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Gómez S, Castellano G, Mayol G, Suñol M, Queiros A, Bibikova M, Nazor KL, Loring JF, Lemos I, Rodríguez E, de Torres C, Mora J, Martín-Subero JI, Lavarino C. DNA methylation fingerprint of neuroblastoma reveals new biological and clinical insights. Epigenomics 2015; 7:1137-53. [PMID: 26067621 DOI: 10.2217/epi.15.49] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
AIM To define the DNA methylation landscape of neuroblastoma and its clinicopathological impact. MATERIALS & METHODS Microarray DNA methylation data were analyzed and associated with functional/regulatory genome annotation data, transcriptional profiles and clinicobiological parameters. RESULTS DNA methylation changes in neuroblastoma affect not only promoters but also intragenic and intergenic regions at cytosine-phosphate-guanine (CpG) and non-CpG sites, and target functional chromatin domains of development and cancer-related genes such as CCND1. Tumors with diverse clinical risk showed differences affecting CpG and, remarkably, non-CpG sites. Non-CpG methylation observed essentially in clinically favorable cases was associated with the differentiation status of neuroblastoma and expression of key genes such as ALK. CONCLUSION This epigenetic fingerprint of neuroblastoma provides new insights into the pathogenesis and clinical behavior of this pediatric tumor.
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Affiliation(s)
- Soledad Gómez
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Edificio Docente 4th floor, C/Santa Rosa 39-57, 08950 Esplugues de Llobregat, Barcelona, Spain
| | - Giancarlo Castellano
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, 08036, Spain
| | - Gemma Mayol
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Edificio Docente 4th floor, C/Santa Rosa 39-57, 08950 Esplugues de Llobregat, Barcelona, Spain
| | - Mariona Suñol
- Department of Pathology, Hospital Sant Joan de Déu, Barcelona, 08950, Spain
| | - Ana Queiros
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, 08036, Spain
| | | | - Kristopher L Nazor
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeanne F Loring
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Isadora Lemos
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Edificio Docente 4th floor, C/Santa Rosa 39-57, 08950 Esplugues de Llobregat, Barcelona, Spain
| | - Eva Rodríguez
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Edificio Docente 4th floor, C/Santa Rosa 39-57, 08950 Esplugues de Llobregat, Barcelona, Spain
| | - Carmen de Torres
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Edificio Docente 4th floor, C/Santa Rosa 39-57, 08950 Esplugues de Llobregat, Barcelona, Spain
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Edificio Docente 4th floor, C/Santa Rosa 39-57, 08950 Esplugues de Llobregat, Barcelona, Spain
| | - José I Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, 08036, Spain.,Department of Anatomic Pathology, Pharmacology & Microbiology, University of Barcelona, Barcelona, 08036, Spain
| | - Cinzia Lavarino
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Edificio Docente 4th floor, C/Santa Rosa 39-57, 08950 Esplugues de Llobregat, Barcelona, Spain
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Rogers DA, Schor NF. Kidins220/ARMS is expressed in neuroblastoma tumors and stabilizes neurotrophic signaling in a human neuroblastoma cell line. Pediatr Res 2013; 74:517-24. [PMID: 23999075 PMCID: PMC3968798 DOI: 10.1038/pr.2013.146] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Accepted: 05/21/2013] [Indexed: 12/26/2022]
Abstract
BACKGROUND Neurotrophic signaling is an important factor in the survival of developing neurons, and the expression of neurotrophic receptors correlates with prognosis in neuroblastoma. Kinase D-interacting substrate of 220 kDa (Kidins220) associates with neurotrophic receptors and stabilizes them, but the expression and function of Kidins220 in neuroblastoma are unknown. METHODS We study Kidins220 expression in human neuroblastoma cell lines and tumor samples by western blotting and microarray analyses. We determine the functional consequences of downregulation of Kidins220 for response of cell lines to oxidative stress, chemotherapeutic treatment, and neurotrophins using small interfering RNA silencing and by measuring cell survival, signaling, and migration. RESULTS Kidins220 is expressed in all neuroblastoma tumors and cell lines studied. Downregulation of Kidins220 leads to attenuation of nerve growth factor (NGF)-induced, but not brain-derived neurotrophic factor (BDNF)-induced, MAPK signaling. However, downregulation of Kidins220 does not alter the response to chemotherapeutic drugs or oxidative stress or affect cellular motility. CONCLUSION Kidins220 is expressed in neuroblastoma tumors and stabilizes NGF-induced, but not BDNF-induced, survival signaling in neuroblastoma cell lines.
