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Erdoğan ÖŞ, Ödemiş DA, Kayım ZY, Gürbüz O, Tunçer ŞB, Kılıç S, Çelik B, Tuncer S, Bay SB, Kebudi R, Yazıcı H. Investigation of the methylation changes in the promoter region of RB1 gene in retinoblastoma: Unraveling the epigenetic puzzle in retinoblastoma. Pathol Res Pract 2024; 253:154939. [PMID: 38006838 DOI: 10.1016/j.prp.2023.154939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/27/2023]
Abstract
Retinoblastoma is an infrequent neoplasm that arises during childhood from retinal nerve cells and is attributed to the biallelic inactivation of the RB1 gene. In conjunction with anatomical anomalies, it is widely acknowledged that epigenetic modifications play a significant role in the pathogenesis of cancer. The association between methylation of the RB1 gene promoter and tumor formation has been established; however, there is currently no scholarly evidence to substantiate the claim that it is responsible for the inheritance of retinoblastoma. The initial hypothesis posited for this work was that familial retinoblastoma disease would be similarly observed in cases with RB1 promotor gene methylation, akin to RB1 mutations. The RB1 gene promoter region was subjected to methylation screening using real-time PCR in individuals diagnosed with familial retinoblastoma but lacking RB1 mutations. The study involved a comparison of the germline methylation status of the RB1 gene in the peripheral blood samples of 50 retinoblastoma patients and 52 healthy individuals. The healthy individuals were carefully selected to match the retinoblastoma patients in terms of age, sex, and ethnicity. The data obtained from both groups were subjected to statistical analysis. The study revealed that the methylation level in a cohort of 50 individuals diagnosed with retinoblastoma and 52 healthy control participants was determined to be 36.1% and 33.9%, respectively. As a result, there was no statistically significant disparity observed in RB1 promoter methylation between the patient and control groups (p = 0.126). The methylation of the promoter region of the RB1 gene in familial retinoblastoma does not exert any influence on the hereditary transmission of the disease.
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Affiliation(s)
- Özge Şükrüoğlu Erdoğan
- Istanbul University, Oncology Institute, Department of Basic Oncology, Division of Cancer Genetics, Fatih, 34093 Istanbul, Turkey.
| | - Demet Akdeniz Ödemiş
- Istanbul University, Oncology Institute, Department of Basic Oncology, Division of Cancer Genetics, Fatih, 34093 Istanbul, Turkey
| | - Zübeyde Yalnız Kayım
- Istanbul University, Oncology Institute, Department of Basic Oncology, Division of Cancer Genetics, Fatih, 34093 Istanbul, Turkey
| | - Orkun Gürbüz
- Istanbul University, Oncology Institute, Department of Basic Oncology, Division of Cancer Genetics, Fatih, 34093 Istanbul, Turkey; İstinye University, Vocational School of Health Care Services
| | - Şeref Buğra Tunçer
- Istanbul University, Oncology Institute, Department of Basic Oncology, Division of Cancer Genetics, Fatih, 34093 Istanbul, Turkey
| | - Seda Kılıç
- Istanbul University, Oncology Institute, Department of Basic Oncology, Division of Cancer Genetics, Fatih, 34093 Istanbul, Turkey
| | - Betül Çelik
- Istanbul University, Oncology Institute, Department of Basic Oncology, Division of Cancer Genetics, Fatih, 34093 Istanbul, Turkey
| | - Samuray Tuncer
- Department of Ophthalmology, Istanbul Medical Faculty, Istanbul University, Fatih, 34093 Istanbul, Turkey
| | - Sema Büyükkapu Bay
- Department of Pediatric and Hematologic Oncology, Oncology Institute, Istanbul University, Fatih, 34093 Istanbul, Turkey
| | - Rejin Kebudi
- Department of Pediatric and Hematologic Oncology, Oncology Institute, Istanbul University, Fatih, 34093 Istanbul, Turkey
| | - Hülya Yazıcı
- Istanbul University, Oncology Institute, Department of Basic Oncology, Division of Cancer Genetics, Fatih, 34093 Istanbul, Turkey; Arel University Faculty of Medicine, Department of Basic Medical Sciences / Medical Biology
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Srivastava A, Srivastava A, Singh RK. Insight into the Epigenetics of Kaposi's Sarcoma-Associated Herpesvirus. Int J Mol Sci 2023; 24:14955. [PMID: 37834404 PMCID: PMC10573522 DOI: 10.3390/ijms241914955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 10/15/2023] Open
Abstract
Epigenetic reprogramming represents a series of essential events during many cellular processes including oncogenesis. The genome of Kaposi's sarcoma-associated herpesvirus (KSHV), an oncogenic herpesvirus, is predetermined for a well-orchestrated epigenetic reprogramming once it enters into the host cell. The initial epigenetic reprogramming of the KSHV genome allows restricted expression of encoded genes and helps to hide from host immune recognition. Infection with KSHV is associated with Kaposi's sarcoma, multicentric Castleman's disease, KSHV inflammatory cytokine syndrome, and primary effusion lymphoma. The major epigenetic modifications associated with KSHV can be labeled under three broad categories: DNA methylation, histone modifications, and the role of noncoding RNAs. These epigenetic modifications significantly contribute toward the latent-lytic switch of the KSHV lifecycle. This review gives a brief account of the major epigenetic modifications affiliated with the KSHV genome in infected cells and their impact on pathogenesis.
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Affiliation(s)
- Anusha Srivastava
- Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Ankit Srivastava
- Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Rajnish Kumar Singh
- Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
- Faculty of Medical Sciences, Charotar University of Science and Technology, Changa 388421, Gujarat, India
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Janostiak R, Torres-Sanchez A, Posas F, de Nadal E. Understanding Retinoblastoma Post-Translational Regulation for the Design of Targeted Cancer Therapies. Cancers (Basel) 2022; 14:cancers14051265. [PMID: 35267571 PMCID: PMC8909233 DOI: 10.3390/cancers14051265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Rb1 is a regulator of cell cycle progression and genomic stability. This review focuses on post-translational modifications, their effect on Rb1 interactors, and their role in intracellular signaling in the context of cancer development. Finally, we highlight potential approaches to harness these post-translational modifications to design novel effective anticancer therapies. Abstract The retinoblastoma protein (Rb1) is a prototypical tumor suppressor protein whose role was described more than 40 years ago. Together with p107 (also known as RBL1) and p130 (also known as RBL2), the Rb1 belongs to a family of structurally and functionally similar proteins that inhibits cell cycle progression. Given the central role of Rb1 in regulating proliferation, its expression or function is altered in most types of cancer. One of the mechanisms underlying Rb-mediated cell cycle inhibition is the binding and repression of E2F transcription factors, and these processes are dependent on Rb1 phosphorylation status. However, recent work shows that Rb1 is a convergent point of many pathways and thus the regulation of its function through post-translational modifications is more complex than initially expected. Moreover, depending on the context, downstream signaling can be both E2F-dependent and -independent. This review seeks to summarize the most recent research on Rb1 function and regulation and discuss potential avenues for the design of novel cancer therapies.
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Affiliation(s)
- Radoslav Janostiak
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; (R.J.); (A.T.-S.)
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Ariadna Torres-Sanchez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; (R.J.); (A.T.-S.)
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Francesc Posas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; (R.J.); (A.T.-S.)
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Correspondence: (F.P.); (E.d.N.); Tel.: +34-93-403-4810 (F.P.); +34-93-403-9895 (E.d.N.)
| | - Eulàlia de Nadal
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; (R.J.); (A.T.-S.)
