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Epp S, Chuah SM, Halasz M. Epigenetic Dysregulation in MYCN-Amplified Neuroblastoma. Int J Mol Sci 2023; 24:17085. [PMID: 38069407 PMCID: PMC10707345 DOI: 10.3390/ijms242317085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Neuroblastoma (NB), a childhood cancer arising from the neural crest, poses significant clinical challenges, particularly in cases featuring amplification of the MYCN oncogene. Epigenetic factors play a pivotal role in normal neural crest and NB development, influencing gene expression patterns critical for tumorigenesis. This review delves into the multifaceted interplay between MYCN and known epigenetic modifications during NB genesis, shedding light on the intricate regulatory networks underlying the disease. We provide an extensive survey of known epigenetic mechanisms, encompassing DNA methylation, histone modifications, non-coding RNAs, super-enhancers (SEs), bromodomains (BET), and chromatin modifiers in MYCN-amplified (MNA) NB. These epigenetic changes collectively contribute to the dysregulated gene expression landscape observed in MNA NB. Furthermore, we review emerging therapeutic strategies targeting epigenetic regulators, including histone deacetylase inhibitors (HDACi), histone methyltransferase inhibitors (HMTi), and DNA methyltransferase inhibitors (DNMTi). We also discuss and summarize current drugs in preclinical and clinical trials, offering insights into their potential for improving outcomes for MNA NB patients.
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Affiliation(s)
- Soraya Epp
- Systems Biology Ireland, UCD School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (S.E.)
| | - Shin Mei Chuah
- Systems Biology Ireland, UCD School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (S.E.)
| | - Melinda Halasz
- Systems Biology Ireland, UCD School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (S.E.)
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
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2
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Hassn Mesrati M, Syafruddin SE, Mohtar MA, Syahir A. CD44: A Multifunctional Mediator of Cancer Progression. Biomolecules 2021; 11:1850. [PMID: 34944493 PMCID: PMC8699317 DOI: 10.3390/biom11121850] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/23/2021] [Accepted: 11/02/2021] [Indexed: 12/15/2022] Open
Abstract
CD44, a non-kinase cell surface transmembrane glycoprotein, has been widely implicated as a cancer stem cell (CSC) marker in several cancers. Cells overexpressing CD44 possess several CSC traits, such as self-renewal and epithelial-mesenchymal transition (EMT) capability, as well as a resistance to chemo- and radiotherapy. The CD44 gene regularly undergoes alternative splicing, resulting in the standard (CD44s) and variant (CD44v) isoforms. The interaction of such isoforms with ligands, particularly hyaluronic acid (HA), osteopontin (OPN) and matrix metalloproteinases (MMPs), drive numerous cancer-associated signalling. However, there are contradictory results regarding whether high or low CD44 expression is associated with worsening clinicopathological features, such as a higher tumour histological grade, advanced tumour stage and poorer survival rates. Nonetheless, high CD44 expression significantly contributes to enhanced tumourigenic mechanisms, such as cell proliferation, metastasis, invasion, migration and stemness; hence, CD44 is an important clinical target. This review summarises current research regarding the different CD44 isoform structures and their roles and functions in supporting tumourigenesis and discusses CD44 expression regulation, CD44-signalling pathways and interactions involved in cancer development. The clinical significance and prognostic value of CD44 and the potential of CD44 as a therapeutic target in cancer are also addressed.
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Affiliation(s)
- Malak Hassn Mesrati
- Nanobiotechnology Research Group, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia;
| | - Saiful Effendi Syafruddin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur 56000, Malaysia; (S.E.S.); (M.A.M.)
| | - M. Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur 56000, Malaysia; (S.E.S.); (M.A.M.)
| | - Amir Syahir
- Nanobiotechnology Research Group, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia;
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia
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MYCN in Neuroblastoma: "Old Wine into New Wineskins". Diseases 2021; 9:diseases9040078. [PMID: 34842635 PMCID: PMC8628738 DOI: 10.3390/diseases9040078] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
MYCN Proto-Oncogene, BHLH Transcription Factor (MYCN) has been one of the most studied genes in neuroblastoma. It is known for its oncogenetic mechanisms, as well as its role in the prognosis of the disease and it is considered one of the prominent targets for neuroblastoma therapy. In the present work, we attempted to review the literature, on the relation between MYCN and neuroblastoma from all possible mechanistic sites. We have searched the literature for the role of MYCN in neuroblastoma based on the following topics: the references of MYCN in the literature, the gene's anatomy, along with its transcripts, the protein's anatomy, the epigenetic mechanisms regulating MYCN expression and function, as well as MYCN amplification. MYCN plays a significant role in neuroblastoma biology. Its functions and properties range from the forming of G-quadraplexes, to the interaction with miRNAs, as well as the regulation of gene methylation and histone acetylation and deacetylation. Although MYCN is one of the most primary genes studied in neuroblastoma, there is still a lot to be learned. Our knowledge on the exact mechanisms of MYCN amplification, etiology and potential interventions is still limited. The knowledge on the molecular mechanisms of MYCN in neuroblastoma, could have potential prognostic and therapeutic advantages.
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Sanfilippo V, Caruso VCL, Cucci LM, Inturri R, Vaccaro S, Satriano C. Hyaluronan-Metal Gold Nanoparticle Hybrids for Targeted Tumor Cell Therapy. Int J Mol Sci 2020; 21:E3085. [PMID: 32349323 PMCID: PMC7247672 DOI: 10.3390/ijms21093085] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/16/2020] [Accepted: 04/25/2020] [Indexed: 12/18/2022] Open
Abstract
In this study, a novel multifunctional nanoplatform based on core-shell nanoparticles of spherical gold nanoparticles (AuNPs) capped with low and high molecular weight (200 and 700 kDa) hyaluronic acid (HA), was assembled via a green, one-pot redox synthesis method at room temperature. A multitechnique characterization approach by UV-visible spectroscopy, dynamic light scattering and atomic force microscopy pointed to the effective 'surface decoration' of the gold nanoparticles by HA, resulting in different grafting densities of the biopolymer chains at the surface of the metal nanoparticle, which in turn affected the physicochemical properties of the nanoparticles. Specifically, the spectral features of the gold plasmonic peak (and the related calculated optical size), the hydrodynamic diameter and the nanoparticle stability were found to depend on the molecular weight of the HA. The CD44-targeting capability of HA-functionalized gold nanoparticles was tested in terms of antibacterial activity and cytotoxicity. An enhanced inhibitory activity against both Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus was found, with a HA molecular weight (MW)-dependent trend for the HA-capped AuNPs compared to the bare, glucose-capped AuNPs. Cell viability assays performed on two CD44-positive cell models, namely normal human umbilical vein endothelial (HUVEC) and prostate tumor (PC-3) cells, in comparison with neuroblastoma cells (SH-SY5Y), which do not express the CD44 receptor, demonstrated an increased cytotoxicity in neuroblastoma compared to prostate cancer cells upon the cellular treatments by HA-AuNP compared to the bare AuNP, but a receptor-dependent perturbation effect on cytoskeleton actin and lysosomal organelles, as detected by confocal microscopy. These results highlighted the promising potentialities of the HA-decorated gold nanoparticles for selective cytotoxicity in cancer therapy. Confocal microscopy imaging of the two human tumor cell models demonstrated a membrane-confined uptake of HA-capped AuNP in the cancer cells that express CD44 receptors and the different perturbation effects related to molecular weight of HA wrapping the metallic core of the plasmonic nanoparticles on cellular organelles and membrane mobility.
