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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] [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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Wang HS, Lao J, Jiang RS, Wang B, Ma XP, Wang JY. Summary of biological research on hepatoblastoma: a scoping review. Front Pediatr 2024; 12:1309693. [PMID: 38390281 PMCID: PMC10881832 DOI: 10.3389/fped.2024.1309693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Background Hepatoblastoma is the most prevalent primary hepatic malignancy in children, comprising 80% of pediatric hepatic malignancies and 1% of all pediatric malignancies. However, traditional treatments have proven inadequate in effectively curing hepatoblastoma, leading to a poor prognosis. Methods A literature search was conducted on multiple electronic databases (PubMed and Google Scholar). A total of 86 articles were eligible for inclusion in this review. Result This review aims to consolidate recent developments in hepatoblastoma research, focusing on the latest advances in cancer-associated genomics, epigenetic studies, transcriptional programs and molecular subtypes. We also discuss the current treatment approaches and forthcoming strategies to address cancer-associated biological challenges. Conclusion To provide a comprehensive summary of the molecular mechanisms associated with hepatoblastoma occurrence, this review highlights three key aspects: genomics, epigenetics, and transcriptomics. Our review aims to facilitate the exploration of novel molecular mechanisms and the development of innovative clinical treatment strategies for hepatoblastoma.
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Affiliation(s)
- Huan-Sheng Wang
- Department of General Surgery, Shenzhen Children's Hospital of China Medical University, Shenzhen, Guangdong Province, China
| | - Jing Lao
- Department of General Surgery, Shenzhen Children's Hospital of China Medical University, Shenzhen, Guangdong Province, China
| | - Ren-Sen Jiang
- Department of General Surgery, Shenzhen Children's Hospital of ShanTou University, Shenzhen, Guangdong Province, China
| | - Bin Wang
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
| | - Xiao-Peng Ma
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
| | - Jian-Yao Wang
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, China
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Kahana-Edwin S, Torpy J, Cain LE, Mullins A, McCowage G, Woodfield SE, Vasudevan SA, Shea DPT, Minoche AE, Espinoza AF, Kummerfeld S, Goldstein LD, Karpelowsky J. Quantitative ctDNA Detection in Hepatoblastoma: Implications for Precision Medicine. Cancers (Basel) 2023; 16:12. [PMID: 38201440 PMCID: PMC10778269 DOI: 10.3390/cancers16010012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Hepatoblastoma is characterized by driver mutations in CTNNB1, making it an attractive biomarker for a liquid biopsy approach utilizing circulating tumor DNA (ctDNA). This prospective observational study sought to ascertain the feasibility of ctDNA detection in patients with hepatoblastoma and explore its associations with established clinical indicators and biomarkers, including serum Alpha-fetoprotein (AFP). We obtained 38 plasma samples and 17 tumor samples from 20 patients with hepatoblastoma. These samples were collected at various stages: 10 at initial diagnosis, 17 during neoadjuvant chemotherapy, 6 post-operatively, and 5 at disease recurrence. Utilizing a bespoke sequencing assay we developed called QUENCH, we identified single nucleotide variants and deletions in CTNNB1 ctDNA. Our study demonstrated the capability to quantitate ctDNA down to a variant allele frequency of 0.3%, achieving a sensitivity of 90% for patients at initial diagnosis, and a specificity of 100% at the patient level. Notably, ctDNA positivity correlated with tumor burden, and ctDNA levels exhibited associations with macroscopic residual disease and treatment response. Our findings provide evidence for the utility of quantitative ctDNA detection in hepatoblastoma management. Given the distinct detection targets, ctDNA and AFP-based stratification and monitoring approaches could synergize to enhance clinical decision-making. Further research is needed to elucidate the interplay between ctDNA and AFP and determine the optimal clinical applications for both methods in risk stratification and residual disease detection.
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Affiliation(s)
- Smadar Kahana-Edwin
- Children’s Cancer Research Unit, Kids Research, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - James Torpy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Lucy E. Cain
- Cancer Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Anna Mullins
- Cancer Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Geoffrey McCowage
- Cancer Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Sarah E. Woodfield
- Divisions of Pediatric Surgery and Surgical Research, Michael E. DeBakey Department of Surgery, Pediatric Surgical Oncology Laboratory, Texas Children’s Surgical Oncology Program, Texas Children’s Liver Tumor Program, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sanjeev A. Vasudevan
- Divisions of Pediatric Surgery and Surgical Research, Michael E. DeBakey Department of Surgery, Pediatric Surgical Oncology Laboratory, Texas Children’s Surgical Oncology Program, Texas Children’s Liver Tumor Program, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dan P. T. Shea
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Andre E. Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Andres F. Espinoza
- Divisions of Pediatric Surgery and Surgical Research, Michael E. DeBakey Department of Surgery, Pediatric Surgical Oncology Laboratory, Texas Children’s Surgical Oncology Program, Texas Children’s Liver Tumor Program, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah Kummerfeld
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- St Vincent’s Clinical School, UNSW Sydney, Sydney, NSW 2217, Australia
| | - Leonard D. Goldstein
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- St Vincent’s Clinical School, UNSW Sydney, Sydney, NSW 2217, Australia
| | - Jonathan Karpelowsky
- Children’s Cancer Research Unit, Kids Research, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
- Paediatric Oncology and Thoracic Surgery, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
- Division of Child and Adolescent Health, The University of Sydney, Sydney, NSW 2050, Australia
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Whitby A, Pabla P, Shastri B, Amugi L, Del Río-Álvarez Á, Kim DH, Royo L, Armengol C, Dandapani M. Characterisation of Aberrant Metabolic Pathways in Hepatoblastoma Using Liquid Chromatography and Tandem Mass Spectrometry (LC-MS/MS). Cancers (Basel) 2023; 15:5182. [PMID: 37958356 PMCID: PMC10648437 DOI: 10.3390/cancers15215182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Hepatoblastoma (HB) is a rare childhood tumour with an evolving molecular landscape. We present the first comprehensive metabolomic analysis using untargeted and targeted liquid chromatography coupled to high-resolution tandem mass spectrometry (LC-MS/MS) of paired tumour and non-tumour surgical samples in HB patients (n = 8 pairs). This study demonstrates that the metabolomic landscape of HB is distinct from that of non-tumour (NT) liver tissue, with 35 differentially abundant metabolites mapping onto pathways such as fatty acid transport, glycolysis, the tricarboxylic acid (TCA) cycle, branched-chain amino acid degradation and glutathione synthesis. Targeted metabolomics demonstrated reduced short-chain acylcarnitines and a relative accumulation of branched-chain amino acids. Medium- and long-chain acylcarnitines in HB were similar to those in NT. The metabolomic changes reported are consistent with previously reported transcriptomic data from tumour and non-tumour samples (49 out of 54 targets) as well as metabolomic data obtained using other techniques. Gene set enrichment analysis (GSEA) from RNAseq data (n = 32 paired HB and NT samples) demonstrated a downregulation of the carnitine metabolome and immunohistochemistry showed a reduction in CPT1a (n = 15 pairs), which transports fatty acids into the mitochondria, suggesting a lack of utilisation of long-chain fatty acids in HB. Thus, our findings suggest a reduced metabolic flux in HB which is corroborated at the gene expression and protein levels. Further work could yield novel insights and new therapeutic targets.