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Correspondence: (F.P.); (E.d.N.); Tel.: +34-93-403-4810 (F.P.); +34-93-403-9895 (E.d.N.)
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Tanaka H, Kuwano Y, Nishikawa T, Rokutan K, Nishida K. ZNF350 promoter methylation accelerates colon cancer cell migration. Oncotarget 2018; 9:36750-36769. [PMID: 30613364 PMCID: PMC6298409 DOI: 10.18632/oncotarget.26353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022] Open
Abstract
Diversification of transcriptomic and epigenomic states may occur during the expansion of colorectal cancers. Certain cancer cells lose their epithelial characters and gain mesenchymal properties, known as epithelial-mesenchymal transition (EMT), and they aggressively migrate into the non-tumorigenic extracellular matrix. In this study, we isolated a subpopulation with accelerated baseline motility (MG cells) and an immotile one (non-MG cells) from a colon cancer cell line (HCT116). Gene expression signatures of the MG cells indicated that this subpopulation was likely an EMT hybrid. The MG cells substantially lost their migratory properties after treatment with a methyltransferase inhibitor, 5-azacytidine, suggesting a role of DNA methylation in this process. Global transcriptome assays of both types of cells with or without 5-azacytidine treatment identified 640 genes, whose expression might be methylation-dependently down-regulated in the MG cells. Global methylation analysis revealed that 35 out of the 640 genes were hyper-methylated in the MG cells. Among them, we focused on the anti-oncogene ZNF350, which encodes a zinc-finger and BRCA1-interacting protein. Notably, ZNF350 knockdown accelerated migration of the non-MG cells, while overexpression of ZNF350 in the MG cells significantly impaired their migration. Finally, pyrosequence analysis together with dual luciferase assays of serially truncated fragments of the ZNF350 promoter (-268 to +49 bp) indicated that three hyper-methylated sites were possibly responsible for the basal promoter activity of ZNF350. Taken together, our results suggest that hyper-methylation of the ZNF350 proximal promoter may be one of the crucial determinants for acquiring increased migratory capabilities in colon cancer cells.
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Affiliation(s)
- Hiroki Tanaka
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Yuki Kuwano
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Tatsuya Nishikawa
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Kazuhito Rokutan
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Kensei Nishida
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
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Khani P, Nasri F, Khani Chamani F, Saeidi F, Sadri Nahand J, Tabibkhooei A, Mirzaei H. Genetic and epigenetic contribution to astrocytic gliomas pathogenesis. J Neurochem 2018; 148:188-203. [PMID: 30347482 DOI: 10.1111/jnc.14616] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/16/2018] [Accepted: 10/17/2018] [Indexed: 12/30/2022]
Abstract
Astrocytic gliomas are the most common and lethal form of intracranial tumors. These tumors are characterized by a significant heterogeneity in terms of cytopathological, transcriptional, and (epi)genomic features. This heterogeneity has made these cancers one of the most challenging types of cancers to study and treat. To uncover these complexities and to have better understanding of the disease initiation and progression, identification, and characterization of underlying cellular and molecular pathways related to (epi)genetics of astrocytic gliomas is crucial. Here, we discuss and summarize molecular and (epi)genetic mechanisms that provide clues as to the pathogenesis of astrocytic gliomas.
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Affiliation(s)
- Pouria Khani
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran.,Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Farzad Nasri
- Department of Medical Immunology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Fateme Khani Chamani
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzane Saeidi
- Department of Medical Genetics, School of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Javid Sadri Nahand
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Tabibkhooei
- Department of Neurosurgery, Iran University of Medical Sciences, Tehran, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
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Abstract
The retinoblastoma protein (pRb) plays a central role in the regulation of cell cycle by interaction with members of the E2F transcription factor family. As a tumor suppressor protein, pRb is frequently dysregulated in several major cancers. In addition to mutations, inactivation of pRb is also caused by epigenetic mechanisms including alterations of DNA methylation. There are three CpG islands located within the RB1 gene that encodes pRb that are closely associated with the regulation of pRb expression. Aberrant DNA methylation at the RB1 gene has been reported in sporadic retinoblastoma as well as other cancers including glioblastoma, hepatocellular carcinoma, and breast cancer. Recent studies have revealed that the RB1 gene is imprinted. Therefore, quantitative analysis is required to detect aberrations in DNA methylation associated with imprint deregulation. Pyrosequencing® is considered as the method of choice for quantitative and reproducible analysis of DNA methylation with single base resolution. In this chapter, we provide a detailed protocol for the quantitative analysis of RB1 gene methylation using bisulfite Pyrosequencing®.
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Affiliation(s)
- Sumadi Lukman Anwar
- Department of Surgery, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ulrich Lehmann
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany.
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Pérez-Ramírez M, Hernández-Jiménez AJ, Guerrero-Guerrero A, Benadón-Darszon E, Pérezpeña-Díazconti M, Siordia-Reyes AG, García-Méndez A, de León FCP, Salamanca-Gómez FA, García-Hernández N. Genomics and epigenetics: A study of ependymomas in pediatric patients. Clin Neurol Neurosurg 2016; 144:53-8. [PMID: 26971296 DOI: 10.1016/j.clineuro.2016.02.041] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 02/22/2016] [Accepted: 02/28/2016] [Indexed: 12/11/2022]
Abstract
OBJECTIVE We identify chromosomal alterations, the methylation pattern and gene expression changes in pediatric ependymomas. METHODS CGH microarray, methylation and gene expression were performed through the Agilent platform. The results were analyzed with the software MatLab, MapViewer, DAVID, GeneCards and Hippie. RESULTS Amplification was found in 14q32.33, 2p22.3 and 8p22, and deletion was found in 8p11.23-p11.22 and 1q21.3. We observed 42.387 CpG islands with changes in their methylation pattern, in which we found 272 genes involved in signaling pathways related to carcinogenesis. We found 481 genes with altered expression. The genes IMMT, JHDMD1D, ASAH1, ZWINT, IPO7, GNAO1 and CISD3 were found to be altered among the three levels. CONCLUSION The 2p22.3, 8p11.23-p11.22 and 14q32.33 regions were identified as the most important; the changes in the methylation pattern related to cell cycle and cancer genes occurred in MIB2, FGF18 and ITIH5. The IPO7, GNAO1 and ASAH1 genes may play a major role in ependymoma development.