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Affiliation(s)
- Vanessa Sanfilippo
- Nano-Hybrid-BioInterfacesLab (NHBIL), Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Viviana Carmela Linda Caruso
- Nano-Hybrid-BioInterfacesLab (NHBIL), Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Lorena Maria Cucci
- Nano-Hybrid-BioInterfacesLab (NHBIL), Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Rosanna Inturri
- Fidia Farmaceutici S.p.A., R&D Unità locale Fidia Research sud, Contrada Pizzuta, 96017 Noto (SR), Italy
| | - Susanna Vaccaro
- Fidia Farmaceutici S.p.A., R&D Unità locale Fidia Research sud, Contrada Pizzuta, 96017 Noto (SR), Italy
| | - Cristina Satriano
- Nano-Hybrid-BioInterfacesLab (NHBIL), Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
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Stojanović S, Najman S, Korać A. Stem Cells Derived from Lipoma and Adipose Tissue-Similar Mesenchymal Phenotype but Different Differentiation Capacity Governed by Distinct Molecular Signature. Cells 2018; 7:E260. [PMID: 30544806 PMCID: PMC6316974 DOI: 10.3390/cells7120260] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 11/29/2018] [Accepted: 12/06/2018] [Indexed: 01/09/2023] Open
Abstract
Lipomas are benign adipose tissue tumors of unknown etiology, which can vary in size, number, body localization and cell populations within the tissue. Lipoma-derived stem cells (LDSCs) are proposed as a potential tool in regenerative medicine and tissue engineering due to their similar characteristics with adipose-derived stem cells (ADSCs) reported so far. Our study is among the first giving detailed insights into the molecular signature and differences in the differentiation capacity of LDSCs in vitro compared to ADSCs. Mesenchymal stem cell phenotype was analyzed by gene expression and flow cytometric analysis of stem cell markers. Adipogenesis and osteogenesis were analyzed by microscopic analysis, cytochemical and immunocytochemical staining, gene and protein expression analyses. We showed that both LDSCs and ADSCs were mesenchymal stem cells with similar phenotype and stemness state but different molecular basis for potential differentiation. Adipogenesis-related genes expression pattern and presence of more mature adipocytes in ADSCs than in LDSCs after 21 days of adipogenic differentiation, indicated that differentiation capacity of LDSCs was significantly lower compared to ADSCs. Analysis of osteogenesis-related markers after 16 days of osteogenic differentiation revealed that both types of cells had characteristic osteoblast-like phenotype, but were at different stages of osteogenesis. Differences observed between LDSCs and ADSCs are probably due to the distinct molecular signature and their commitment in the tissue that governs their different capacity and fate during adipogenic and osteogenic induction in vitro despite their similar mesenchymal phenotype.
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Affiliation(s)
- Sanja Stojanović
- Department of Biology and Human Genetics and Department for Cell and Tissue Engineering, Faculty of Medicine, University of Niš, 18000 Niš, Serbia.
| | - Stevo Najman
- Department of Biology and Human Genetics and Department for Cell and Tissue Engineering, Faculty of Medicine, University of Niš, 18000 Niš, Serbia.
| | - Aleksandra Korać
- Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia.
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Ram Kumar RM, Schor NF. Methylation of DNA and chromatin as a mechanism of oncogenesis and therapeutic target in neuroblastoma. Oncotarget 2018; 9:22184-22193. [PMID: 29774131 PMCID: PMC5955135 DOI: 10.18632/oncotarget.25084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/21/2018] [Indexed: 12/17/2022] Open
Abstract
Neuroblastoma (NB), a developmental cancer, is often fatal, emphasizing the need to understand its pathogenesis and identify new therapeutic targets. The heterogeneous pathological and clinical phenotype of NB underscores the cryptic biological and genetic features of this tumor that result in outcomes ranging from rapid progression to spontaneous regression. Despite recent genome-wide mutation analyses, most primary NBs do not harbor driver mutations, implicating epigenetically-mediated gene regulatory mechanisms in the initiation and maintenance of NB. Aberrant epigenomic mechanisms, as demonstrated by global changes in DNA methylation signatures, acetylation, re-distribution of histone marks, and change in the chromatin architecture, are hypothesized to play a role in NB oncogenesis. This paper reviews the evidence for, putative mechanisms underlying, and prospects for therapeutic targeting of NB oncogenesis related to DNA methylation.
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Affiliation(s)
- Ram Mohan Ram Kumar
- Department of Pediatrics and Wilmot Cancer Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Nina Felice Schor
- Department of Pediatrics and Wilmot Cancer Center, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Current affiliation: National Institute of Neurological Disorders & Stroke, National Institutes of Health, Bethesda, MD, USA
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Yang G, Fu S, Yao W, Wang X, Zha Q, Tang R. Hyaluronic acid nanogels prepared via ortho ester linkages show pH-triggered behavior, enhanced penetration and antitumor efficacy in 3-D tumor spheroids. J Colloid Interface Sci 2017; 504:25-38. [DOI: 10.1016/j.jcis.2017.05.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/06/2017] [Accepted: 05/11/2017] [Indexed: 02/05/2023]
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Epigenetic basis of cancer health disparities: Looking beyond genetic differences. Biochim Biophys Acta Rev Cancer 2017; 1868:16-28. [PMID: 28108348 DOI: 10.1016/j.bbcan.2017.01.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/07/2017] [Accepted: 01/16/2017] [Indexed: 12/18/2022]
Abstract
Despite efforts at various levels, racial health disparities still exist in cancer patients. These inequalities in incidence and/or clinical outcome can only be explained by a multitude of factors, with genetic basis being one of them. Several investigations have provided convincing evidence to support epigenetic regulation of cancer-associated genes, which results in the differential transcriptome and proteome, and may be linked to a pre-disposition of individuals of certain race/ethnicity to early or more aggressive cancers. Recent technological advancements and the ability to quickly analyze whole genome have aided in these efforts, and owing to their relatively easy detection, methylation events are much well-characterized, than the acetylation events, across human populations. The early trend of investigating a pre-determined set of genes for differential epigenetic regulation is paving way for more unbiased screening. This review summarizes our current understanding of the epigenetic events that have been tied to the racial differences in cancer incidence and mortality. A better understanding of the epigenetics of racial diversity holds promise for the design and execution of novel strategies targeting the human epigenome for reducing the disparity gaps.