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Affiliation(s)
- Alison Whitby
- Children's Brain Tumour Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Pardeep Pabla
- School of Medicine, Royal Derby Hospital Centre, University of Nottingham, Derby DE22 3DT, UK
| | - Bhoomi Shastri
- Children's Brain Tumour Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Laudina Amugi
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Division, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
- Phenome Centre Birmingham, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Álvaro Del Río-Álvarez
- Childhood Liver Oncology Group, Translational Program in Cancer Research (CARE), Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
- Centro de Investigación Biomédica en Red (CIBER) en Enfermedades Hepáticas y Digestivas, 28029 Madrid, Spain
| | - Dong-Hyun Kim
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Division, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Laura Royo
- Childhood Liver Oncology Group, Translational Program in Cancer Research (CARE), Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
| | - Carolina Armengol
- Childhood Liver Oncology Group, Translational Program in Cancer Research (CARE), Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
- Centro de Investigación Biomédica en Red (CIBER) en Enfermedades Hepáticas y Digestivas, 28029 Madrid, Spain
| | - Madhumita Dandapani
- Children's Brain Tumour Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
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5
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Clavería-Cabello A, Herranz JM, Latasa MU, Arechederra M, Uriarte I, Pineda-Lucena A, Prosper F, Berraondo P, Alonso C, Sangro B, García Marin JJ, Martinez-Chantar ML, Ciordia S, Corrales FJ, Francalanci P, Alaggio R, Zucman-Rossi J, Indersie E, Cairo S, Domingo-Sàbat M, Zanatto L, Sancho-Bru P, Armengol C, Berasain C, Fernandez-Barrena MG, Avila MA. Identification and experimental validation of druggable epigenetic targets in hepatoblastoma. J Hepatol 2023; 79:989-1005. [PMID: 37302584 DOI: 10.1016/j.jhep.2023.05.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/25/2023] [Accepted: 05/22/2023] [Indexed: 06/13/2023]
Abstract
BACKGROUND & AIMS Hepatoblastoma (HB) is the most frequent childhood liver cancer. Patients with aggressive tumors have limited therapeutic options; therefore, a better understanding of HB pathogenesis is needed to improve treatment. HBs have a very low mutational burden; however, epigenetic alterations are increasingly recognized. We aimed to identify epigenetic regulators consistently dysregulated in HB and to evaluate the therapeutic efficacy of their targeting in clinically relevant models. METHODS We performed a comprehensive transcriptomic analysis of 180 epigenetic genes. Data from fetal, pediatric, adult, peritumoral (n = 72) and tumoral (n = 91) tissues were integrated. Selected epigenetic drugs were tested in HB cells. The most relevant epigenetic target identified was validated in primary HB cells, HB organoids, a patient-derived xenograft model, and a genetic mouse model. Transcriptomic, proteomic and metabolomic mechanistic analyses were performed. RESULTS Altered expression of genes regulating DNA methylation and histone modifications was consistently observed in association with molecular and clinical features of poor prognosis. The histone methyltransferase G9a was markedly upregulated in tumors with epigenetic and transcriptomic traits of increased malignancy. Pharmacological targeting of G9a significantly inhibited growth of HB cells, organoids and patient-derived xenografts. Development of HB induced by oncogenic forms of β-catenin and YAP1 was ablated in mice with hepatocyte-specific deletion of G9a. We observed that HBs undergo significant transcriptional rewiring in genes involved in amino acid metabolism and ribosomal biogenesis. G9a inhibition counteracted these pro-tumorigenic adaptations. Mechanistically, G9a targeting potently repressed the expression of c-MYC and ATF4, master regulators of HB metabolic reprogramming. CONCLUSIONS HBs display a profound dysregulation of the epigenetic machinery. Pharmacological targeting of key epigenetic effectors exposes metabolic vulnerabilities that can be leveraged to improve the treatment of these patients. IMPACT AND IMPLICATIONS In spite of recent advances in the management of hepatoblastoma (HB), treatment resistance and drug toxicity are still major concerns. This systematic study reveals the remarkable dysregulation in the expression of epigenetic genes in HB tissues. Through pharmacological and genetic experimental approaches, we demonstrate that the histone-lysine-methyltransferase G9a is an excellent drug target in HB, which can also be harnessed to enhance the efficacy of chemotherapy. Furthermore, our study highlights the profound pro-tumorigenic metabolic rewiring of HB cells orchestrated by G9a in coordination with the c-MYC oncogene. From a broader perspective, our findings suggest that anti-G9a therapies may also be effective in other c-MYC-dependent tumors.