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Affiliation(s)
- Monserrat Pérez-Ramírez
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría "Dr. Silvestre Frenk Freud", Centro Médico Nacional "Siglo XXI", IMSS, Av. Cuauhtémoc 330, Col. Doctores, Del. Cuauhtémoc, 06720 México D. F., Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Avenida Ciudad Universitaria 3000, Coyoacán, 04360 México D.F., Mexico
| | - Alejo Justino Hernández-Jiménez
- Servicio de Neurocirugía Pediátrica, Hospital General "Dr. Gaudencio González Garza", Centro Médico Nacional "La Raza", IMSS, Calzada Vallejo y Jacarandas S/N, Col. La Raza, Del. Azcapotzalco, 02980 Mexico D.F, Mexico
| | - Armando Guerrero-Guerrero
- Servicio de Neurocirugía Pediátrica, Hospital General "Dr. Gaudencio González Garza", Centro Médico Nacional "La Raza", IMSS, Calzada Vallejo y Jacarandas S/N, Col. La Raza, Del. Azcapotzalco, 02980 Mexico D.F, Mexico
| | - Eduardo Benadón-Darszon
- Departamento de Pediatría Ambulatoria, Hospital Infantil de México "Federico Gómez", Dr. Márquez 162, Col. Doctores, Del. Cuauhtémoc, 06720 México D.F, Mexico
| | - Mario Pérezpeña-Díazconti
- Departamento de Patología, Hospital Infantil de México "Federico Gómez", Dr. Márquez 162, Col. Doctores, Del. Cuauhtémoc, 06720 México D.F., Mexico
| | - Alicia Georgina Siordia-Reyes
- Servicio de Patología, Hospital de Pediatría "Dr. Silvestre Frenk Freud", Centro Médico Nacional "Siglo XXI", IMSS, Av. Cuauhtémoc 330, Col. Doctores, Del. Cuauhtémoc, 06720 México D.F., Mexico
| | - Antonio García-Méndez
- Servicio de Neurocirugía Pediátrica, Hospital General "Dr. Gaudencio González Garza", Centro Médico Nacional "La Raza", IMSS, Calzada Vallejo y Jacarandas S/N, Col. La Raza, Del. Azcapotzalco, 02980 Mexico D.F, Mexico
| | - Fernando Chico-Ponce de León
- Departamento de Neurocirugía, Hospital Infantil de México "Federico Gómez", Dr. Márquez 162, Col. Doctores, Del. Cuauhtémoc, 06720 México D.F., Mexico
| | - Fabio Abdel Salamanca-Gómez
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría "Dr. Silvestre Frenk Freud", Centro Médico Nacional "Siglo XXI", IMSS, Av. Cuauhtémoc 330, Col. Doctores, Del. Cuauhtémoc, 06720 México D. F., Mexico
| | - Normand García-Hernández
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría "Dr. Silvestre Frenk Freud", Centro Médico Nacional "Siglo XXI", IMSS, Av. Cuauhtémoc 330, Col. Doctores, Del. Cuauhtémoc, 06720 México D. F., Mexico.
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Lee CH, Chung CK, Ohn JH, Kim CH. The Similarities and Differences between Intracranial and Spinal Ependymomas : A Review from a Genetic Research Perspective. J Korean Neurosurg Soc 2016; 59:83-90. [PMID: 26962412 PMCID: PMC4783489 DOI: 10.3340/jkns.2016.59.2.83] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 11/20/2015] [Accepted: 01/01/2016] [Indexed: 11/27/2022] Open
Abstract
Ependymomas occur in both the brain and spine. The prognosis of these tumors sometimes differs for different locations. The genetic landscape of ependymoma is very heterogeneous despite the similarity of histopathologic findings. In this review, we describe the genetic differences between spinal ependymomas and their intracranial counterparts to better understand their prognosis. From the literature review, many studies have reported that spinal cord ependymoma might be associated with NF2 mutation, NEFL overexpression, Merlin loss, and 9q gain. In myxopapillary ependymoma, NEFL and HOXB13 overexpression were reported to be associated. Prior studies have identified HIC-1 methylation, 4.1B deletion, and 4.1R loss as common features in intracranial ependymoma. Supratentorial ependymoma is usually characterized by NOTCH-1 mutation and p75 expression. TNC mutation, no hypermethylation of RASSF1A, and GFAP/NeuN expression may be diagnostic clues of posterior fossa ependymoma. Although MEN1, TP53, and PTEN mutations are rarely reported in ependymoma, they may be related to a poor prognosis, such as recurrence or metastasis. Spinal ependymoma has been found to be quite different from intracranial ependymoma in genetic studies, and the favorable prognosis in spinal ependymoma may be the result of the genetic differences. A more detailed understanding of these various genetic aberrations may enable the identification of more specific prognostic markers as well as the development of customized targeted therapies.
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Affiliation(s)
- Chang-Hyun Lee
- Department of Neurosurgery, Ilsan Paik Hospital, Inje University College of Medicine, Goyang, Korea
| | - Chun Kee Chung
- Department of Neurosurgery, Seoul National University Hospital, Seoul, Korea.; Department of Neurosurgery, Seoul National University College of Medicine, Seoul, Korea.; Neuroscience Research Institute, Seoul National University Medical Research Center, Seoul, Korea.; Clinical Research Institute, Seoul National University Hospital, Seoul, Korea.; Department of Brain and Cognitive Sciences, Seoul National University College of Natural Sciences, Seoul, Korea
| | - Jung Hun Ohn
- Bioinformatics, Samsung Gene Institute, Samsung Medical Center, Seoul, Korea
| | - Chi Heon Kim
- Department of Neurosurgery, Seoul National University Hospital, Seoul, Korea.; Department of Neurosurgery, Seoul National University College of Medicine, Seoul, Korea.; Neuroscience Research Institute, Seoul National University Medical Research Center, Seoul, Korea.; Clinical Research Institute, Seoul National University Hospital, Seoul, Korea
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Abstract
The approval of DNA methylation inhibitors azacytidine and decitabine for the treatment of myelodysplastic syndromes and acute myeloid leukaemia has demonstrated that modulation of relatively broad epigenetic regulatory processes can show beneficial efficacy/safety profiles in defined patient groups. This chapter will focus on the biochemical mechanisms controlling DNA methylation, consequences of aberrant DNA methylation in complex chronic diseases, existing modulators of DNA methylation used in the clinic, and opportunities for new drugs targeting this central epigenetic mechanism.
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Affiliation(s)
- Tom D. Heightman
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Michael McCullar
- Astex Pharmaceuticals Inc. 4140 Dublin Boulevard, Suite 200 Dublin CA 94568 USA
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Expression Analysis of Genes Involved in the RB/E2F Pathway in Astrocytic Tumors. PLoS One 2015; 10:e0137259. [PMID: 26317630 PMCID: PMC4552853 DOI: 10.1371/journal.pone.0137259] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 08/13/2015] [Indexed: 02/08/2023] Open
Abstract
Astrocytic gliomas, which are derived from glial cells, are considered the most common primary neoplasias of the central nervous system (CNS) and are histologically classified as low grade (I and II) or high grade (III and IV). Recent studies have shown that astrocytoma formation is the result of the deregulation of several pathways, including the RB/E2F pathway, which is commonly deregulated in various human cancers via genetic or epigenetic mechanisms. On the basis of the assumption that the study of the mechanisms controlling the INK4/ARF locus can help elucidate the molecular pathogenesis of astrocytic tumors, identify diagnostic and prognostic markers, and help select appropriate clinical treatments, the present study aimed to evaluate and compare methylation patterns using bisulfite sequencing PCR and evaluate the gene expression profile using real-time PCR in the genes CDKN2A, CDKN2B, CDC6, Bmi-1, CCND1, and RB1 in astrocytic tumors. Our results indicate that all the evaluated genes are not methylated independent of the tumor grade. However, the real-time PCR results indicate that these genes undergo progressive deregulation as a function of the tumor grade. In addition, the genes CDKN2A, CDKN2B, and RB1 were underexpressed, whereas CDC6, Bmi-1, and CCND1 were overexpressed; the increase in gene expression was significantly associated with decreased patient survival. Therefore, we propose that the evaluation of the expression levels of the genes involved in the RB/E2F pathway can be used in the monitoring of patients with astrocytomas in clinical practice and for the prognostic indication of disease progression.