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Siapati EK, Rouka E, Kyriakou D, Vassilopoulos G. Neuroblastoma cells negative for CD44 possess tumor-initiating properties. Cell Oncol (Dordr) 2011; 34:189-97. [PMID: 21424816 DOI: 10.1007/s13402-011-0022-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2011] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND CD44 has been linked to favorable prognosis in neuroblastoma and in the present study we investigate if it can be used to prospectively isolate neuroblastoma-initiating cells. METHODS To define the cancer-initiating properties of CD44 positive and negative cells, we FACS-sorted the SK-N-SH neuroblastoma cell line on the basis of CD44 expression and proceeded to phenotypically and molecularly characterize the two cell subpopulations. RESULTS We found that CD44 defines two morphologically distinctive cell populations with different adhesion molecule profiles, and that CD44 negative cells expressed higher levels of the neuroblastoma-initiating cell marker CD24. When inoculated subcutaneously into NOD/SCID animals, the CD44 negative cells were capable of tumor formation and organ infiltration, clearly demonstrating an inverse correlation of CD44 expression and neuroblastoma metastases formation. Gene expression analysis revealed that CD44 defines molecularly discrete cell types with the CD44 negative cells expressing proteins associated with uncontrolled cell cycle progression, immune evasion and a reduced capacity to undergo apoptosis. CONCLUSION Collectively, our findings show that CD44 negative neuroblastoma cells possess all the phenotypic and molecular features required for a cancer-initiating cell.
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Affiliation(s)
- Elena K Siapati
- Cell and Gene Therapy Lab, Basic Research II, Biomedical Research Foundation of the Academy of Athens, Greece.
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Grau E, Martinez F, Orellana C, Canete A, Yañez Y, Oltra S, Noguera R, Hernandez M, Bermúdez JD, Castel V. Hypermethylation of apoptotic genes as independent prognostic factor in neuroblastoma disease. Mol Carcinog 2010; 50:153-62. [PMID: 21104989 DOI: 10.1002/mc.20700] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 09/05/2010] [Accepted: 10/05/2010] [Indexed: 11/08/2022]
Abstract
Neuroblastoma (NB) is an embryonal tumour of neuroectodermal cells, and its prognosis is based on patient age at diagnosis, tumour stage and MYCN amplification, but it can also be classified according to their degree of methylation. Considering that epigenetic aberrations could influence patient survival, we studied the methylation status of a series of 17 genes functionally involved in different cellular pathways in patients with NB and their impact on survival. We studied 82 primary NB tumours and we used methylation-specific-PCR to perform the epigenetic analysis. We evaluated the putative association among the evidence of hypermethylation with the most important NB prognostic factors, as well as to determine the relationship among methylation, clinical classification and survival. CASP8 hypermethylation showed association with relapse susceptibility and, TMS1 and APAF1 hypermethylation are associated with bad prognosis and showed high influence on NB overall survival. Hypermethylation of apoptotic genes has been identified as a good candidate of prognostic factor. We propose the simultaneous analysis of hypermethylation of APAF1, TMS1 and CASP8 apoptotic genes on primary NB tumour as a good prognostic factor of disease progression.
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Affiliation(s)
- Elena Grau
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario La Fe, Valencia, Spain
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George RE, Lahti JM, Adamson PC, Zhu K, Finkelstein D, Ingle AM, Reid JM, Krailo M, Neuberg D, Blaney SM, Diller L. Phase I study of decitabine with doxorubicin and cyclophosphamide in children with neuroblastoma and other solid tumors: a Children's Oncology Group study. Pediatr Blood Cancer 2010; 55:629-38. [PMID: 20589651 PMCID: PMC3025700 DOI: 10.1002/pbc.22607] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Demethylating agents may alter the expression of genes involved in chemotherapy resistance. We conducted a phase I trial to determine the toxicity and molecular effects of the demethylating agent, decitabine, followed by doxorubicin and cyclophosphamide in children with refractory solid tumors. PROCEDURE Stratum A included children with any solid tumor; Stratum B included neuroblastoma patients only. Patients received a 1-hr decitabine infusion for 7 days, followed by doxorubicin (45 mg/m(2)) and cyclophosphamide (1 g/m(2)) on day 7. Pharmacokinetic studies were performed after the first dose of decitabine. Biological studies included methylation and gene expression analyses of caspase-8, MAGE-1 and fetal hemoglobin (HbF), and expression profiling of pre- and post-treatment peripheral blood and bone marrow cells. RESULTS The maximum-tolerated dose of decitabine was 5 mg/m(2)/day for 7 days. Dose-limiting toxicities at 10 mg/m(2)/day were neutropenia and thrombocytopenia. Decitabine exhibited rapid clearance from plasma. Three of 9 patients in Stratum A and 4/12 patients in Stratum B had stable disease for > or = 4 months. Sustained MAGE-1 demethylation and increased HbF expression were observed in the majority of patients post-treatment (12/20 and 14/16, respectively). Caspase-8 promoter demethylation and gene expression were seen in 2/7 bone marrow samples. Differentially expressed genes were identified by microarray analysis. CONCLUSION Low-dose decitabine when combined with doxorubicin/cyclophosphamide has tolerable toxicity in children. However, doses of decitabine capable of producing clinically relevant biologic effects were not well tolerated with this combination. Alternative strategies of combining demethylating agents with non-cytotoxic, biologically targeted agents such as histone deacetylase inhibitors should be explored.
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Affiliation(s)
- Rani E. George
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Children’s Hospital, Boston, Massachusetts,Correspondence: Rani E. George, MD PhD MRCP, Department of Pediatric Hematology and Oncology, Dana 322, Dana-Farber Cancer Institute, 44 Binney St, Boston, MA 02115; Tel: 617 632 5281; Fax: 617 632 4850;
| | - Jill M. Lahti
- St. Jude Children’s Research Hospital, Memphis, Tennessee
| | | | - Kejin Zhu
- St. Jude Children’s Research Hospital, Memphis, Tennessee
| | | | | | - Joel M. Reid
- Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Mark Krailo
- Children’s Oncology Group, Arcadia, California
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Children’s Hospital, Boston, Massachusetts
| | | | - Lisa Diller
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Children’s Hospital, Boston, Massachusetts
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Bmi1 is a MYCN target gene that regulates tumorigenesis through repression of KIF1Bbeta and TSLC1 in neuroblastoma. Oncogene 2010; 29:2681-90. [PMID: 20190806 DOI: 10.1038/onc.2010.22] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent advances in neuroblastoma (NB) research addressed that epigenetic alterations such as hypermethylation of promoter sequences, with consequent silencing of tumor-suppressor genes, can have significant roles in the tumorigenesis of NB. However, the exact role of epigenetic alterations, except for DNA hypermethylation, remains to be elucidated in NB research. In this paper, we clarified the direct binding of MYCN to Bmi1 promoter and upregulation of Bmi1 transcription by MYCN. Mutation introduction into an MYCN binding site in the Bmi1 promoter suggests that MYCN has more important roles in the transcription of Bmi1 than E2F-related Bmi1 regulation. A correlation between MYCN and polycomb protein Bmi1 expression was observed in primary NB tumors. Expression of Bmi1 resulted in the acceleration of proliferation and colony formation in NB cells. Bmi1-related inhibition of NB cell differentiation was confirmed by neurite extension assay and analysis of differentiation marker molecules. Intriguingly, the above-mentioned Bmi1-related regulation of the NB cell phenotype seems not to be mediated only by p14ARF/p16INK4a in NB cells. Expression profiling analysis using a tumor-specific cDNA microarray addressed the Bmi1-dependent repression of KIF1Bbeta and TSLC1, which have important roles in predicting the prognosis of NB. Chromatin immunoprecipitation assay showed that KIF1Bbeta and TSLC1 are direct targets of Bmi1 in NB cells. These findings suggest that MYCN induces Bmi1 expression, resulting in the repression of tumor suppressors through Polycomb group gene-mediated epigenetic chromosome modification. NB cell proliferation and differentiation seem to be partially dependent on the MYCN/Bmi1/tumor-suppressor pathways.