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Affiliation(s)
| | - Jose Maria Herranz
- Hepatology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain; CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Maria Ujue Latasa
- Hepatology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain; CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Maria Arechederra
- Hepatology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain; CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
| | - Iker Uriarte
- Hepatology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain; CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Felipe Prosper
- Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain; Oncohematology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Pedro Berraondo
- Immunology and Immunotherapy Program, CIMA, University of Navarra, Pamplona, Spain; CIBERonc, Madrid, Spain
| | | | - Bruno Sangro
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain; Hepatology Unit, CCUN, Navarra University Clinic, Pamplona, Spain
| | - Jose Juan García Marin
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Experimental Hepatology and Drug Targeting (HEVEFARM), University of Salamanca, IBSAL, Salamanca, Spain
| | - Maria Luz Martinez-Chantar
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CICbioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Sergio Ciordia
- Functional Proteomics Laboratory, CNB-CSIC, Madrid, Spain
| | - Fernando José Corrales
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Functional Proteomics Laboratory, CNB-CSIC, Madrid, Spain
| | - Paola Francalanci
- Pathology Unit, Children's Hospital Bambino Gesù, IRCCS, Rome, Italy
| | - Rita Alaggio
- Pathology Unit, Children's Hospital Bambino Gesù, IRCCS, Sapienza University, Rome, Italy
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, INSERM, Hôpital Européen Georges Pompidou, Paris, France
| | | | - Stefano Cairo
- XenTech, Evry-Courcouronnes, France; Champions Oncology, Rockville, MD, USA
| | - Montserrat Domingo-Sàbat
- Childhood Liver Oncology Group, Program of Predictive and Personalized Medicine of Cancer (PMPCC), Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Laura Zanatto
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Pau Sancho-Bru
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Carolina Armengol
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Childhood Liver Oncology Group, Program of Predictive and Personalized Medicine of Cancer (PMPCC), Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Carmen Berasain
- Hepatology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain; CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
| | - Maite García Fernandez-Barrena
- Hepatology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain; CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain.
| | - Matias Antonio Avila
- Hepatology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain; CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain.
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Silva FLT, Ruas JS, Euzébio MF, Hoffmann IL, Junqueira T, Tedeschi H, Pereira LH, Cassone AE, Cardinalli IA, Seidinger AL, Jotta PY, Maschietto M. 11p15 Epimutations in Pediatric Embryonic Tumors: Insights from a Methylome Analysis. Cancers (Basel) 2023; 15:4256. [PMID: 37686532 PMCID: PMC10486592 DOI: 10.3390/cancers15174256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 09/10/2023] Open
Abstract
Embryonic tumors share few recurrent mutations, suggesting that other mechanisms, such as aberrant DNA methylation, play a prominent role in their development. The loss of imprinting (LOI) at the chromosome region 11p15 is the germline alteration behind Beckwith-Wiedemann syndrome that results in an increased risk of developing several embryonic tumors. This study analyzed the methylome, using EPIC Beadchip arrays from 99 sporadic embryonic tumors. Among these tumors, 46.5% and 14.6% presented alterations at imprinted control regions (ICRs) 1 and 2, respectively. Based on the methylation levels of ICR1 and ICR2, four clusters formed with distinct methylation patterns, mostly for medulloblastomas (ICR1 loss of methylation (LOM)), Wilms tumors, and hepatoblastomas (ICR1 gain of methylation (GOM), with or without ICR2 LOM). To validate the results, the methylation status of 29 cases was assessed with MS-MLPA, and a high level of agreement was found between both methodologies: 93% for ICR1 and 79% for ICR2. The MS-MLPA results indicate that 15 (51.7%) had ICR1 GOM and 11 (37.9%) had ICR2 LOM. To further validate our findings, the ICR1 methylation status was characterized via digital PCR (dPCR) in cell-free DNA (cfDNA) extracted from peripheral blood. At diagnosis, we detected alterations in the methylation levels of ICR1 in 62% of the cases, with an agreement of 76% between the tumor tissue (MS-MLPA) and cfDNA methods. Among the disagreements, the dPCR was able to detect ICR1 methylation level changes presented at heterogeneous levels in the tumor tissue, which were detected only in the methylome analysis. This study highlights the prevalence of 11p15 methylation status in sporadic embryonic tumors, with differences relating to methylation levels (gain or loss), location (ICR1 or ICR2), and tumor types (medulloblastomas, Wilms tumors, and hepatoblastomas).
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Affiliation(s)
- Felipe Luz Torres Silva
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil; (F.L.T.S.); (J.S.R.); (M.F.E.); (P.Y.J.)
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
| | - Juliana Silveira Ruas
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil; (F.L.T.S.); (J.S.R.); (M.F.E.); (P.Y.J.)
| | - Mayara Ferreira Euzébio
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil; (F.L.T.S.); (J.S.R.); (M.F.E.); (P.Y.J.)
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
| | | | - Thais Junqueira
- Boldrini Children’s Hospital, Campinas 13083-210, SP, Brazil
| | - Helder Tedeschi
- Boldrini Children’s Hospital, Campinas 13083-210, SP, Brazil
| | | | | | | | - Ana Luiza Seidinger
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil; (F.L.T.S.); (J.S.R.); (M.F.E.); (P.Y.J.)
| | - Patricia Yoshioka Jotta
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil; (F.L.T.S.); (J.S.R.); (M.F.E.); (P.Y.J.)
| | - Mariana Maschietto
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, SP, Brazil; (F.L.T.S.); (J.S.R.); (M.F.E.); (P.Y.J.)