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Yáñez Y, Grau E, Rodríguez-Cortez VC, Hervás D, Vidal E, Noguera R, Hernández M, Segura V, Cañete A, Conesa A, Font de Mora J, Castel V. Two independent epigenetic biomarkers predict survival in neuroblastoma. Clin Epigenetics 2015; 7:16. [PMID: 25767620 PMCID: PMC4357365 DOI: 10.1186/s13148-015-0054-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/09/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Neuroblastoma (NB) is the most common extracranial pediatric solid tumor with a highly variable clinical course, ranging from spontaneous regression to life-threatening disease. Survival rates for high-risk NB patients remain disappointingly low despite multimodal treatment. Thus, there is an urgent clinical need for additional biomarkers to improve risk stratification, treatment management, and survival rates in children with aggressive NB. RESULTS Using gene promoter methylation analysis in 48 neuroblastoma tumors with microarray technology, we found a strong association between survival and gene promoter hypermethylation (P = 0.036). Hypermethylation of 70 genes significantly differentiated high-risk survivor patients from those who died during follow-up time. Sixteen genes with relevant roles in cancer biology were further validated in an additional cohort of 83 neuroblastoma tumors by bisulfite pyrosequencing. High promoter methylation rates of these genes were found in patients with metastatic tumors (either stage metastatic (M) or metastatic special (MS)), 18 months or older at first diagnosis, MYCN amplification, relapsed, and dead. Notably, the degree of methylation of retinoblastoma 1 (RB1) and teratocarcinoma-derived growth factor 1 (TDGF1) predicts event-free and overall survival independently of the established risk factors. In addition, low RB1 mRNA expression levels associate with poor prognosis suggesting that promoter methylation could contribute to the transcriptional silencing of this gene in NB. CONCLUSIONS We found a new epigenetic signature predictive for NB patients' outcome: the methylation status of RB1 and TDGF1 associate with poorer survival. This information is useful to assess prognosis and improve treatment selection.
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Affiliation(s)
- Yania Yáñez
- Pediatric Oncology Unit, Hospital Universitari i Politècnic La Fe, Avda Fernando Abril Martorell, Valencia, 46026 Spain
| | - Elena Grau
- Pediatric Oncology Unit, Hospital Universitari i Politècnic La Fe, Avda Fernando Abril Martorell, Valencia, 46026 Spain
| | - Virginia C Rodríguez-Cortez
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC) Bellvitge Biomedical Research Institute (IDIBELL), Gran Via de L'Hospitalet, Barcelona, 08908 Spain
| | - David Hervás
- Biostatistics Unit, Instituto de Investigación Sanitaria La Fe, Avda Fernando Abril Martorell, Valencia, 46026 Spain
| | - Enrique Vidal
- Genomics of Gene Expression Lab, Centro de Investigaciones Príncipe Felipe, Carrer d'Eduardo Primo Yúfera, Valencia, 46012 Spain
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia, Avda Blasco Ibáñez, Valencia, 46010 Spain
| | - Miguel Hernández
- Department of Pathology, Hospital Universitari i Politècnic La Fe, Avda Fernando Abril Martorell, Valencia, 46026 Spain
| | - Vanessa Segura
- Pediatric Oncology Unit, Hospital Universitari i Politècnic La Fe, Avda Fernando Abril Martorell, Valencia, 46026 Spain
| | - Adela Cañete
- Pediatric Oncology Unit, Hospital Universitari i Politècnic La Fe, Avda Fernando Abril Martorell, Valencia, 46026 Spain
| | - Ana Conesa
- Genomics of Gene Expression Lab, Centro de Investigaciones Príncipe Felipe, Carrer d'Eduardo Primo Yúfera, Valencia, 46012 Spain
| | - Jaime Font de Mora
- Laboratory of Cellular and Molecular Biology, Instituto de Investigación Sanitaria La Fe, Avda Fernando Abril Martorell, Valencia, 46026 Spain
| | - Victoria Castel
- Pediatric Oncology Unit, Hospital Universitari i Politècnic La Fe, Avda Fernando Abril Martorell, Valencia, 46026 Spain
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Charlton J, Williams RD, Sebire NJ, Popov S, Vujanic G, Chagtai T, Alcaide-German M, Morris T, Butcher LM, Guilhamon P, Beck S, Pritchard-Jones K. Comparative methylome analysis identifies new tumour subtypes and biomarkers for transformation of nephrogenic rests into Wilms tumour. Genome Med 2015; 7:11. [PMID: 25763109 PMCID: PMC4354990 DOI: 10.1186/s13073-015-0136-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/21/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Wilms tumours (WTs) are characterised by several hallmarks that suggest epimutations such as aberrant DNA methylation are involved in tumour progression: loss of imprinting at 11p15, lack of recurrent mutations and formation of nephrogenic rests (NRs), which are lesions of retained undifferentiated embryonic tissue that can give rise to WTs. METHODS To identify such epimutations, we performed a comprehensive methylome analysis on 20 matched trios of micro-dissected WTs, NRs and surrounding normal kidneys (NKs) using Illumina Infinium HumanMethylation450 Bead Chips and functionally validated findings using RNA sequencing. RESULTS Comparison of NRs with NK revealed prominent tissue biomarkers: 629 differentially methylated regions, of which 55% were hypermethylated and enriched for domains that are bivalent in embryonic stem cells and for genes expressed during development (P = 2.49 × 10(-5)). Comparison of WTs with NRs revealed two WT subgroups; group-2 WTs and NRs were epigenetically indistinguishable whereas group-1 WTs showed an increase in methylation variability, hypomethylation of renal development genes, hypermethylation and relative loss of expression of cell adhesion genes and known and potential new WT tumour suppressor genes (CASP8, H19, MIR195, RB1 and TSPAN32) and was strongly associated with bilateral disease (P = 0.032). Comparison of WTs and NRs to embryonic kidney highlighted the significance of polycomb target methylation in Wilms tumourigenesis. CONCLUSIONS Methylation levels vary during cancer evolution. We have described biomarkers related to WT evolution from its precursor NRs which may be useful to differentiate between these tissues for patients with bilateral disease.
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Affiliation(s)
- Jocelyn Charlton
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
| | - Richard D Williams
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
| | - Neil J Sebire
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
| | - Sergey Popov
- />The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG UK
| | - Gordan Vujanic
- />Department of Pathology, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN UK
| | - Tasnim Chagtai
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
| | - Marisa Alcaide-German
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
| | - Tiffany Morris
- />UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK
| | - Lee M Butcher
- />UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK
| | - Paul Guilhamon
- />UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK
| | - Stephan Beck
- />UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK
| | - Kathy Pritchard-Jones
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
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13
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Retinoblastoma (RB1) pocket domain mutations and promoter hyper-methylation in head and neck cancer. Cell Oncol (Dordr) 2014; 37:203-13. [PMID: 24888624 DOI: 10.1007/s13402-014-0173-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2014] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The RB1 gene plays a pivotal role in cell cycle regulation. In this case-control study we searched for alterations in the RB1 pocket domain and its promoter region in head and neck cancer (HNC) patients in the Pakistani population. METHODS For germline mutation analyses, 380 blood samples from HNC patients and 350 blood samples from control individuals were included. Polymerase chain reaction (PCR) and single strand conformational polymorphism (SSCP) assays, followed by sequence analyses, were used for the RB1 pocket domain mutation screens. For the RB1 promoter methylation screens, 72 HNC tumor samples along with adjacent uninvolved tissues were tested using a methylation-specific polymerase chain reaction (MSP) assay. RESULTS RB1 (pocket domain and spacer region) sequence analysis revealed one frameshift and seven non-synonymous missense mutations. The frequency of missense mutations in exon 14, i.e., g76474C > T, g76475G > C and g76476A > G, resulting in Arg455Ser, was found to be highest (0.10). Missense mutations g76467G > C (exon14), g76468T > C (exon14), g77041A > T and g77043A > T (exon 16), when analyzed via Alamut biosoftware version 2.0, were found to be present in highly conserved amino acids with Align GVGD scores C15 (GV: 0.00-GD: 21.82), C65 (GV: 0.00-GD: 83.33) and C65 (GV: 0.00-GD: 98.69), respectively. These missense mutations were found to be deleterious by SIFT score: 0.00 (median 3.64). RB1 promoter methylation analysis revealed that 16% of its cytosines (3% in CpG) were methylated in the HNC tumor samples. CONCLUSION Our findings indicate that both genetic and epigenetic RB1 changes may contribute to the pathogenesis of HNC in the Pakistani population.