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Crea F, Danesi R, Farrar WL. Cancer stem cell epigenetics and chemoresistance. Epigenomics 2009; 1:63-79. [DOI: 10.2217/epi.09.4] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Cancer stem cells (CSCs) are thought to sustain cancer progression, metastasis and recurrence after therapy. There is in vitro and in vivo evidence supporting the idea that CSCs are highly chemoresistant. Epigenetic gene regulation is crucial for both stem cell biology and chemoresistance. In this review, we summarize current data on epigenetic mechanisms of chemoresistance in cancer stem cells. We propose a model integrating classical CSC pathways (Wnt, Hedgehog and Notch), epigenetic effectors (Polycomb) and drug resistance genes (ABCG2, CD44). Moreover, we analyze the potential of epigenetic drugs to reverse CSC chemoresistance. In the future, CSC epigenomic profiling could help to dissect specific chemoresistance pathways, and have a significant clinical impact for patient stratification and rational design of therapeutic regimens.
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Yi JM, Tsai HC, Glöckner SC, Lin S, Ohm JE, Easwaran H, James CD, Costello JF, Riggins G, Eberhart CG, Laterra J, Vescovi AL, Ahuja N, Herman JG, Schuebel KE, Baylin SB. Abnormal DNA methylation of CD133 in colorectal and glioblastoma tumors. Cancer Res 2008; 68:8094-103. [PMID: 18829568 DOI: 10.1158/0008-5472.can-07-6208] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Much recent effort has focused on identifying and characterizing cellular markers that distinguish tumor propagating cells (TPC) from more differentiated progeny. We report here an unusual promoter DNA methylation pattern for one such marker, the cell surface antigen CD133 (Prominin 1). This protein has been extensively used to enrich putative cancer propagating stem-like cell populations in epithelial tumors and, especially, glioblastomas. We find that, within individual cell lines of cultured colon cancers and glioblastomas, the promoter CpG island of CD133 is DNA methylated, primarily, in cells with absent or low expression of the marker protein, whereas lack of such methylation is evident in purely CD133+ cells. Differential histone modification marks of active versus repressed genes accompany these DNA methylation changes. This heterogeneous CpG island DNA methylation status in the tumors is unusual in that other DNA hypermethylated genes tested in such cultures preserve their methylation patterns between separated CD133+ and CD133- cell populations. Furthermore, the CD133 DNA methylation seems to constitute an abnormal promoter signature because it is not found in normal brain and colon but only in cultured and primary tumors. Thus, the DNA methylation is imposed on the transition between the active versus repressed transcription state for CD133 only in tumors. Our findings provide additional insight for the dynamics of aberrant DNA methylation associated with aberrant gene silencing in human tumors.
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Affiliation(s)
- Joo Mi Yi
- Cancer Biology Division, Johns Hopkins Kimmel Cancer Center, USA
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Hoebeeck J, Michels E, Pattyn F, Combaret V, Vermeulen J, Yigit N, Hoyoux C, Laureys G, De Paepe A, Speleman F, Vandesompele J. Aberrant methylation of candidate tumor suppressor genes in neuroblastoma. Cancer Lett 2008; 273:336-46. [PMID: 18819746 DOI: 10.1016/j.canlet.2008.08.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Revised: 07/19/2008] [Accepted: 08/18/2008] [Indexed: 11/29/2022]
Abstract
CpG island hypermethylation has been recognized as an alternative mechanism for tumor suppressor gene inactivation. In this study, we performed methylation-specific PCR (MSP) to investigate the methylation status of 10 selected tumor suppressor genes in neuroblastoma. Seven of the investigated genes (CD44, RASSF1A, CASP8, PTEN, ZMYND10, CDH1, PRDM2) showed high frequencies (> or =30%) of methylation in 33 neuroblastoma cell lines. In 42 primary neuroblastoma tumors, the frequencies of methylation were 69%, CD44; 71%, RASSF1A; 56%, CASP8; 25%, PTEN; 15%, ZMYND10; 8%, CDH1; and 0%, PRDM2. Furthermore, CASP8 and CDH1 hypermethylation was significantly associated with poor event-free survival. Meta-analysis of 115 neuroblastoma tumors demonstrated a significant correlation between CASP8 methylation and MYCN amplification. In addition, there was a correlation between ZMYND10 methylation and MYCN amplification. The MSP data, together with optimized mRNA re-expression experiments (in terms of concentration and time of treatment and use of proper reference genes) further strengthen the notion that epigenetic alterations could play a significant role in NB oncogenesis. This study thus warrants the need for a global profiling of gene promoter hypermethylation to identify genome-wide aberrantly methylated genes in order to further understand neuroblastoma pathogenesis and to identify prognostic methylation markers.
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Affiliation(s)
- Jasmien Hoebeeck
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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16
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Novakovic B, Rakyan V, Ng HK, Manuelpillai U, Dewi C, Wong NC, Morley R, Down T, Beck S, Craig JM, Saffery R. Specific tumour-associated methylation in normal human term placenta and first-trimester cytotrophoblasts. Mol Hum Reprod 2008; 14:547-54. [PMID: 18708652 DOI: 10.1093/molehr/gan046] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Human placentation displays many similarities with tumourigenesis, including rapid cell division, migration and invasion, overlapping gene expression profiles and escape from immune detection. Recent data have identified promoter methylation in the Ras association factor and adenomatous polyposis coli tumour suppressor genes as part of this process. However, the extent of tumour-associated methylation in the placenta remains unclear. Using whole genome methylation data as a starting point, we have examined this phenomenon in placental tissue. We found no evidence for methylation of the majority of common tumour suppressor genes in term placentas, but identified methylation in several genes previously described in some human tumours. Notably, promoter methylation of four independent negative regulators of Wnt signalling has now been identified in human placental tissue and purified trophoblasts. Methylation is present in baboon, but not in mouse placentas. This supports a role for elevated Wnt signalling in primate trophoblast invasiveness and placentation. Examination of invasive choriocarcinoma cell lines revealed altered methylation patterns consistent with a role of methylation change in gestational trophoblastic disease. This distinct pattern of tumour-associated methylation implicates a coordinated series of epigenetic silencing events, similar to those associated with some tumours, in the distinct features of normal human placental invasion and function.