- Genetics and Molecular Biology, Institute of Biology, State University of Campinas, Campinas 13083-862, SP, Brazil
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7
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Zhou S, Li M, Ostrow D, Ruble D, Mascarenhas L, Pawel B, Buckley JD, Triche TJ. Potential methylation-regulated genes and pathways in hepatocellular neoplasm, not otherwise specified. Front Oncol 2022; 12:952325. [PMID: 36212481 PMCID: PMC9532972 DOI: 10.3389/fonc.2022.952325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background and Aims The molecular basis of hepatocellular neoplasm, not otherwise specified (HCN-NOS) is unknown. We aimed to identify gene expression patterns, potential methylation-regulated genes and pathways that characterize the tumor, and its possible relationship to hepatoblastoma and hepatocellular carcinoma (HCC). Approach & Results Parallel genome-wide profiling of gene expression (RNAseq) and DNA methylation (EPIC850) was performed on 4 pairs of pre-treatment HCN-NOS tumors and adjacent non-tumor controls. 2530 significantly differentially expressed genes (DEGs) were identified between tumors and controls. Many of these DEGs were associated with hepatoblastoma and/or HCC. Analysis Match in Ingenuity Pathway Analysis determined that the gene expression profile of HCN-NOS was unique but significantly similar to that of both hepatoblastoma and HCC. A total of 27,195 CpG sites (CpGs) were significantly differentially methylated (DM) between tumors and controls, with a global hypomethylation pattern and predominant CpG island hypermethylation in promotor regions. Aberrant DNA methylation predominated in Developmental Process and Molecular Function Regulator pathways. Embryonic stem cell pathways were significantly enriched. In total, 1055 aberrantly methylated (at CpGs) and differentially expressed genes were identified, including 25 upstream regulators and sixty-one potential CpG island methylation-regulated genes. Eight methylation-regulated genes (TCF3, MYBL2, SRC, HMGA2, PPARGC1A, SLC22A1, COL2A1 and MYCN) had highly consistent gene expression patterns and prognostic value in patients with HCC, based on comparison to publicly available datasets. Conclusions HCN-NOS has a unique, stem-cell like gene expression and DNA methylation profile related to both hepatoblastoma and HCC but distinct therefrom. Further, 8 methylation-regulated genes associated with prognosis in HCC were identified.
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Affiliation(s)
- Shengmei Zhou
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- *Correspondence: Shengmei Zhou,
| | - Meng Li
- USC Libraries Bioinformatics Services, University of Southern California, Los Angeles, CA, United States
| | - Dejerianne Ostrow
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - David Ruble
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Leo Mascarenhas
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Cancer and Blood Disease Institute, Division of Hematology/Oncology, Department of Pediatrics, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Bruce Pawel
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jonathan David Buckley
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Timothy J. Triche
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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8
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Feng J, Zhao D, Lv F, Yuan Z. Epigenetic Inheritance From Normal Origin Cells Can Determine the Aggressive Biology of Tumor-Initiating Cells and Tumor Heterogeneity. Cancer Control 2022; 29:10732748221078160. [PMID: 35213254 PMCID: PMC8891845 DOI: 10.1177/10732748221078160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The acquisition of genetic- and epigenetic-abnormalities during transformation has been recognized as the two fundamental factors that lead to tumorigenesis and determine the aggressive biology of tumor cells. However, there is a regularity that tumors derived from less-differentiated normal origin cells (NOCs) usually have a higher risk of vascular involvement, lymphatic and distant metastasis, which can be observed in both lymphohematopoietic malignancies and somatic cancers. Obviously, the hypothesis of genetic- and epigenetic-abnormalities is not sufficient to explain how the linear relationship between the cellular origin and the biological behavior of tumors is formed, because the cell origin of tumor is an independent factor related to tumor biology. In a given system, tumors can originate from multiple cell types, and tumor-initiating cells (TICs) can be mapped to different differentiation hierarchies of normal stem cells, suggesting that the heterogeneity of the origin of TICs is not completely chaotic. TIC’s epigenome includes not only genetic- and epigenetic-abnormalities, but also established epigenetic status of genes inherited from NOCs. In reviewing previous studies, we found much evidence supporting that the status of many tumor-related “epigenetic abnormalities” in TICs is consistent with that of the corresponding NOC of the same differentiation hierarchy, suggesting that they may not be true epigenetic abnormalities. So, we speculate that the established statuses of genes that control NOC’s migration, adhesion and colonization capabilities, cell-cycle quiescence, expression of drug transporters, induction of mesenchymal formation, overexpression of telomerase, and preference for glycolysis can be inherited to TICs through epigenetic memory and be manifested as their aggressive biology. TICs of different origins can maintain different degrees of innate stemness from NOC, which may explain why malignancies with stem cell phenotypes are usually more aggressive.
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Affiliation(s)
- Jiliang Feng
- Clinical-Pathology Center, Capital Medical University Affiliated Beijing Youan Hospital, Beijing, China
| | - Dawei Zhao
- Medical Imaging Department, Capital Medical University Affiliated Beijing Youan Hospital, Beijing, China
| | - Fudong Lv
- Clinical-Pathology Center, Capital Medical University Affiliated Beijing Youan Hospital, Beijing, China
| | - Zhongyu Yuan
- Clinical-Pathology Center, Capital Medical University Affiliated Beijing Youan Hospital, Beijing, China
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9
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Abstract
Hepatoblastoma (HB) is the most common malignancy within the rare cohort of
pediatric primary liver tumors. It may arise sporadically or in association with
germline mutations in specific genetic syndromes. Histogenesis recapitulates
fetal hepatic development, however, this tumor can exhibit a markedly
heterogeneous appearance both macroscopically and under the microscope.
Histologic subtypes are classified based on morphologic appearance, with
additional discrimination based on emerging molecular and immunohistochemical
features. Numerous diagnostic pitfalls exist from clinical presentation through
to ancillary testing; at all stages, the surgical pathologist must be discerning
and open to collaboration with colleagues of different specialties. Problematic
areas include the adequacy of tissue sampling, correlation of histology with
radiologic appearance and alpha feto-protein (AFP) serology, forming a
diagnostic consensus within the pediatric pathology community and choosing a
shrewd immunohistochemical panel. This review discusses the sequence of events
leading up to histologic assessment, and the nuances of microscopic evaluation.
Along the way, pitfalls are highlighted, providing a tool for the surgical
pathologists to support their individual approach.
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Affiliation(s)
| | - Consolato M. Sergi
- Anatomic Pathology Division, Children's Hospital of Eastern Ontario,
Ottawa, ON, Canada
- Consolato M. Sergi, Chief, Anatomic
Pathology Division, Pediatric Pathologist, Children’s Hospital of Eastern
Ontario (CHEO), 401 Smyth Road Ottawa, ON, K1H 8L1, Canada.