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Foulks JM, Parnell KM, Nix RN, Chau S, Swierczek K, Saunders M, Wright K, Hendrickson TF, Ho KK, McCullar MV, Kanner SB. Epigenetic drug discovery: targeting DNA methyltransferases. ACTA ACUST UNITED AC 2011; 17:2-17. [PMID: 21965114 DOI: 10.1177/1087057111421212] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Epigenetic modification of DNA leads to changes in gene expression. DNA methyltransferases (DNMTs) comprise a family of nuclear enzymes that catalyze the methylation of CpG dinucleotides, resulting in an epigenetic methylome distinguished between normal cells and those in disease states such as cancer. Disrupting gene expression patterns through promoter methylation has been implicated in many malignancies and supports DNMTs as attractive therapeutic targets. This review focuses on the rationale of targeting DNMTs in cancer, the historical approach to DNMT inhibition, and current marketed hypomethylating therapeutics azacytidine and decitabine. In addition, we address novel DNMT inhibitory agents emerging in development, including CP-4200 and SGI-110, analogs of azacytidine and decitabine, respectively; the oligonucleotides MG98 and miR29a; and a number of reversible inhibitors, some of which appear to be selective against particular DNMT isoforms. Finally, we discuss future opportunities and challenges for next-generation therapeutics.
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Affiliation(s)
- Jason M Foulks
- Astex Pharmaceuticals, Inc., Salt Lake City, UT 84109, USA.
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15
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Paradise WA, Vesper BJ, Goel A, Waltonen JD, Altman KW, Haines GK, Radosevich JA. Nitric oxide: perspectives and emerging studies of a well known cytotoxin. Int J Mol Sci 2010; 11:2715-45. [PMID: 20717533 PMCID: PMC2920563 DOI: 10.3390/ijms11072715] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 06/17/2010] [Accepted: 07/13/2010] [Indexed: 12/19/2022] Open
Abstract
The free radical nitric oxide (NO•) is known to play a dual role in human physiology and pathophysiology. At low levels, NO• can protect cells; however, at higher levels, NO• is a known cytotoxin, having been implicated in tumor angiogenesis and progression. While the majority of research devoted to understanding the role of NO• in cancer has to date been tissue-specific, we herein review underlying commonalities of NO• which may well exist among tumors arising from a variety of different sites. We also discuss the role of NO• in human physiology and pathophysiology, including the very important relationship between NO• and the glutathione-transferases, a class of protective enzymes involved in cellular protection. The emerging role of NO• in three main areas of epigenetics—DNA methylation, microRNAs, and histone modifications—is then discussed. Finally, we describe the recent development of a model cell line system in which human tumor cell lines were adapted to high NO• (HNO) levels. We anticipate that these HNO cell lines will serve as a useful tool in the ongoing efforts to better understand the role of NO• in cancer.
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Affiliation(s)
- William A. Paradise
- Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, Chicago, IL 60612, USA; E-Mails: (W.A.P.); (B.J.V.)
- Department of Jesse Brown, Veterans Administration Medical Center, Chicago, IL 60612, USA
| | - Benjamin J. Vesper
- Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, Chicago, IL 60612, USA; E-Mails: (W.A.P.); (B.J.V.)
- Department of Jesse Brown, Veterans Administration Medical Center, Chicago, IL 60612, USA
| | - Ajay Goel
- Division of Gastroenterology, Department of Internal Medicine, Charles A. Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75246, USA; E-Mail:
| | - Joshua D. Waltonen
- Department of Otolaryngology, Wake Forest University, Winston-Salem, NC 27157, USA; E-Mail:
| | | | - G. Kenneth Haines
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA; E-Mail:
| | - James A. Radosevich
- Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois at Chicago, Chicago, IL 60612, USA; E-Mails: (W.A.P.); (B.J.V.)
- Department of Jesse Brown, Veterans Administration Medical Center, Chicago, IL 60612, USA
- Author to whom correspondence should be addressed; E-Mail:
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16
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Kanu OO, Mehta A, Di C, Lin N, Bortoff K, Bigner DD, Yan H, Adamson DC. Glioblastoma multiforme: a review of therapeutic targets. Expert Opin Ther Targets 2009; 13:701-18. [PMID: 19409033 DOI: 10.1517/14728220902942348] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Glioblastoma is the commonest primary brain tumor, as well as the deadliest. Malignant gliomas such as glioblastoma multiforme (GBM) present some of the greatest challenges in the management of cancer patients worldwide, despite notable recent achievements in oncology. Even with aggressive surgical resections using state-of-the-art preoperative and intraoperative neuroimaging, along with recent advances in radiotherapy and chemotherapy, the prognosis for GBM patients remains dismal: survival after diagnosis is about 1 year. Established prognostic factors are limited, but include age, Karnofsky performance status, mini-mental status examination score, O6-methylguanine methyltransferase promoter methylation and extent of surgery. Standard treatment includes resection of > 95% of the tumor, followed by concurrent chemotherapy and radiotherapy. Nevertheless, GBM research is being conducted worldwide at a remarkable pace, in the laboratory and at the bedside, with some of the more recent promising studies focused on identification of aberrant genetic events and signaling pathways to develop molecular-based targeted therapies, tumor stem cell identification and characterization, modulation of tumor immunological responses and understanding of the rare long-term survivors. With this universally fatal disease, any small breakthrough will have a significant impact on survival and provide hope to the thousands of patients who receive this diagnosis annually. This review describes the epidemiology, clinical presentation, pathology and tumor immunology, with a focus on understanding the molecular biology that underlies the current targeted therapeutics being tested.
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Affiliation(s)
- Okezie O Kanu
- Duke and Durham VAMC, Neurosurgery, DUMC Box 2624, NC 27710, USA
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17
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Kanu OO, Hughes B, Di C, Lin N, Fu J, Bigner DD, Yan H, Adamson C. Glioblastoma Multiforme Oncogenomics and Signaling Pathways. Clin Med Oncol 2009; 3:39-52. [PMID: 19777070 PMCID: PMC2748278 DOI: 10.4137/cmo.s1008] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In the adult population, glioblastoma multiforme is one of the most common primary brain tumors encountered. Unfortunately, this highly malignant tumor represents over 50% of all types of primary central nervous system gliomas. The vast majority of GBMs develops quite rapidly without clinical, radiological, or morphologic evidence of a less malignant precursor lesion (primary or de novo GBMs), as compared to secondary GBMs that develop slowly by progression from diffuse low-grade astrocytomas. These GBM subtypes must be kept in mind because they may constitute distinct disease entities. Even though they look histologically quite similar, they likely involve different genetic alterations and signaling pathways. Decades of surgical therapy, radiotherapy, and chemotherapy have failed to drastically change survival. Clearly, we do not fully understand this tumor; however, the exciting genetic revolution in glioma research over the past decade is providing a promising outlook for exploring this tumor at the genetic level. Science has begun to elucidate the numerous genetic alterations and critical signaling pathways, and it has opened new exciting areas of research such as glioma stem cell biology and neoangiogenesis. This work has already begun to improve our understanding of GBM cell proliferation, migration, and invasion. Indeed, exciting novel targeted therapies are making their way to clinical trials based on this increased knowledge. This review provides the current understanding of GBM oncogenomics, signaling pathways, and glioma stem cell biology and discusses the potential new therapeutic targets on the horizon.