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Affiliation(s)
- B Novakovic
- Developmental Epigenetics Research, Murdoch Children's Research Institute, Royal Children's Hospital, VIC 3052, Australia
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17
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de Bruijn DRH, Nap JP, van Kessel AG. The (epi)genetics of human synovial sarcoma. Genes Chromosomes Cancer 2007; 46:107-17. [PMID: 17117414 DOI: 10.1002/gcc.20399] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Human synovial sarcomas are aggressive soft tissue tumors with relatively high rates of recurrences and metastases. They display a variable response to common treatment protocols such as radiation and chemotherapy. For the development of novel diagnostic, prognostic, and therapeutic approaches, detailed information on the molecular mechanisms underlying the development of these tumors is of imperative importance. Fusion of the SS18 and (one of the) SSX genes is a molecular hallmark of human synovial sarcomas. The SS18 and SSX genes encode nuclear proteins that exhibit opposite transcription regulatory activities, likely through epigenetic mechanisms. The SS18 protein functions as a transcriptional coactivator and interacts directly with members of the epigenetic chromatin remodeling and modification machineries. In contrast, the SSX proteins function as transcriptional corepressors and are associated with several Polycomb group proteins. Since the domains involved in these apparently opposite transcription regulatory activities are retained in the SS18-SSX fusion proteins, we hypothesize that these fusion proteins function as "activator-repressors" of transcription. The implications of this model for human synovial sarcoma development and future treatment are discussed.
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Affiliation(s)
- Diederik R H de Bruijn
- Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen Center for Molecular Life Sciences, Nijmegen, The Netherlands
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18
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Yang Q, Kiernan CM, Tian Y, Salwen HR, Chlenski A, Brumback BA, London WB, Cohn SL. Methylation of CASP8, DCR2, and HIN-1 in neuroblastoma is associated with poor outcome. Clin Cancer Res 2007; 13:3191-7. [PMID: 17545522 DOI: 10.1158/1078-0432.ccr-06-2846] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Epigenetic aberrations have been shown to play an important role in the pathogenesis of most cancers. To investigate the clinical significance of epigenetic changes in neuroblastoma, we evaluated the relationship between clinicopathologic variables and the pattern of gene methylation in neuroblastoma cell lines and tumors. EXPERIMENTAL DESIGN Methylation-specific PCR was used to evaluate the gene methylation status of 19 genes in 14 neuroblastoma cell lines and 8 genes in 70 primary neuroblastoma tumors. Associations between gene methylation, established prognostic factors, and outcome were evaluated. Log-rank tests were used to identify the number of methylated genes that was most predictive of overall survival. RESULTS Epigenetic changes were detected in the neuroblastoma cell lines and primary tumors, although the pattern of methylation varied. Eight of the 19 genes analyzed were methylated in >70% of the cell lines. Epigenetic changes of four genes were detected in only small numbers of cell lines. None of the cell lines had methylation of the other seven genes analyzed. In primary neuroblastoma tumors, high-risk disease and poor outcome were associated with methylation of DCR2, CASP8, and HIN-1 individually. Although methylation of the other five individual genes was not predictive of poor outcome, a trend toward decreased survival was seen in patients with a methylation phenotype, defined as > or =4 methylated genes (P = 0.055). CONCLUSION Our study indicates that clinically aggressive neuroblastoma tumors have aberrant methylation of multiple genes and provides a rationale for exploring treatment strategies that include demethylating agents.
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Affiliation(s)
- Qiwei Yang
- The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
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19
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Sugino Y, Misawa A, Inoue J, Kitagawa M, Hosoi H, Sugimoto T, Imoto I, Inazawa J. Epigenetic silencing of prostaglandin E receptor 2 (PTGER2) is associated with progression of neuroblastomas. Oncogene 2007; 26:7401-13. [PMID: 17533365 DOI: 10.1038/sj.onc.1210550] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We previously identified a cluster of prostanoid receptor genes, prostaglandin D2 receptor (PTGDR) and prostaglandin E receptor 2 (PTGER2), as possible targets for DNA methylation in advanced types of neuroblastoma (NB) using bacterial artificial chromosome array-based methylated CpG island amplification method. Among them, in this study, we found that PTGER2 was frequently silenced in NB cell lines, especially in those with MYCN amplification, through epigenetic mechanisms. In NB cell lines, DNA methylation pattern within a part of CpG island was inversely correlated with PTGER2 expression, and histone H3 and H4 deacetylation and histone H3 lysine 9 methylation within the putative promoter region were more directly correlated with silencing of this gene. Methylation of PTGER2 was observed more frequently in advanced-type of primary NBs compared with early-stage tumors. Growth of NB cells lacking endogenous PTGER2 expression was inhibited by restoration of the gene product by transient and stable transfection. A PTGER2-selective agonist, butaprost, increased intracellular cyclic adenosine monophosphate (cAMP) level, inhibited cell growth and induced apoptosis of NB cells stably expressing exogenous PTGER2. 8-Bromo-cAMP also inhibited growth of NB cells lacking PTGER2 expression, but not cells expressing this gene. Taken together, it is suggested that NB cells may lose responsiveness to PTGER2-mediated growth inhibition/apoptosis through epigenetic silencing of PTGER2 and/or disruption of downstream cAMP-dependent pathway during the neuroblastomagenesis.
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MESH Headings
- 8-Bromo Cyclic Adenosine Monophosphate/pharmacology
- Alprostadil/analogs & derivatives
- Alprostadil/pharmacology
- Cell Growth Processes/drug effects
- Cell Growth Processes/genetics
- Cell Line, Tumor
- Chromatin Immunoprecipitation
- CpG Islands
- DNA Methylation
- Dinoprostone/pharmacology
- Disease Progression
- Epigenesis, Genetic
- Gene Expression Regulation, Neoplastic
- Gene Silencing
- Genes, Tumor Suppressor
- Humans
- Neuroblastoma/genetics
- Neuroblastoma/metabolism
- Neuroblastoma/pathology
- Promoter Regions, Genetic
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Receptors, Immunologic/biosynthesis
- Receptors, Immunologic/genetics
- Receptors, Prostaglandin/biosynthesis
- Receptors, Prostaglandin/genetics
- Receptors, Prostaglandin E/biosynthesis
- Receptors, Prostaglandin E/genetics
- Receptors, Prostaglandin E, EP2 Subtype
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Affiliation(s)
- Y Sugino
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
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20
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Lázcoz P, Muñoz J, Nistal M, Pestaña A, Encío IJ, Castresana JS. Loss of heterozygosity and microsatellite instability on chromosome arm 10q in neuroblastoma. ACTA ACUST UNITED AC 2007; 174:1-8. [PMID: 17350460 DOI: 10.1016/j.cancergencyto.2006.08.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Revised: 07/31/2006] [Accepted: 08/07/2006] [Indexed: 01/12/2023]
Abstract
Tumor suppressor genes can be inactivated by various mechanisms, including promoter hypermethylation and loss of heterozygosity. We screened the 10q locus for loss of heterozygosity and the promoter methylation status of PTEN, MGMT, MXI1, and FGFR2 in neuroblastic tumors and neuroblastoma cell lines. Expression of these genes in cell lines was analyzed with reverse transcriptase-polymerase chain reaction. Loss of heterozygosity at 10q was detected in 18% of tumors and microsatellite instability in 14%. Promoter hypermethylation of MGMT appeared in 8% of tumors and 25% of cell lines. Correlation between methylation status and lack of expression was evident for PTEN, FGFR2, and MXI1 and was less clear for MGMT. No associations between these alterations and MYCN amplification, 1p deletion, or aggressive tumor histology could be demonstrated, singly or in combination. These data suggest that 10q alterations might be implicated in the development of a small number of neuroblastomas.