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10
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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] [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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11
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Wang JY, Lao J, Luo Y, Guo JJ, Cheng H, Zhang HY, Yao J, Ma XP, Wang B. Integrative Analysis of DNA Methylation and Gene Expression Profiling Data Reveals Candidate Methylation-Regulated Genes in Hepatoblastoma. Int J Gen Med 2021; 14:9419-9431. [PMID: 34908869 PMCID: PMC8664605 DOI: 10.2147/ijgm.s331178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/09/2021] [Indexed: 11/24/2022] Open
Abstract
Purpose This study aimed to identify novel methylation-regulated genes as diagnostic biomarkers and therapeutic targets for hepatoblastoma (HB). Materials and Methods The DNA methylation data of 19 HB tumor samples and 10 normal liver samples from the GSE78732 dataset and gene expression profiling data of 53 HB tumor samples and 14 normal liver samples from the GSE131329 dataset and 31 HB tumor samples and 32 normal liver samples from the GSE133039 dataset were downloaded form the Gene Expression Omnibus database. Next, differentially methylated genes (DMGs) and differentially expressed genes (DEGs) were identified. Venn diagrams were used to identify methylation-regulated genes. The VarElect online tool was selected to identify key methylation-regulated genes, and a protein–protein interaction (PPI) network was constructed to show the interactions among key methylation-regulated genes and DEGs. Finally, Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed to investigate the potential regulatory mechanisms of key methylation-regulated genes. Results A total of 457 DMGs and 1597 DEGs were identified between the HB and normal liver samples. After DMGs and DEGs overlapping, 22 hypomethylated and upregulated genes and 19 hypermethylated and downregulated genes in HB were screened. Survival analysis revealed that 13 methylation-regulated genes were associated with the prognosis of liver cancer. Moreover, SPP1, UHRF1, and HEY1 were selected as the key DNA methylation-regulated genes. The PPI network revealed that all of them could affect TP53, while both UHRF1 and HEY1 could influence BMP4. Enrichment analysis suggested that the DEGs were involved in TP53-related pathways, including the cell cycle and p53 signaling pathway. Finally, SPP1, UHRF1, and HEY1 were hypomethylated and upregulated in the HB samples compared with those in the normal liver samples. Conclusion SPP1, UHRE1, and HEY1 may play important roles in HB and be used as biomarkers for its diagnosis and treatment.
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Affiliation(s)
- Jian-Yao Wang
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, 518026, Guangdong Province, People's Republic of China
| | - Jing Lao
- Shenzhen Children's Hospital of China Medical University, Shenzhen, 518026, Guangdong Province, People's Republic of China
| | - Yu Luo
- Zhuhai Campus of Zunyi Medical University, Zhuhai, 519090, Guangdong Province, People's Republic of China
| | - Jing-Jie Guo
- Shenzhen Children's Hospital of China Medical University, Shenzhen, 518026, Guangdong Province, People's Republic of China
| | - Hao Cheng
- Shenzhen Children's Hospital of China Medical University, Shenzhen, 518026, Guangdong Province, People's Republic of China
| | - Hong-Yan Zhang
- Shenzhen Children's Hospital of China Medical University, Shenzhen, 518026, Guangdong Province, People's Republic of China
| | - Jun Yao
- Department of Gastroenterology, Jinan University of Medical Sciences, Shenzhen Municipal People's Hospital, Shenzhen, 518020, Guangdong Province, People's Republic of China
| | - Xiao-Peng Ma
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, 518026, Guangdong Province, People's Republic of China
| | - Bin Wang
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, 518026, Guangdong Province, People's Republic of China
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12
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Rivas M, Johnston ME, Gulati R, Kumbaji M, Margues Aguiar TF, Timchenko L, Krepischi A, Shin S, Bondoc A, Tiao G, Geller J, Timchenko N. HDAC1-Dependent Repression of Markers of Hepatocytes and P21 Is Involved in Development of Pediatric Liver Cancer. Cell Mol Gastroenterol Hepatol 2021; 12:1669-1682. [PMID: 34245919 PMCID: PMC8536541 DOI: 10.1016/j.jcmgh.2021.06.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Epigenetic regulation of gene expression plays a critical role in the development of liver cancer; however, the molecular mechanisms of epigenetic-driven liver cancers are not well understood. The aims of this study were to examine molecular mechanisms that cause the dedifferentiation of hepatocytes into cancer cells in aggressive hepatoblastoma and test if the inhibition of these mechanisms inhibits tumor growth. METHODS We have analyzed CCAAT/Enhancer Binding Protein alpha (C/EBPα), Transcription factor Sp5, and histone deacetylase (HDAC)1 pathways from a large biobank of fresh hepatoblastoma (HBL) samples using high-pressure liquid chromatography-based examination of protein-protein complexes and have examined chromatin remodeling on the promoters of markers of hepatocytes and p21. The HDAC1 activity was inhibited in patient-derived xenograft models of HBL and in cultured hepatoblastoma cells and expression of HDAC1-dependent markers of hepatocytes was examined. RESULTS Analyses of a biobank showed that a significant portion of HBL patients have increased levels of an oncogenic de-phosphorylated-S190-C/EBPα, Sp5, and HDAC1 compared with amounts of these proteins in adjacent regions. We found that the oncogenic de-phosphorylated-S190-C/EBPα is created in aggressive HBL by protein phosphatase 2A, which is increased within the nucleus and dephosphorylates C/EBPα at Ser190. C/EBPα-HDAC1 and Sp5-HDAC1 complexes are abundant in hepatocytes, which dedifferentiate into cancer cells. Studies in HBL cells have shown that C/EBPα-HDAC1 and Sp5-HDAC1 complexes reduce markers of hepatocytes and p21 via repression of their promoters. Pharmacologic inhibition of C/EBPα-HDAC1 and Sp5-HDAC1 complexes by Suberoylanilide hydroxamic acid (SAHA) and small interfering RNA-mediated inhibition of HDAC1 increase expression of hepatocyte markers, p21, and inhibit proliferation of cancer cells. CONCLUSIONS HDAC1-mediated repression of markers of hepatocytes is an essential step for the development of HBL, providing background for generation of therapies for aggressive HBL by targeting HDAC1 activities.