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18
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Tolmacheva EN, Kashevarova AA, Sukhanova NN, Sazhenova EA, Lebedev IN. Epigenetic inactivation of the RB1 gene as a factor of genomic instability: A possible contribution to etiology of chromosomal mosaicism during human embryo development. RUSS J GENET+ 2009. [DOI: 10.1134/s1022795408110033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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19
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Shai RM, Reichardt JKV, Chen TC. Pharmacogenomics of brain cancer and personalized medicine in malignant gliomas. Future Oncol 2008; 4:525-34. [PMID: 18684063 DOI: 10.2217/14796694.4.4.525] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The pharmacogenetics of cancer treatment has been aimed at identifying genetic components of interindividual variability in patients' response to cancer chemotherapy and toxicity. This, in turn, will establish an individually based treatment, and also elucidate the molecular basis of the treatment regimen for further improvements. Brain cancer is an instructive example for the potential contributions of pharmacogenomics to improved treatment in the 21st century. Patients with oligodendrogliomas have benefited from phamacogenomics, as there is a clear relationship between response to chemotherapy and chromosomal profile. Drug efficacy, safety and response could be improved by using pharmacogenomics to identify genetic markers that differentiate responder from nonresponder patient groups, as well as identifying patients likely to develop adverse drug reactions. This review will focus on how pharmacogenomics by microarray studies may lead to much more accurate tumor classification, drug and biomarker discovery, and drug efficacy testing. We will discuss relevant scientific advances in pharmacogenetics for more personalized chemotherapy.
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Affiliation(s)
- Ruty Mehrian Shai
- USC Keck School of Medicine, Department of Biochemistry and Molecular Biology, Institute for Genetic Medicine, Los Angeles, CA 90089, USA.
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20
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Loss of Rb1 in the gastrointestinal tract of Apc1638N mice promotes tumors of the cecum and proximal colon. Proc Natl Acad Sci U S A 2008; 105:15493-8. [PMID: 18832169 DOI: 10.1073/pnas.0802933105] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
To examine the role of Rb1 in gastrointestinal (GI) tumors, we generated mice with an Apc(1638N) allele, Rb(tm2brn) floxed alleles, and a villin-cre transgene (RBVCA). These animals had exon 19 deleted from Rb1 throughout the GI tract. We have shown previously that Rb1 deficiency is insufficient for GI tumor initiation, with inactivation of an Apc allele capable of overcoming the insufficiency. In this study we demonstrate that RBVCA mice have reduced median survival because of an increase in tumor incidence and multiplicity in the cecum and the proximal colon. Large intestinal tumors are predominantly adenomas, whereas the tumors of the small intestine are a mixture of adenomas and adenocarcinomas. We find truncation mutations to the second Apc allele in tumors of both the large and small intestine. Expression profiles of duodenal and cecal tumors relative to each other show unique gene subsets up and down regulated. Substantial expression patterns compare to human colorectal cancer, including recapitulation of embryonic genes. Our results indicate that Rb1 has significant influence over tumor location in the GI tract, and that both cecal and duodenal tumors initiate through inactivation of Apc. Expression profile analysis indicates the two tumor types differentially regulate distinct sets of genes that are over-expressed in a majority of human colorectal carcinomas.
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21
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Abstract
Epigenetics are defined, in broad-terms, as alterations in gene expression without changes in DNA sequence. While histone modifications and DNA methylation are two classical means to regulate gene expression, miRNA has also recently been documented to govern gene expression in normal as well as cancer cells. In this review, we will first describe briefly histone modifications, DNA methylation and miRNAs and the functions of these epigenetic marks during different cellular processes involving DNA metabolism. We will then highlight some epigenetic changes in glioblastomas, a malignant form of brain tumor, and potential application of epigenetic means for diagnosis, prognosis, and treatment of gliomas. We expect that novel therapies will be developed to counter epigenetic changes in this deadly disease.
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Affiliation(s)
- Rebecca Burgess
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
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22
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de Bont JM, Packer RJ, Michiels EM, den Boer ML, Pieters R. Biological background of pediatric medulloblastoma and ependymoma: a review from a translational research perspective. Neuro Oncol 2008; 10:1040-60. [PMID: 18676356 DOI: 10.1215/15228517-2008-059] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Survival rates of pediatric brain tumor patients have significantly improved over the years due to developments in diagnostic techniques, neurosurgery, chemotherapy, radiotherapy, and supportive care. However, brain tumors are still an important cause of cancer-related deaths in children. Prognosis is still highly dependent on clinical characteristics, such as the age of the patient, tumor type, stage, and localization, but increased knowledge about the genetic and biological features of these tumors is being obtained and might be useful to further improve outcome for these patients. It has become clear that the deregulation of signaling pathways essential in brain development, for example, sonic hedgehog (SHH), Wnt, and Notch pathways, plays an important role in pathogenesis and biological behavior, especially for medulloblastomas. More recently, data have become available about the cells of origin of brain tumors and the possible existence of brain tumor stem cells. Newly developed array-based techniques for studying gene expression, protein expression, copy number aberrations, and epigenetic events have led to the identification of other potentially important biological abnormalities in pediatric medulloblastomas and ependymomas.
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Affiliation(s)
- Judith M de Bont
- Department of Pediatric Oncology and Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands.
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24
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Lai PS, Cheah PY, Kadam P, Chua CLM, Lie DKH, Li HH, Eu KW, Seow-Choen F, Lee ASG. Overexpression of RB1 transcript is significantly correlated with 13q14 allelic imbalance in colorectal carcinomas. Int J Cancer 2006; 119:1061-6. [PMID: 16570290 DOI: 10.1002/ijc.21945] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
RB1 gene expression has been reported to be upregulated in colorectal carcinomas (CRC) at both the mRNA and protein levels when compared to normal colonic mucosa. However, allelic loss at the genomic level has been detected in CRC with widely differing frequencies ranging from 11.5% to 50%. To determine whether there is indeed a correlation between RB1 allelic imbalance (AI) and expression, a consecutive series of 55 CRC from Singapore patients were analysed by microsatellite analysis, real-time RT-PCR and immunohistochemistry. Microsatellite analysis using 3 RB1 intragenic microsatellite markers and 2 markers flanking RB1 detected AI in 32.7% (18/55) of the cases, in at least 1 locus. The highest AI frequency (22.9%) was observed at the microsatellite marker D13S137 (Cu13), which maps 5 cM distal to RB1. AI was present in both early and late Dukes stages. Real-time RT-PCR revealed that all 40 cases analysed expressed RB1 mRNA, with mRNA overexpression in 37.5% (15/40) and pRB protein expression in 88.2% (30/34) of cases. Notably, a statistically significant correlation was found between AI of RB1 and mRNA overexpression of RB1 (p < 0.001, Fishers exact test). These findings provide evidence that despite AI, RB1 expression is not abrogated. Thus, our data suggests that RB1 may play a role in colorectal tumorigenesis through functional regulation of the transcript and protein rather than through its tumour suppressor role by gene inactivation.