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Affiliation(s)
- Danny A. Rogers
- Departments of Pediatrics, Neurology, and Neurobiology & Anatomy, University of Rochester Medical Center, Rochester, NY
| | - Nina F. Schor
- Departments of Pediatrics, Neurology, and Neurobiology & Anatomy, University of Rochester Medical Center, Rochester, NY
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Mayol G, Martín-Subero JI, Ríos J, Queiros A, Kulis M, Suñol M, Esteller M, Gómez S, Garcia I, de Torres C, Rodríguez E, Galván P, Mora J, Lavarino C. DNA hypomethylation affects cancer-related biological functions and genes relevant in neuroblastoma pathogenesis. PLoS One 2012; 7:e48401. [PMID: 23144874 PMCID: PMC3492354 DOI: 10.1371/journal.pone.0048401] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 10/01/2012] [Indexed: 02/06/2023] Open
Abstract
Neuroblastoma (NB) pathogenesis has been reported to be closely associated with numerous genetic alterations. However, underlying DNA methylation patterns have not been extensively studied in this developmental malignancy. Here, we generated microarray-based DNA methylation profiles of primary neuroblastic tumors. Stringent supervised differential methylation analyses allowed us to identify epigenetic changes characteristic for NB tumors as well as for clinical and biological subtypes of NB. We observed that gene-specific loss of DNA methylation is more prevalent than promoter hypermethylation. Remarkably, such hypomethylation affected cancer-related biological functions and genes relevant to NB pathogenesis such as CCND1, SPRR3, BTC, EGF and FGF6. In particular, differential methylation in CCND1 affected mostly an evolutionary conserved functionally relevant 3′ untranslated region, suggesting that hypomethylation outside promoter regions may play a role in NB pathogenesis. Hypermethylation targeted genes involved in cell development and proliferation such as RASSF1A, POU2F2 or HOXD3, among others. The results derived from this study provide new candidate epigenetic biomarkers associated with NB as well as insights into the molecular pathogenesis of this tumor, which involves a marked gene-specific hypomethylation.
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Affiliation(s)
- Gemma Mayol
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - José I. Martín-Subero
- Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Barcelona, Spain
| | - José Ríos
- Laboratory of Biostatistics and Epidemiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Clinical Pharmacology Service, IDIBAPS, Hospital Clinic, Barcelona, Spain
| | - Ana Queiros
- Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Barcelona, Spain
| | - Marta Kulis
- Hematopathology Unit, Hospital Clinic, Barcelona, Spain
| | - Mariona Suñol
- Department of Pathology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL),L'Hospitalet, Barcelona, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Soledad Gómez
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Idoia Garcia
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Carmen de Torres
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Eva Rodríguez
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Patricia Galván
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
| | - Cinzia Lavarino
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
- * E-mail:
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Casalà C, Gil-Guiñón E, Ordóñez JL, Miguel-Queralt S, Rodríguez E, Galván P, Lavarino C, Munell F, de Alava E, Mora J, de Torres C. The calcium-sensing receptor is silenced by genetic and epigenetic mechanisms in unfavorable neuroblastomas and its reactivation induces ERK1/2-dependent apoptosis. Carcinogenesis 2012; 34:268-76. [PMID: 23108190 DOI: 10.1093/carcin/bgs338] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Neuroblastic tumors (NTs) include the neuroblastomas, ganglioneuroblastomas and ganglioneuromas. We have reported previously that the calcium-sensing receptor is expressed in differentiated, favorable NTs but almost undetectable in unfavorable neuroblastomas. We have now detected hypermethylation of a particular region within the CpG island encompassing the CaSR gene promoter 2 in neuroblastoma cell lines and 25% primary neuroblastomas. Hypermethylation of this region was associated with reduced CaSR messenger RNA expression and several predictors of poor outcome in neuroblastomas, including MYCN amplification. Treatment with 5'aza-2-deoxycitidine and/or trichostatin A restored CaSR expression in MYCN-amplified cell lines. Following 5'aza-2-deoxycitidine exposure, decreased percentages of methylated CpG sites were observed at the above-mentioned region. By interphase fluorescence in situ hybridization, variable percentages of nuclei with monosomy of chromosome 3, where the human CaSR gene resides, were observed in more than 90% of primary NTs of all subgroups. Nuclei harboring this alteration were heterogeneously distributed among tumor cells. Ectopic overexpression of the calcium-sensing receptor in two MYCN-amplified neuroblastoma cell lines in which this gene is silenced by promoter hypermethylation significantly reduced their in vitro proliferation rates and almost abolished their capacity to generate xenografts in immunocompromised mice. Finally, upon acute exposure to calcium, the primary activator of this receptor, calcium-sensing receptor-overexpressing neuroblastoma cells underwent apoptosis, a process dependent on sustained activation of ERK1/2. These data would support the hypothesis that epigenetic silencing of the CaSR gene is neither an in vitro artefact in neuroblastoma cell lines nor an irrelevant, secondary event in primary NTs, but a significant mechanism for neuroblastoma survival.