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Affiliation(s)
- Maria Rivas
- Division of General and Thoracic Surgery, Cincinnati, Ohio,Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Michael E. Johnston
- Division of General and Thoracic Surgery, Cincinnati, Ohio,Department of Surgery, University of Cincinnati College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Ruhi Gulati
- Division of General and Thoracic Surgery, Cincinnati, Ohio
| | | | | | | | - Ana Krepischi
- Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Soona Shin
- Division of General and Thoracic Surgery, Cincinnati, Ohio,Department of Surgery, University of Cincinnati College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | | | - Gregory Tiao
- Division of General and Thoracic Surgery, Cincinnati, Ohio,Department of Surgery, University of Cincinnati College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - James Geller
- Department of Oncology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Nikolai Timchenko
- Division of General and Thoracic Surgery, Cincinnati, Ohio,Department of Surgery, University of Cincinnati College of Medicine, University of Cincinnati, Cincinnati, Ohio,Correspondence Address correspondence to: Nikolai Timchenko, PhD, Liver Tumor Program, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, Ohio 45229. fax: (513) 636-4200.
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13
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Pischedda S, O'Connor D, Fairfax BP, Salas A, Martinon-Torres F, Pollard AJ, Trück J. Changes in epigenetic profiles throughout early childhood and their relationship to the response to pneumococcal vaccination. Clin Epigenetics 2021; 13:29. [PMID: 33541404 PMCID: PMC7860179 DOI: 10.1186/s13148-021-01012-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/11/2021] [Indexed: 02/07/2023] Open
Abstract
Background Pneumococcal infections are a major cause of morbidity and mortality in young children and immaturity of the immune system partly underlies poor vaccine responses seen in the young. Emerging evidence suggests a key role for epigenetics in the maturation and regulation of the immune system in health and disease. The study aimed to investigate epigenetic changes in early life and to understand the relationship between the epigenome and antigen-specific antibody responses to pneumococcal vaccination. Methods The epigenetic profiles from 24 healthy children were analyzed at 12 months prior to a booster dose of the 13-valent pneumococcal conjugate vaccine (PCV-13), and at 24 months of age, using the Illumina Methylation 450 K assay and assessed for differences over time and between high and low vaccine responders. Results Our analysis revealed 721 significantly differentially methylated positions between 12 and 24 months (FDR < 0.01), with significant enrichment in pathways involved in the regulation of cell–cell adhesion and T cell activation. Comparing high and low vaccine responders, we identified differentially methylated CpG sites (P value < 0.01) associated with HLA-DPB1 and IL6. Conclusion These data imply that epigenetic changes that occur during early childhood may be associated with antigen-specific antibody responses to pneumococcal vaccines.
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Affiliation(s)
- Sara Pischedda
- Genetics, Vaccines and Infections and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain. .,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain. .,Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Galicia, Spain.
| | - Daniel O'Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and The NIHR Oxford Biomedical Research Centre, Oxford, UK.
| | - Benjamin P Fairfax
- MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Antonio Salas
- Genetics, Vaccines and Infections and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain.,Hospital Clínico Universitario de Santiago (SERGAS), Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Galicia, Spain
| | - Federico Martinon-Torres
- Genetics, Vaccines and Infections and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and The NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Johannes Trück
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and The NIHR Oxford Biomedical Research Centre, Oxford, UK. .,Division of Immunology and Children's Research Center, University Children's Hospital Zurich, University of Zurich (UZH), Zurich, Switzerland.
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14
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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] [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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15
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Shen G, Shen H, Zhang J, Yan Q, Liu H. DNA methylation in Hepatoblastoma-a literature review. Ital J Pediatr 2020; 46:113. [PMID: 32758256 PMCID: PMC7409486 DOI: 10.1186/s13052-020-00877-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 07/29/2020] [Indexed: 12/19/2022] Open
Abstract
Hepatoblastoma (HB) is the most common malignant liver tumor in children. Abnormal activation of the Wnt/β-catenin signaling pathway plays an important role in the formation and development of HB. Genes in HB show a global hypomethylation change, accompanied by hypermethylation of specific tumor suppressor genes (TSGs). This article reviews the hypermethylation changes in several TSGs, such as RASSF1A, SOCS1, APC, HHIP, and P16, and analyzes the pathways and mechanisms of TSGs regulating gene expression. The role of the methylation-regulating enzymes DNA methyltransferases (DNMTs) and ten-eleven translocation (TET) family members enzymes in the methylation changes of HB was analyzed, and it was speculated that the occurrence of HB is partly due to the obstruction of liver differentiation in the early stage of differentiation. The origin cells may be incompletely differentiated hepatocytes remaining in the liver of children after birth. Therefore, further studying the role of methylation regulating enzymes in methylation changes in HB is a promising future research direction.
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Affiliation(s)
- Gang Shen
- Pediatric Surgery Department, Weifang Peoples' Hospital, Weifang, China
| | - Hongyu Shen
- Ultrasound Department, Weifang Haifushan Hospital, Weifang, China
| | - Jing Zhang
- Pediatric Surgery Department, Weifang Peoples' Hospital, Weifang, China
| | - Qingtao Yan
- Pediatric Surgery Department, Weifang Peoples' Hospital, Weifang, China
| | - Huixian Liu
- Dermatology Department, Weifang Peoples' Hospital, No. 151, Guangwen Street, Kuiwen District, Weifang, 261041, China.