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Affiliation(s)
- Poh-San Lai
- Department of Paediatrics, National University of Singapore, Singapore
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25
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Anselmo NP, Bello MJ, Gonzalez-Gomez P, Dias LAA, Almeida JRWD, Santos MJD, Rey JA, Casartelli C. Epigenetic alterations in human brain tumors in a Brazilian population. Genet Mol Biol 2006. [DOI: 10.1590/s1415-47572006000300001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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26
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Bello MJ, Rey JA. The p53/Mdm2/p14ARF cell cycle control pathway genes may be inactivated by genetic and epigenetic mechanisms in gliomas. ACTA ACUST UNITED AC 2006; 164:172-3. [PMID: 16434325 DOI: 10.1016/j.cancergencyto.2005.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2005] [Accepted: 07/01/2005] [Indexed: 10/25/2022]
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Liu H, Liu W, Wu Y, Zhou Y, Xue R, Luo C, Wang L, Zhao W, Jiang JD, Liu J. Loss of epigenetic control of synuclein-gamma gene as a molecular indicator of metastasis in a wide range of human cancers. Cancer Res 2005; 65:7635-43. [PMID: 16140929 DOI: 10.1158/0008-5472.can-05-1089] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Metastasis is a major contributing factor to poor prognosis in cancer. Reliable and sensitive biomarkers that indicate the development of metastasis of primary tumors would be of great clinical use. In this study, we show that the neuronal protein synuclein-gamma (SNCG) is abnormally expressed in a high percentage (67.5%) of tumor tissues of diversified cancer types, including liver, esophagus, colon, gastric, lung, prostate, cervical, and breast cancer, but rarely expressed in tumor-matched nonneoplastic adjacent tissues (0.6%). Expressions of SNCG protein in different cancer types all display stage-specific patterns of very low expression in stage I and high expression in stages II to IV. Importantly, we observe a strong association between SNCG protein expression in primary tumors with distant metastasis in patients regardless of the cancer type (60.6%, P < 0.001). By performing genomic sequencing and methylation-specific PCR assays, we identify an inclusive demethylation of CpG sites within the CpG island of SNCG gene in every tumor sample (100%) across all cancer types, illustrating a universal loss of the epigenetic control of SNCG gene expression in tumors and further demonstrating that the demethylation of SNCG CpG island is primarily responsible for the aberrant expression of SNCG protein in cancerous tissues. These new findings strongly suggest that reactivation of SNCG gene expression by DNA demethylation is a common critical contributing factor to malignant progression of many solid tumors and its expression in primary carcinomas is an effective molecular indicator of distant metastasis. Our studies also suggest that the methylation status of SNCG gene can be used as a sensitive molecular tool in early detections of tumorigenesis.
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Affiliation(s)
- Haiyan Liu
- Research Service, Department of Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA
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Takahira T, Oda Y, Tamiya S, Yamamoto H, Kobayashi C, Izumi T, Ito K, Iwamoto Y, Tsuneyoshi M. Alterations of the RB1 gene in dedifferentiated liposarcoma. Mod Pathol 2005; 18:1461-70. [PMID: 15933756 DOI: 10.1038/modpathol.3800447] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Dedifferentiated liposarcoma is a malignant adipocytic neoplasm containing a non-lipogenic sarcoma of variable histological grade that arises against the background of a pre-existing well-differentiated liposarcoma. The phenomenon of dedifferentiation is considered to be time-dependent, but the mechanism is not well known. The retinoblastoma protein, encoded by the RB1 gene located at 13q14, is a key regulator of proliferation, development, and differentiation of certain cell types, including adipocytes. In the current study, we investigated the genetic alterations of the RB1 gene, such as mutation (the essential promoter region and the protein-binding pocket domain; exons 20-24) and methylation of the promoter region, in addition to pRB expression and loss of heterozygosity (LOH) status, in two morphologically distinct areas (non-lipogenic dedifferentiated and well-differentiated components) in 27 patients. As a control, 11 undifferentiated high-grade pleomorphic sarcoma/pleomorphic malignant fibrous histiocytoma samples and 11 well-differentiated liposarcoma samples were also evaluated. Dedifferentiated components showed LOH (15/25; 60%) and abnormal retinoblastoma protein expression (18/27; 66.7%) more frequently than noted in the well-differentiated components (3/24; 12.5% and 9/27; 33.3%, respectively). Five and four out of the 27 dedifferentiated components harbored mutations and promoter methylation, respectively, whereas none of these alterations were seen in the well-differentiated components. These results suggest that retinoblastoma protein has a major role to play in dedifferentiation and that a 'two-hit' mechanism is involved in the altered retinoblastoma protein expression in dedifferentiated liposarcoma.
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Affiliation(s)
- Tomonari Takahira
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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Hodge DR, Peng B, Cherry JC, Hurt EM, Fox SD, Kelley JA, Munroe DJ, Farrar WL. Interleukin 6 supports the maintenance of p53 tumor suppressor gene promoter methylation. Cancer Res 2005; 65:4673-82. [PMID: 15930285 DOI: 10.1158/0008-5472.can-04-3589] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A strong association exists between states of chronic inflammation and cancer, and it is believed that mediators of inflammation may be responsible for this phenomenon. Interleukin 6 (IL-6) is an inflammatory cytokine known to play a role in the growth and survival of many types of tumors, yet the mechanisms employed by this pleomorphic cytokine to accomplish this feat are still poorly understood. Another important factor in tumor development seems to be the hypermethylation of CpG islands located within the promoter regions of tumor suppressor genes. This common epigenetic alteration enables tumor cells to reduce or inactivate the expression of important tumor suppressor and cell cycle regulatory genes. Here we show that in the IL-6-responsive human multiple myeloma cell line KAS 6/1, the promoter region of p53 is epigenetically modified by methyltransferases, resulting in decreased levels of expression. Furthermore, cells treated with IL-6 exhibit an increase in the expression of the DNA maintenance methylation enzyme, DNMT-1. The DNA methyltransferase inhibitor zebularine reverses the methylation of the p53 promoter, allowing the resumption of its expression. However, when zebularine is withdrawn from the cells, the reestablishment of the original CpG island methylation within the p53 promoter does not occur in the absence of IL-6, and cells which do not receive IL-6 eventually die, as p53 expression continues unchecked by remethylation. Interestingly, this loss of viability seems to involve not the withdrawal of cytokine, but the inability of the cell to resilence the promoter. Consistent with this model, when cells that express IL-6 in an autocrine fashion are subjected to identical treatment, p53 expression is reduced shortly after withdrawal of zebularine. Therefore, it seems IL-6 is capable of maintaining promoter methylation thus representing one of the possible mechanisms used by inflammatory mediators in the growth and survival of tumors.
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Affiliation(s)
- David R Hodge
- Laboratory of Molecular Immunoregulation, Cytokine Molecular Mechanisms Section, Center for Cancer Research, National Cancer Institute at Frederick, MD 21702, USA.