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Affiliation(s)
- Carla Casalà
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu and Fundació Sant Joan de Déu, Barcelona, Spain
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Garcia I, Mayol G, Ríos J, Domenech G, Cheung NKV, Oberthuer A, Fischer M, Maris JM, Brodeur GM, Hero B, Rodríguez E, Suñol M, Galvan P, de Torres C, Mora J, Lavarino C. A three-gene expression signature model for risk stratification of patients with neuroblastoma. Clin Cancer Res 2012; 18:2012-23. [PMID: 22328561 DOI: 10.1158/1078-0432.ccr-11-2483] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
PURPOSE Neuroblastoma is an embryonal tumor with contrasting clinical courses. Despite elaborate stratification strategies, precise clinical risk assessment still remains a challenge. The purpose of this study was to develop a PCR-based predictor model to improve clinical risk assessment of patients with neuroblastoma. EXPERIMENTAL DESIGN The model was developed using real-time PCR gene expression data from 96 samples and tested on separate expression data sets obtained from real-time PCR and microarray studies comprising 362 patients. RESULTS On the basis of our prior study of differentially expressed genes in favorable and unfavorable neuroblastoma subgroups, we identified three genes, CHD5, PAFAH1B1, and NME1, strongly associated with patient outcome. The expression pattern of these genes was used to develop a PCR-based single-score predictor model. The model discriminated patients into two groups with significantly different clinical outcome [set 1: 5-year overall survival (OS): 0.93 ± 0.03 vs. 0.53 ± 0.06, 5-year event-free survival (EFS): 0.85 ± 0.04 vs. 0.042 ± 0.06, both P < 0.001; set 2 OS: 0.97 ± 0.02 vs. 0.61 ± 0.1, P = 0.005, EFS: 0.91 ± 0.8 vs. 0.56 ± 0.1, P = 0.005; and set 3 OS: 0.99 ± 0.01 vs. 0.56 ± 0.06, EFS: 0.96 ± 0.02 vs. 0.43 ± 0.05, both P < 0.001]. Multivariate analysis showed that the model was an independent marker for survival (P < 0.001, for all). In comparison with accepted risk stratification systems, the model robustly classified patients in the total cohort and in different clinically relevant risk subgroups. CONCLUSION We propose for the first time in neuroblastoma, a technically simple PCR-based predictor model that could help refine current risk stratification systems.