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16
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Epigenetic footprint enables molecular risk stratification of hepatoblastoma with clinical implications. J Hepatol 2020; 73:328-341. [PMID: 32240714 DOI: 10.1016/j.jhep.2020.03.025] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Hepatoblastoma (HB) is a rare disease. Nevertheless, it is the predominant pediatric liver cancer, with limited therapeutic options for patients with aggressive tumors. Herein, we aimed to uncover the mechanisms of HB pathobiology and to identify new biomarkers and therapeutic targets in a move towards precision medicine for patients with advanced HB. METHODS We performed a comprehensive genomic, transcriptomic and epigenomic characterization of 159 clinically annotated samples from 113 patients with HB, using high-throughput technologies. RESULTS We discovered a widespread epigenetic footprint of HB that includes hyperediting of the tumor suppressor BLCAP concomitant with a genome-wide dysregulation of RNA editing and the overexpression of mainly non-coding genes of the oncogenic 14q32 DLK1-DIO3 locus. By unsupervised analysis, we identified 2 epigenomic clusters (Epi-CA, Epi-CB) with distinct degrees of DNA hypomethylation and CpG island hypermethylation that are associated with the C1/C2/C2B transcriptomic subtypes. Based on these findings, we defined the first molecular risk stratification of HB (MRS-HB), which encompasses 3 main prognostic categories and improves the current clinical risk stratification approach. The MRS-3 category (28%), defined by strong 14q32 locus expression and Epi-CB methylation features, was characterized by CTNNB1 and NFE2L2 mutations, a progenitor-like phenotype and clinical aggressiveness. Finally, we identified choline kinase alpha as a promising therapeutic target for intermediate and high-risk HBs, as its inhibition in HB cell lines and patient-derived xenografts strongly abrogated tumor growth. CONCLUSIONS These findings provide a detailed insight into the molecular features of HB and could be used to improve current clinical stratification approaches and to develop treatments for patients with HB. LAY SUMMARY Hepatoblastoma is a rare childhood liver cancer that has been understudied. We have used cutting-edge technologies to expand our molecular knowledge of this cancer. Our biological findings can be used to improve clinical management and pave the way for the development of novel therapies for this cancer.
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17
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Sekiguchi M, Seki M, Kawai T, Yoshida K, Yoshida M, Isobe T, Hoshino N, Shirai R, Tanaka M, Souzaki R, Watanabe K, Arakawa Y, Nannya Y, Suzuki H, Fujii Y, Kataoka K, Shiraishi Y, Chiba K, Tanaka H, Shimamura T, Sato Y, Sato-Otsubo A, Kimura S, Kubota Y, Hiwatari M, Koh K, Hayashi Y, Kanamori Y, Kasahara M, Kohashi K, Kato M, Yoshioka T, Matsumoto K, Oka A, Taguchi T, Sanada M, Tanaka Y, Miyano S, Hata K, Ogawa S, Takita J. Integrated multiomics analysis of hepatoblastoma unravels its heterogeneity and provides novel druggable targets. NPJ Precis Oncol 2020; 4:20. [PMID: 32656360 PMCID: PMC7341754 DOI: 10.1038/s41698-020-0125-y] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
Although hepatoblastoma is the most common pediatric liver cancer, its genetic heterogeneity and therapeutic targets are not well elucidated. Therefore, we conducted a multiomics analysis, including mutatome, DNA methylome, and transcriptome analyses, of 59 hepatoblastoma samples. Based on DNA methylation patterns, hepatoblastoma was classified into three clusters exhibiting remarkable correlation with clinical, histological, and genetic features. Cluster F was largely composed of cases with fetal histology and good outcomes, whereas clusters E1 and E2 corresponded primarily to embryonal/combined histology and poor outcomes. E1 and E2, albeit distinguishable by different patient age distributions, were genetically characterized by hypermethylation of the HNF4A/CEBPA-binding regions, fetal liver-like expression patterns, upregulation of the cell cycle pathway, and overexpression of NQO1 and ODC1. Inhibition of NQO1 and ODC1 in hepatoblastoma cells induced chemosensitization and growth suppression, respectively. Our results provide a comprehensive description of the molecular basis of hepatoblastoma and rational therapeutic strategies for high-risk cases.
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Affiliation(s)
- Masahiro Sekiguchi
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masafumi Seki
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Misa Yoshida
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoya Isobe
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noriko Hoshino
- Department of Pediatric Surgery, The University of Tokyo Hospital, Tokyo, Japan
| | - Ryota Shirai
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Mio Tanaka
- Department of Pathology, Kanagawa Children's Medical Center, Kanagawa, Japan
| | - Ryota Souzaki
- Department of Pediatric Surgery, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kentaro Watanabe
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuki Arakawa
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiromichi Suzuki
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoichi Fujii
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuichi Shiraishi
- Center for Cancer Genomics and Advanced Therapeutics, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenichi Chiba
- Center for Cancer Genomics and Advanced Therapeutics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Teppei Shimamura
- Department of Systems Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Yusuke Sato
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Aiko Sato-Otsubo
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shunsuke Kimura
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasuo Kubota
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mitsuteru Hiwatari
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | | | - Yutaka Kanamori
- Division of Surgery, Department of Surgical Specialties, National Center for Child Health and Development, Tokyo, Japan
| | - Mureo Kasahara
- Transplantation Center, National Center for Child Health and Development, Tokyo, Japan
| | - Kenichi Kohashi
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Motohiro Kato
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Takako Yoshioka
- Department of Pathology, National Center for Child Health and Development, Tokyo, Japan
| | - Kimikazu Matsumoto
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoaki Taguchi
- Department of Pediatric Surgery, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masashi Sanada
- Department of Advanced Diagnosis, Clinical Research Center, Nagoya Medical Center, Nagoya, Japan
| | - Yukichi Tanaka
- Department of Pathology, Kanagawa Children's Medical Center, Kanagawa, Japan
| | - Satoru Miyano
- Center for Cancer Genomics and Advanced Therapeutics, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto, Japan.,Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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18
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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] [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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19
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Quintero Escobar M, Maschietto M, Krepischi ACV, Avramovic N, Tasic L. Insights into the Chemical Biology of Childhood Embryonal Solid Tumors by NMR-Based Metabolomics. Biomolecules 2019; 9:biom9120843. [PMID: 31817982 PMCID: PMC6995504 DOI: 10.3390/biom9120843] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/30/2019] [Accepted: 12/02/2019] [Indexed: 01/19/2023] Open
Abstract
Most childhood cancers occur as isolated cases and show very different biological behavior when compared with cancers in adults. There are some solid tumors that occur almost exclusively in children among which stand out the embryonal solid tumors. These cancers main types are neuroblastoma, nephroblastoma (Wilms tumors), retinoblastoma and hepatoblastomas and tumors of the central nervous system (CNS). Embryonal solid tumors represent a heterogeneous group of cancers supposedly derived from undifferentiated cells, with histological features that resemble tissues of origin during embryogenesis. This key observation suggests that tumorigenesis might begin during early fetal or child life due to the errors in growth or pathways differentiation. There are not many literature data on genomic, transcriptomic, epigenetic, proteomic, or metabolomic differences in these types of cancers when compared to the omics- used in adult cancer research. Still, metabolomics by nuclear magnetic resonance (NMR) in childhood embryonal solid tumors research can contribute greatly to understand better metabolic pathways alterations and biology of the embryonal solid tumors and potential to be used in clinical applications. Different types of samples, such as tissues, cells, biofluids, mostly blood plasma and serum, can be analyzed by NMR to detect and identify cancer metabolic signatures and validated biomarkers using enlarged group of samples. The literature search for biomarkers points to around 20-30 compounds that could be associated with pediatric cancer as well as metastasis.