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Affiliation(s)
- Paula Lázcoz
- Department of Health Sciences, Public University of Navarra, 31006 Pamplona, Spain
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21
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Abstract
Neuroblastoma is the second most common solid tumor in children that is metastatic in 70% of patients at the time of diagnosis. The ability of neuroblastoma cells to colonize distant organs like the bone marrow and the bone is the result of close interactions between tumor cells and the microenvironment. Significant progress has been recently made in our understanding of the mechanisms that promote the colonization and invasion of the bone by neuroblastoma cells and these mechanisms are reviewed in this article. How this understanding is now allowing us to test new therapeutic agents specifically targeted at interfering with neuroblastoma metastasis is then discussed.
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Affiliation(s)
- Tasnim Ara
- Division of Hematology-Oncology, Department of Pediatrics and Biochemistry and Molecular Biology, USC Keck School of Medicine and The Saban Research Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
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22
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Lázcoz P, Muñoz J, Nistal M, Pestaña Á, Encío I, Castresana JS. Frequent promoter hypermethylation of RASSF1A and CASP8 in neuroblastoma. BMC Cancer 2006; 6:254. [PMID: 17064406 PMCID: PMC1634754 DOI: 10.1186/1471-2407-6-254] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Accepted: 10/25/2006] [Indexed: 01/09/2023] Open
Abstract
Background Epigenetic alterations and loss of heterozygosity are mechanisms of tumor suppressor gene inactivation. A new carcinogenic pathway, targeting the RAS effectors has recently been documented. RASSF1A, on 3p21.3, and NORE1A, on 1q32.1, are among the most important, representative RAS effectors. Methods We screened the 3p21 locus for the loss of heterozygosity and the hypermethylation status of RASSF1A, NORE1A and BLU (the latter located at 3p21.3) in 41 neuroblastic tumors. The statistical relationship of these data was correlated with CASP8 hypermethylation. The expression levels of these genes, in cell lines, were analyzed by RT-PCR. Results Loss of heterozygosity and microsatellite instability at 3p21 were detected in 14% of the analyzed tumors. Methylation was different for tumors and cell lines (tumors: 83% in RASSF1A, 3% in NORE1A, 8% in BLU and 60% in CASP8; cell lines: 100% in RASSF1A, 50% in NORE1A, 66% in BLU and 92% in CASP8). In cell lines, a correlation with lack of expression was evident for RASSF1A, but less clear for NORE1A, BLU and CASP8. We could only demonstrate a statistically significant association between hypermethylation of RASSF1A and hypermethylation of CASP8, while no association with MYCN amplification, 1p deletion, and/or aggressive histological pattern of the tumor was demonstrated. Conclusion 1) LOH at 3p21 appears in a small percentage of neuroblastomas, indicating that a candidate tumor suppressor gene of neuroblastic tumors is not located in this region. 2) Promoter hypermethylation of RASSF1A and CASP8 occurs at a high frequency in neuroblastomas.
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Affiliation(s)
- Paula Lázcoz
- Departamento de Ciencias de la Salud, Universidad Pública de Navarra, Pamplona, Spain
| | - Jorge Muñoz
- Laboratorio de Neuro-Oncología Molecular, Universidad de Navarra, Pamplona, Spain
| | - Manuel Nistal
- Departamento de Anatomía Patológica, Hospital La Paz, Madrid, Spain
| | - Ángel Pestaña
- Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, Madrid, Spain
| | - Ignacio Encío
- Departamento de Ciencias de la Salud, Universidad Pública de Navarra, Pamplona, Spain
| | - Javier S Castresana
- Laboratorio de Neuro-Oncología Molecular, Universidad de Navarra, Pamplona, Spain
- Unidad de Biología de Tumores Cerebrales, Universidad de Navarra, Irunlarrea 1, E-31008 Pamplona, Spain
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23
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de Bruijn DRH, Allander SV, van Dijk AHA, Willemse MP, Thijssen J, van Groningen JJM, Meltzer PS, van Kessel AG. The Synovial Sarcoma–Associated SS18-SSX2 Fusion Protein Induces Epigenetic Gene (De)Regulation. Cancer Res 2006; 66:9474-82. [PMID: 17018603 DOI: 10.1158/0008-5472.can-05-3726] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fusion of the SS18 and either one of the SSX genes is a hallmark of human synovial sarcoma. The SS18 and SSX genes encode nuclear proteins that exhibit opposite transcriptional activities. The SS18 protein functions as a transcriptional coactivator and is associated with the SWI/SNF complex, whereas the SSX proteins function as transcriptional corepressors and are associated with the polycomb complex. The domains involved in these opposite transcriptional activities are retained in the SS18-SSX fusion proteins. Here, we set out to determine the direct transcriptional consequences of conditional SS18-SSX2 fusion protein expression using complementary DNA microarray-based profiling. By doing so, we identified several clusters of SS18-SSX2-responsive genes, including a group of genes involved in cholesterol synthesis, which is a general characteristic of malignancy. In addition, we identified a group of SS18-SSX2-responsive genes known to be specifically deregulated in primary synovial sarcomas, including IGF2 and CD44. Furthermore, we observed an uncoupling of EGR1, JUNB, and WNT signaling in response to SS18-SSX2 expression, suggesting that the SWI/SNF-associated coactivation functions of the SS18 moiety are impaired. Finally, we found that SS18-SSX2 expression affects histone modifications in the CD44 and IGF2 promoters and DNA methylation levels in the IGF2 imprinting control region. Together, we conclude that the SS18-SSX2 fusion protein may act as a so-called transcriptional "activator-repressor," which induces downstream target gene deregulation through epigenetic mechanisms. Our results may have implications for both the development and clinical management of synovial sarcomas.