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Affiliation(s)
- Idoia Garcia
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Deu, Edificio Docente 4th Floor, 08950 Esplugues de Llobregat, Barcelona 08950, Spain
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Garcia I, Mayol G, Rodríguez E, Suñol M, Gershon TR, Ríos J, Cheung NKV, Kieran MW, George RE, Perez-Atayde AR, Casala C, Galván P, de Torres C, Mora J, Lavarino C. Expression of the neuron-specific protein CHD5 is an independent marker of outcome in neuroblastoma. Mol Cancer 2010; 9:277. [PMID: 20950435 PMCID: PMC2992029 DOI: 10.1186/1476-4598-9-277] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 10/15/2010] [Indexed: 11/30/2022] Open
Abstract
Background The chromodomain, helicase DNA-binding protein 5 (CHD5) is a potential tumor suppressor gene located on chromosome 1p36, a region recurrently deleted in high risk neuroblastoma (NB). Previous data have shown that CHD5 mRNA is present in normal neural tissues and in low risk NB, nevertheless, the distribution of CHD5 protein has not been explored. The aim of this study was to investigate CHD5 protein expression as an immunohistochemical marker of outcome in NB. With this purpose, CHD5 protein expression was analyzed in normal neural tissues and neuroblastic tumors (NTs). CHD5 gene and protein expression was reexamined after induction chemotherapy in a subset of high risk tumors to identify potential changes reflecting tumor response. Results We provide evidence that CHD5 is a neuron-specific protein, absent in glial cells, with diverse expression amongst neuron types. Within NTs, CHD5 immunoreactivity was found restricted to differentiating neuroblasts and ganglion-like cells, and absent in undifferentiated neuroblasts and stromal Schwann cells. Correlation between protein and mRNA levels was found, suggesting transcriptional regulation of CHD5. An immunohistochemical analysis of 90 primary NTs highlighted a strong association of CHD5 expression with favorable prognostic variables (age at diagnosis <12 months, low clinical stage, and favorable histology; P < 0.001 for all), overall survival (OS) (P < 0.001) and event-free survival (EFS) (P < 0.001). Multivariate analysis showed that CHD5 prognostic value is independent of other clinical and biologically relevant parameters, and could therefore represent a marker of outcome in NB that can be tested by conventional immunohistochemistry. The prognostic value of CHD5 was confirmed in an independent, blinded set of 32 NB tumors (P < 0.001). Reactivation of CHD5 expression after induction chemotherapy was observed mainly in those high risk tumors with induced tumor cell differentiation features. Remarkably, these NB tumors showed good clinical response and prolonged patient survival. Conclusions The neuron-specific protein CHD5 may represent a marker of outcome in NB that can be tested by conventional immunohistochemistry. Re-establishment of CHD5 expression induced by chemotherapy could be a surrogate marker of treatment response.
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Affiliation(s)
- Idoia Garcia
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Fundación Sant Joan de Déu, Barcelona, Spain
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Lavarino C, Cheung NKV, Garcia I, Domenech G, de Torres C, Alaminos M, Rios J, Gerald WL, Kushner B, LaQuaglia M, Mora J. Specific gene expression profiles and chromosomal abnormalities are associated with infant disseminated neuroblastoma. BMC Cancer 2009; 9:44. [PMID: 19192278 PMCID: PMC2642835 DOI: 10.1186/1471-2407-9-44] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Accepted: 02/03/2009] [Indexed: 12/14/2022] Open
Abstract
Background Neuroblastoma (NB) tumours have the highest incidence of spontaneous remission, especially among the stage 4s NB subgroup affecting infants. Clinical distinction of stage 4s from lethal stage 4 can be difficult, but critical for therapeutic decisions. The aim of this study was to investigate chromosomal alterations and differential gene expression amongst infant disseminated NB subgroups. Methods Thirty-five NB tumours from patients diagnosed at < 18 months (25 stage 4 and 10 stage 4s), were evaluated by allelic and gene expression analyses. Results All stage 4s patients underwent spontaneous remission, only 48% stage 4 patients survived despite combined modality therapy. Stage 4 tumours were 90% near-diploid/tetraploid, 44% MYCN amplified, 77% had 1p LOH (50% 1p36), 23% 11q and/or 14q LOH (27%) and 47% had 17q gain. Stage 4s were 90% near-triploid, none MYCN amplified and LOH was restricted to 11q. Initial comparison analyses between stage 4s and 4 < 12 months tumours revealed distinct gene expression profiles. A significant portion of genes mapped to chromosome 1 (P < 0.0001), 90% with higher expression in stage 4s, and chromosome 11 (P = 0.0054), 91% with higher expression in stage 4. Less definite expression profiles were observed between stage 4s and 4 < 18m, yet, association with chromosomes 1 (P < 0.0001) and 11 (P = 0.005) was maintained. Distinct gene expression profiles but no significant association with specific chromosomal region localization was observed between stage 4s and stage 4 < 18 months without MYCN amplification. Conclusion Specific chromosomal aberrations are associated with distinct gene expression profiles which characterize spontaneously regressing or aggressive infant NB, providing the biological basis for the distinct clinical behaviour.
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Affiliation(s)
- Cinzia Lavarino
- Developmental tumour biology laboratory, Hospital Sant Joan de Déu, Fundació Sant Joan de Deu, Barcelona, Spain.
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