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Affiliation(s)
- Melissa Quintero Escobar
- Biological Chemistry Group, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas 13083-970, Brazil;
- Laboratory of Blood Coagulation, Department of Medical Physiopathology, Hemocentro, University of Campinas (UNICAMP), Campinas 13083-878, Brazil
| | - Mariana Maschietto
- Research Center, Boldrini Children’s Hospital, Campinas 13083-884, Brazil;
| | - Ana C. V. Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo (USP), Sao Paulo 05508-0970, Brazil;
| | - Natasa Avramovic
- Institute of Medical Chemistry, Faculty of Medicine, University of Belgrade, Belgrade 11000, Serbia;
| | - Ljubica Tasic
- Biological Chemistry Group, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas 13083-970, Brazil;
- Correspondence: ; Tel.: +55-19-3521-1106
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20
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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] [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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21
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de Sá Pereira BM, Montalvão-de-Azevedo R, Faria PA, de Paula Silva N, Nicolau-Neto P, Maschietto M, de Camargo B, Soares Lima SC. Association between long interspersed nuclear element-1 methylation levels and relapse in Wilms tumors. Clin Epigenetics 2017; 9:128. [PMID: 29255497 PMCID: PMC5728012 DOI: 10.1186/s13148-017-0431-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/30/2017] [Indexed: 12/18/2022] Open
Abstract
Background Wilms tumor (WT) is a curable pediatric renal malignancy, but there is a need for new molecular biomarkers to improve relapse risk-directed therapy. Somatic alterations occur at relatively low frequencies whereas epigenetic changes at 11p15 are the most common aberration. We analyzed long interspersed element-1 (LINE-1) methylation levels in the blastemal component of WT and normal kidney samples to explore their prognostic significance. Results WT samples presented a hypomethylated pattern at all five CpG sites compared to matched normal kidney samples; therefore, the averaged methylation levels of the five CpG sites were used for further analyses. WT presented a hypomethylation profile (median 65.0%, 47.4–73.2%) compared to normal kidney samples (median 71.8%, 51.5–77.5%; p < 0.0001). No significant associations were found between LINE-1 methylation levels and clinical–pathological characteristics. We observed that LINE-1 methylation levels were lower in tumor samples from patients with relapse (median methylation 60.5%) compared to patients without relapse (median methylation 66.5%; p = 0.0005), and a receiving operating characteristic curve analysis was applied to verify the ability of LINE-1 methylation levels to discriminate WT samples from these patients. Using a cut-off value of 62.71% for LINE-1 methylation levels, the area under the curve was 0.808, with a sensitivity of 76.5% and a specificity of 83.3%. Having identified differences in LINE-1 methylation between WT samples from patients with and without relapse in this cohort, we evaluated other prognostic factors using a logistic regression model. This analysis showed that in risk stratification, LINE-1 methylation level was an independent variable for relapse risk: the lower the methylation levels, the higher the risk of relapse. The logistic regression model indicated a relapse risk increase of 30% per decreased unit of methylation (odds ratio 1.30; 95% confidence interval 1.07–1.57). Conclusion Our results reinforce previous data showing a global hypomethylation profile in WT. LINE-1 methylation levels can be suggested as a marker of relapse after chemotherapy treatment in addition to risk classification, helping to guide new treatment approaches. Electronic supplementary material The online version of this article (10.1186/s13148-017-0431-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bruna M de Sá Pereira
- Post Graduate Program of Instituto Nacional do Cancer (INCA), Rio de Janeiro, Brazil.,Pediatric Hematology-Oncology Research Program, Research Center (CPQ), Instituto Nacional de Câncer (INCA), Rua Andre Cavalcanti 37, Centro, Rio de Janeiro, 20231-050 Brazil
| | - Rafaela Montalvão-de-Azevedo
- Post Graduate Program of Instituto Nacional do Cancer (INCA), Rio de Janeiro, Brazil.,Pediatric Hematology-Oncology Research Program, Research Center (CPQ), Instituto Nacional de Câncer (INCA), Rua Andre Cavalcanti 37, Centro, Rio de Janeiro, 20231-050 Brazil
| | - Paulo Antônio Faria
- Pathology Division of Instituto Nacional do Câncer (DIPAT-INCA), Rua Cordeiro da Graça 156, Santo Cristo, Rio de Janeiro, 20220-400 Brazil
| | - Neimar de Paula Silva
- Post Graduate Program of Instituto Nacional do Cancer (INCA), Rio de Janeiro, Brazil.,Pediatric Hematology-Oncology Research Program, Research Center (CPQ), Instituto Nacional de Câncer (INCA), Rua Andre Cavalcanti 37, Centro, Rio de Janeiro, 20231-050 Brazil
| | - Pedro Nicolau-Neto
- Molecular Carcinogenesis Program, Research Center (CPQ), Instituto Nacional do Câncer (INCA), Rua André Cavalcanti 37, Centro, Rio de Janeiro, 20231-050 Brazil
| | - Mariana Maschietto
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), Rua Giuseppe Máximo Scolfaro 10.000, Bosque das Palmeiras, Campinas, Sao Paulo 13083-970 Brazil
| | - Beatriz de Camargo
- Pediatric Hematology-Oncology Research Program, Research Center (CPQ), Instituto Nacional de Câncer (INCA), Rua Andre Cavalcanti 37, Centro, Rio de Janeiro, 20231-050 Brazil
| | - Sheila Coelho Soares Lima
- Molecular Carcinogenesis Program, Research Center (CPQ), Instituto Nacional do Câncer (INCA), Rua André Cavalcanti 37, Centro, Rio de Janeiro, 20231-050 Brazil
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