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Affiliation(s)
- Diederik R H de Bruijn
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
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24
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Misawa A, Inoue J, Sugino Y, Hosoi H, Sugimoto T, Hosoda F, Ohki M, Imoto I, Inazawa J. Methylation-Associated Silencing of the Nuclear Receptor 1I2 Gene in Advanced-Type Neuroblastomas, Identified by Bacterial Artificial Chromosome Array-Based Methylated CpG Island Amplification. Cancer Res 2005; 65:10233-42. [PMID: 16288011 DOI: 10.1158/0008-5472.can-05-1073] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To identify genes whose expression patterns are altered by methylation of DNA, we established a method for scanning human genomes for methylated DNA sequences, namely bacterial artificial chromosome array-based methylated CpG island amplification (BAMCA). In the course of a program using BAMCA to screen neuroblastoma cell lines for aberrant DNA methylation compared with stage I primary neuroblastoma tumors, we identified CpG methylation-dependent silencing of the nuclear receptor 1I2 (NR1I2) gene. NR1I2 was methylated in a subset of neuroblastoma cell lines and also in advanced-stage primary tumors with amplification of MYCN. Its methylation status was inversely associated with gene expression. Treatment with the demethylating agent 5-aza-2'-deoxycytidine restored NR1I2 transcription in neuroblastoma cell lines lacking endogenous expression of this gene. A CpG island located around exon 3 of NR1I2 showed promoter activity, and its methylation status was clearly and inversely correlated with NR1I2 expression status. The gene product, NR1I2, has a known function in regulating response to xenobiotic agents but it also suppressed growth of neuroblastoma cells in our experiments. We identified some possible transcriptional targets of NR1I2 by expression array analysis. The high prevalence of NR1I2 silencing by methylation in aggressive neuroblastomas, together with the growth-suppressive activity of NR1I2, suggests that this molecule could serve as a diagnostic marker to predict prognosis for neuroblastomas.
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Affiliation(s)
- Akiko Misawa
- Department of Molecular Cytogenetics, Medical Research Institute and Graduate School of Biomedical Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan
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25
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Wang Y, Yu Q, Cho AH, Rondeau G, Welsh J, Adamson E, Mercola D, McClelland M. Survey of differentially methylated promoters in prostate cancer cell lines. Neoplasia 2005; 7:748-60. [PMID: 16207477 PMCID: PMC1501885 DOI: 10.1593/neo.05289] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Revised: 04/15/2005] [Accepted: 04/22/2005] [Indexed: 12/31/2022]
Abstract
DNA methylation and copy number in the genomes of three immortalized prostate epithelial and five cancer cell lines (LNCaP, PC3, PC3M, PC3M-Pro4, and PC3M-LN4) were compared using a microarray-based technique. Genomic DNA is cut with a methylation-sensitive enzyme HpaII, followed by linker ligation, polymerase chain reaction (PCR) amplification, labeling, and hybridization to an array of promoter sequences. Only those parts of the genomic DNA that have unmethylated restriction sites within a few hundred base pairs generate PCR products detectable on an array. Of 2732 promoter sequences on a test array, 504 (18.5%) showed differential hybridization between immortalized prostate epithelial and cancer cell lines. Among candidate hypermethylated genes in cancer-derived lines, there were eight (CD44, CDKN1A, ESR1, PLAU, RARB, SFN, TNFRSF6, and TSPY) previously observed in prostate cancer and 13 previously known methylation targets in other cancers (ARHI, bcl-2, BRCA1, CDKN2C, GADD45A, MTAP, PGR, SLC26A4, SPARC, SYK, TJP2, UCHL1, and WIT-1). The majority of genes that appear to be both differentially methylated and differentially regulated between prostate epithelial and cancer cell lines are novel methylation targets, including PAK6, RAD50, TLX3, PIR51, MAP2K5, INSR, FBN1, and GG2-1, representing a rich new source of candidate genes used to study the role of DNA methylation in prostate tumors.
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Affiliation(s)
- Yipeng Wang
- Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, CA 92121, USA
| | - Qiuju Yu
- Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, CA 92121, USA
| | - Ann H Cho
- Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, CA 92121, USA
| | - Gaelle Rondeau
- Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, CA 92121, USA
| | - John Welsh
- Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, CA 92121, USA
| | - Eileen Adamson
- The Burnham Institute, Cancer Research Center, La Jolla, CA, USA
| | - Dan Mercola
- Department of Pathology, University of California at Irvine, Irvine, CA 92697, USA
| | - Michael McClelland
- Sidney Kimmel Cancer Center, 10835 Road to the Cure, San Diego, CA 92121, USA
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26
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Banine F, Bartlett C, Gunawardena R, Muchardt C, Yaniv M, Knudsen ES, Weissman BE, Sherman LS. SWI/SNF chromatin-remodeling factors induce changes in DNA methylation to promote transcriptional activation. Cancer Res 2005; 65:3542-7. [PMID: 15867346 DOI: 10.1158/0008-5472.can-04-3554] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Brahma (Brm) and brahma-related gene-1 (Brg1) are mammalian homologues of SWI/SNF chromatin-remodeling factor subunits that can regulate both transcriptional activation and repression. Both Brg1 and Brm are mutated or deleted in numerous cancer cell lines, leading to the altered expression of genes that influence cell proliferation and metastasis. Here, we find that the promoters of two such genes, CD44 and E-cadherin, are hypermethylated in cells that have lost Brg1 or Brm. In two carcinoma cell lines that lack functional Brg1 and Brm, CD44 and E-cadherin expression are induced by the demethylating agent 5-aza-2'-deoxycytidine. Transfection with either Brg1 or Brm also induces CD44 and E-cadherin transcription and protein expression in these cells, as well as loss of methylation at sequences in the promoters of both genes. Chromatin immunoprecipitation assays show that Brg1 and Brm associate with these regions of the CD44 and E-cadherin promoters, suggesting that SWI/SNF protein complexes may directly influence the loss of DNA methylation. In vivo, Brm-deficient mice also show methylation and silencing of the CD44 promoter. Collectively, these data implicate loss of SWI/SNF-mediated transcriptional activation as a novel mechanism to increase DNA methylation in cancer cells and provide insight into the mechanisms underlying aberrant gene induction and repression during tumor progression.
