfunction, taken together with a relatively small number of driver genetic mutations reported for both adult and pediatric liver cancers, shed light on the relevance of epigenetic mechanisms for hepatic tumorigenesis.
Collapse
Affiliation(s)
- Mariana Maschietto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Tatiane Cristina Rodrigues
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | | | | | | | | | - Luciana Dos Reis Vasques
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Monica Cypriano
- Department of Pediatrics, Pediatric Oncology Institute (GRAACC), Federal University of São Paulo, São Paulo, Brazil
| | - Helena Brentani
- Department of Psychiatry, School of Medicine, University of São Paulo, São Paulo, Brazil
| | | | - Peter Lees Pearson
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Dirce Maria Carraro
- International Research Center, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana C V Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
13
|
Cypriano M, Spinola Castro AM, Monteiro Caran EM, Siviero-Miachon AA, Pires AL, Petrilli AS. Late effects in children treated for Wilms tumor at a single center in Brazil. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.e21034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
14
|
Santos MVC, Paiva MG, Macedo CRDP, Petrilli AS, Azeka E, Jatene IB, Castro Junior CG, Seber A, Miachon AS, Tanaka ACS, Castro MAS, Carvalho AC, Nars CCF, Terzian CN, Santos CCL, Guerra CCS, Silva DCB, Bassi DU, Feitosa FA, Hamamoto F, Szarf G, Lederman HM, Rigon Junior HJ, Mota ICF, Perrud JÁ, Soares Junior J, Gutierrez JA, Perin JPM, Catani LH, Tsai LY, Vianna LC, Santos MJ, Ishigai MMS, Diógenes MSB, Alves MTS, Piedade MTC, Parreiras M, Cypriano M, Negrini NS, Campos Filho O, Figueiredo PA, Novaes PE, Camargo PR, Maia OS, Petrilli R, Arduini RG, Gouveia RV, Teruya SBM, Moisés VA, Morais VLL. I Diretriz Brasileira de Cardio-Oncologia Pediátrica da Sociedade Brasileira de Cardiologia. Arq Bras Cardiol 2013; 100:1-68. [DOI: 10.5935/abc.2013s005] [Citation(s) in RCA: 8] [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] [Indexed: 11/20/2022] Open
|
15
|
Abib SDCV, Leite MTC, Ribeiro RC, Fachin CG, Demuner MS, Cypriano M, Schettini ST. Renal tumor and trauma: a pitfall for conversative management. Int Braz J Urol 2011; 37:514-8. [DOI: 10.1590/s1677-55382011000400011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2011] [Indexed: 11/21/2022] Open
|
16
|
Cypriano M, Ferraro A, Costa CMJ, Odone V, Lustosa D, Borsato ML, Brunetto AL, Calheiros LM, Barreto JH, Epelman S, Carvalho E, Pereira WV, Pontes EM, Garcia Filho RJ, Alves MTDS, Macedo CR, de Camargo OP, Pericles P, Penna V, Petrilli AS. Proposal of a prognostic score system for the Brazilian Osteosarcoma Treatment Group (BOTG) patients. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.9528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
17
|
Petrilli AS, Cypriano M, Dantas LS, Lee LM, Vercillo Luisi MFA, Torres B Silva KV, Pires Pereira CA. Evaluation of ticarcillin/clavulanic acid versus ceftriaxone plus amikacin for fever and neutropenia in pediatric patients with leukemia and lymphoma. Braz J Infect Dis 2003; 7:111-20. [PMID: 12959681 DOI: 10.1590/s1413-86702003000200003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The empirical use of antibiotic treatments is widely accepted as a means to treat cancer patients in chemotherapy who have fever and neutropenia. Intravenous monotherapy, with broad spectrum antibiotics, of patients with a high risk of complications is a possible alternative. METHODS We conducted a prospective open-label, randomized study of patients with lymphoma or leukemia who had fever and neutropenia during chemotherapy. Patients received either monotherapy with ticarcillin/clavulanic acid (T) or ceftriaxone plus amikacin (C+A). RESULTS Seventy patients who presented 136 episodes were evaluated, 68 in each arm of the study. The mean neutrophil counts at admission were 217cells/mm(3) (T) and 201cells/mm(3) (C+A). The mean duration of neutropenia was 8.7 days (T) and 7.6 days (C+A). Treatment was successful without the need for modifications in 71% of the episodes in the T group and 81% in the C+A group (p=0.23). Treatment was considered to have failed because of death in two episodes (3%) in the T group and three episodes (4%) in the C+A group, and because of a change in the drug applied in one episode in the T group and two episodes in the C+A group. Overall success was 96% (T) and 93% (C+A). Adverse events that occurred in group T were not related to the drugs used in this study. CONCLUSION In pediatric and adolescent patients with leukemia or lymphoma, who presented with fever and neutropenia, during chemotherapy, ticarcillin/clavulanic acid was as successful as the combination of ceftriaxone plus amikacin. It should be considered an appropriate option for this group of patients at high risk for infections.
Collapse
Affiliation(s)
- Antonio Sérgio Petrilli
- Pediatric Oncology Institute (GRAACC) Division of Infectious Disease, Federal University of São Paulo (UNIFESP), São Paulo/SP, Brazil.
| | | | | | | | | | | | | |
Collapse
|