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Affiliation(s)
- Fatima Banine
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Oregon 97006, USA
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27
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Tang XX, Robinson ME, Riceberg JS, Kim DY, Kung B, Titus TB, Hayashi S, Flake AW, Carpentieri D, Ikegaki N. Favorable neuroblastoma genes and molecular therapeutics of neuroblastoma. Clin Cancer Res 2005; 10:5837-44. [PMID: 15355914 DOI: 10.1158/1078-0432.ccr-04-0395] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE AND EXPERIMENTAL DESIGN Neuroblastoma (NB) is a common pediatric solid tumor that exhibits a striking clinical bipolarity: favorable and unfavorable. Favorable NB genes (EPHB6, EFNB2, EFNB3, NTRK1, and CD44) are genes whose high-level expression predicts favorable NB outcome, and forced expression of these genes inhibits growth of unfavorable NB cells. In this study, we investigated whether favorable NB gene expression could be augmented in unfavorable NB cells by chemical compounds and whether an increased expression of these genes was associated with suppression of NB growth and metastasis. RESULTS We found that inhibitors of DNA methylation [5-aza-2'-deoxycytidine (5AdC)], histone deacetylase (HDAC) [4-phenylbutyrate (4PB)], and proteasome (MG262) enhanced the expression of favorable NB genes in NB cell lines and inhibited the growth of these cells in vitro (P < 0.0005). The growth-inhibitory effects of 5AdC and 4PB in vitro were in part due to caspase-dependent cell death and inhibition of DNA synthesis. Administration of 5AdC and/or 4PB also suppressed growth of subcutaneous NB xenografts in nude mice (P < 0.001), which was accompanied by enhanced favorable NB gene expression and an increase in apoptosis. Moreover, 4PB suppressed bone marrow and liver metastases of NB cells in severe combined immunodeficient/Beige mice (P = 0.007 and P = 0.008, respectively). The growth-suppressive activity of HDAC inhibitors on NB was further confirmed by the efficacy of trichostatin A, a potent and specific HDAC inhibitor. CONCLUSIONS Collectively, these observations further emphasize the link between the elevated favorable NB gene expression and a benign phenotype of NB.
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Affiliation(s)
- Xao X Tang
- Divisions of Neurology, Surgery Research, and Pathology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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28
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Yang Q, Zage P, Kagan D, Tian Y, Seshadri R, Salwen HR, Liu S, Chlenski A, Cohn SL. Association of Epigenetic Inactivation of RASSF1A with Poor Outcome in Human Neuroblastoma. Clin Cancer Res 2004; 10:8493-500. [PMID: 15623630 DOI: 10.1158/1078-0432.ccr-04-1331] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To investigate the prevalence and potential clinical significance of epigenetic aberrations in neuroblastoma (NB). EXPERIMENTAL DESIGN The methylation status of 11 genes that are frequently epigenetically inactivated in adult cancers was assayed in 13 NB cell lines. The prevalence of RASSF1A and TSP-1 methylation was also analyzed in 56 NBs and 5 ganglioneuromas by methylation-specific PCR. Associations between the methylation status of RASSF1A and TSP-1 and patient age, tumor stage, tumor MYCN status, and patient survival were evaluated. RESULTS Epigenetic changes were detected in all 13 NB cell lines, although the pattern of gene methylation varied. The putative tumor suppressor gene RASSF1A was methylated in all 13 cell lines, and TSP-1 and CASP8 were methylated in 11 of 13 cell lines. Epigenetic changes of DAPK and FAS were detected in only small numbers of cell lines, whereas none of the cell lines had methylation of p16, p21, p73, RAR-beta2, SPARC, or TIMP-3. RASSF1A was also methylated in 70% of the primary NB tumors tested, and TSP-1 methylation was detected in 55% of the tumors. RASSF1A methylation was significantly associated with age >1 year (P < 0.01), high-risk disease (P < 0.016), and poor survival (P < 0.001). In contrast, no association between TSP-1 methylation and prognostic factors or survival was observed. CONCLUSIONS Our results suggest that epigenetic inactivation of RASSF1A may contribute to the clinically aggressive phenotype of high-risk NB.
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Affiliation(s)
- Qiwei Yang
- The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
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29
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Yang Q, Liu S, Tian Y, Hasan C, Kersey D, Salwen HR, Chlenski A, Perlman EJ, Cohn SL. Methylation-Associated Silencing of theHeat Shock Protein 47Gene in Human Neuroblastoma. Cancer Res 2004; 64:4531-8. [PMID: 15231663 DOI: 10.1158/0008-5472.can-04-0956] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Hypermethylation of gene promoter CpG islands is a frequent mechanism for gene inactivation in a variety of human cancers, including neuroblastoma (NB). We demonstrated recently that treatment with the demethylating agent 5'-aza-2'-deoxycytidine (5-Aza-dC) significantly inhibited NB growth in vivo. In an effort to identify the genes and biological pathways that are responsible for the impaired NB tumor growth observed after treatment with 5-Aza-dC, we performed genome-wide gene expression analysis of control and treated NBL-W-S NB cells. We found >or=3-fold changes in expression of 44 genes that play roles in angiogenesis, apoptosis, cell adhesion, transcriptional regulation, and signal transduction. The gene encoding heat shock protein 47 (Hsp47), a collagen-specific molecular chaperon, was up-regulated >80-fold after 5-Aza-dC treatment. Expression studies confirmed that Hsp47 is silenced in a subset of NB cell lines and tumors. We also show that silencing of Hsp47 in NB cells is associated with aberrant methylation of promoter CpG islands and that Hsp47 expression can be restored after treatment with 5-Aza-dC. A strong correlation between Hsp47 and collagen type I and IV expression was seen in NB cells. Interestingly, tumorigenicity was inversely correlated with the level of collagen expression in NB cell lines, and higher levels of collagen were detected in mature NB tumors that are associated with favorable outcome compared with undifferentiated, advanced-stage NBs. Our studies support a role for Hsp47 in the regulation of collagen type I and IV production in NB cells and suggest that the level of collagen expression may influence NB tumor phenotype.
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Affiliation(s)
- Qiwei Yang
- The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
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Wesley UV, Tiwari S, Houghton AN. Role for dipeptidyl peptidase IV in tumor suppression of human non small cell lung carcinoma cells. Int J Cancer 2004; 109:855-66. [PMID: 15027119 DOI: 10.1002/ijc.20091] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Lung cancer is the leading cause of cancer death. Lung cancers produce a variety of mitogenic growth factors that stimulate tumor cell proliferation and migration. The cell surface protease, dipeptidyl peptidase IV (DPPIV), is involved in diverse biologic functions, including peptide-mediated cellular growth and differentiation. DPPIV is expressed in various normal tissues, including lung tissue, and its expression is lost in many types of human cancers. DPPIV expression and its enzymatic activity are detected in normal bronchial and alveolar epithelium but different histologic subtypes of lung carcinomas lose DPPIV expression. To investigate the role of DPPIV in lung carcinoma, we examined the expression of DPPIV at both mRNA and protein levels in non small cell lung cancer (NSCLC) cell lines and normal human bronchial epithelial cells. DPPIV expression was detectable in normal lung epithelial cells, but was absent or markedly reduced in all NSCLC cell lines at both mRNA and protein levels. Restoration of DPPIV expression in NSCLC cells resulted in profound morphologic changes, inhibition of cell proliferation, anchorage-independent growth, in vitro cell migration and tumorigenicity in nude mice. DPPIV reexpression also correlated with increased p21 expression, leading to induction of apoptosis and cell cycle arrest in G1 stage. These effects were accompanied by increased expression of cell surface proteins, fibroblast-activating protein (Fapalpha) and CD44 that are associated with suppression of tumor growth and metastasis. Thus, DPPIV functions as a tumor suppressor, and its downregulation may contribute to the loss of growth control in NSCLC cells.
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Affiliation(s)
- Umadevi V Wesley
- Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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