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Waha A, Güntner S, Huang THM, Yan PS, Arslan B, Pietsch T, Wiestler OD, Waha A. Epigenetic silencing of the protocadherin family member PCDH-gamma-A11 in astrocytomas. Neoplasia 2005; 7:193-9. [PMID: 15799819 PMCID: PMC1501138 DOI: 10.1593/neo.04490] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In a microarray-based methylation analysis of astrocytomas [World Health Organization (WHO) grade II], we identified a CpG island within the first exon of the protocadherin-gamma subfamily A11 (PCDH-gamma-A11) gene that showed hypermethylation compared to normal brain tissue. Bisulfite sequencing and combined bisulfite restriction analysis (COBRA) was performed to screen low- and high-grade astrocytomas for the methylation status of this CpG island. Hypermethylation was detected in 30 of 34 (88%) astrocytomas (WHO grades II and III), 20 of 23 (87%) glioblastomas (WHO grade IV), and 8 of 8 (100%) glioma cell lines. There was a highly significant correlation (P = .00028) between PCDH-gamma-A11 hypermethylation and decreased transcription as determined by competitive reverse transcription polymerase chain reaction in WHO grades II and III astrocytomas. After treatment of glioma cell lines with a demethylating agent, transcription of PCDH-gamma-A11 was restored. In summary, we have identified PCDH-gamma-A11 as a new target silenced epigenetically in astrocytic gliomas. The inactivation of this cell-cell contact molecule might be involved in the invasive growth of astrocytoma cells into normal brain parenchyma.
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Affiliation(s)
- Anke Waha
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Stefanie Güntner
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Tim Hui-Ming Huang
- Division of Human Cancer Genetics, Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | - Pearlly S Yan
- Division of Human Cancer Genetics, Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | - Bülent Arslan
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Torsten Pietsch
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Otmar D Wiestler
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas Waha
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
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Jeanblanc M, Mousli M, Hopfner R, Bathami K, Martinet N, Abbady AQ, Siffert JC, Mathieu E, Muller CD, Bronner C. The retinoblastoma gene and its product are targeted by ICBP90: a key mechanism in the G1/S transition during the cell cycle. Oncogene 2005; 24:7337-45. [PMID: 16007129 DOI: 10.1038/sj.onc.1208878] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The retinoblastoma protein (pRB) is encoded by the RB1 gene whose promoter contains several putative binding sites for ICBP90 (Inverted CCAAT box Binding Protein of 90 kDa), a transcriptional regulator of the topoisomerase IIalpha gene. ICBP90 has two consensus binding sites for pRB in its primary sequence. Here, we show that pRB and ICBP90 co-immunoprecipitate in cell extracts of proliferating human lung fibroblasts and of proliferating or confluent Jurkat cells. GST pull-down assays and immunocytochemistry, after cell synchronization in late G1 phase, confirmed this interaction. Overexpression of ICBP90 induces downregulation of pRB expression in lung fibroblasts as a result of mRNA decrease. DNA chromatin immunoprecipitation experiment shows that ICBP90 binds to the RB1 gene promoter under its methylated status. Overexpression of ICBP90 increases the S and G2/M phase cell fractions of serum-starved lung fibroblasts as assessed by flow cytometry analysis and increases topoisomerase IIalpha expression. Together, these results show that ICBP90 regulates pRB at the protein and gene transcription levels, thus favoring the entry into the S phase of the cells. We propose that ICBP90 overexpression, found in cancer cells, is involved in the altered checkpoint controls occurring in cancerogenesis.
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Affiliation(s)
- Michaël Jeanblanc
- Inserm UMR S392, Faculté de Pharmacie, 74 route du Rhin, BP 60024, 67401 Illkirch Cedex, France
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Hamilton DW, Lusher ME, Lindsey JC, Ellison DW, Clifford SC. Epigenetic inactivation of the RASSF1A tumour suppressor gene in ependymoma. Cancer Lett 2004; 227:75-81. [PMID: 16051033 DOI: 10.1016/j.canlet.2004.11.044] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2004] [Revised: 11/26/2004] [Accepted: 11/28/2004] [Indexed: 12/31/2022]
Abstract
To investigate the role of aberrant epigenetic events in ependymoma and identify critical genes in its pathogenesis, the methylation status of nine tumour suppressor genes (TSGs: p14(ARF), p15(INK4B), p16(INK4A), CASP8, MGMT, TIMP3, TP73, RB1 and RASSF1A) was assessed. Extensive hypermethylation across the RASSF1A CpG island was detected frequently in ependymomas of all clinical and pathological disease subtypes (86% of cases, n=35), but not in non-neoplastic brain tissues (n=6). Less frequent methylation was observed for CASP8, MGMT and TP73 (5-20%). The remaining TSGs showed no evidence of methylation. RASSF1A hypermethylation represents the most common gene-specific defect identified in ependymoma highlighting the importance of its further investigation in this disease.
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Affiliation(s)
- David W Hamilton
- Northern Institute for Cancer Research, Paul O'Gorman Building, The Medical School, University of Newcastle, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK
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Lomas J, Bello MJ, Arjona D, Alonso ME, Martinez-Glez V, Lopez-Marin I, Amiñoso C, de Campos JM, Isla A, Vaquero J, Rey JA. Genetic and epigenetic alteration of theNF2gene in sporadic meningiomas. Genes Chromosomes Cancer 2004; 42:314-9. [PMID: 15609345 DOI: 10.1002/gcc.20141] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The role of the NF2 gene in the development of meningiomas has recently been documented; inactivating mutations plus allelic loss at 22q, the site of this gene (at 22q12), have been identified in both sporadic and neurofibromatosis type 2-associated tumors. Although epigenetic inactivation through aberrant CpG island methylation of the NF2 5' flanking region has been documented in schwannoma (another NF2-associated neoplasm), data on participation of this epigenetic modification in meningiomas are not yet widely available. Using methylation-specific PCR (MSP) plus sequencing, we assessed the presence of aberrant promoter NF2 methylation in a series of 88 meningiomas (61 grade I, 24 grade II, and 3 grade III), in which the allelic constitution at 22q and the NF2 mutational status also were determined by RFLP/microsatellite and PCR-SSCP analyses. Chromosome 22 allelic loss, NF2 gene mutation, and aberrant NF2 promoter methylation were detected in 49%, 24%, and 26% of cases, respectively. Aberrant NF2 methylation with loss of heterozygosity (LOH) at 22q was found in five cases, and aberrant methylation with NF2 mutation in another; LOH 22q and the mutation were found in 16 samples. The aberrant methylation of the NF2 gene also was the sole alteration in 15 samples, most of which were from grade I tumors. These results indicate that aberrant NF2 hypermethylation may participate in the development of a significant proportion of sporadic meningiomas, primarily those of grade I.
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Affiliation(s)
- Jesus Lomas
- Laboratorio de Oncogenética Molecular y Epigenética del Cáncer, Departamento de C. Experimental, Unidad de Investigación, Hospital Universitario La Paz, Madrid, Spain
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Abstract
DNA methylation is an important regulator of gene transcription, and its role in carcinogenesis has been a topic of considerable interest in the last few years. Alterations in DNA methylation are common in a variety of tumors as well as in development. Of all epigenetic modifications, hypermethylation, which represses transcription of the promoter regions of tumor suppressor genes leading to gene silencing, has been most extensively studied. However, global hypomethylation has also been recognized as a cause of oncogenesis. New information concerning the mechanism of methylation and its control has led to the discovery of many regulatory proteins and enzymes. The contribution of dietary folate and methylene terahydrofolate reductase polymorphisms to methylation patterns in normal and cancer tissues is under intense investigation. As methylation occurs early and can be detected in body fluids, it may be of potential use in early detection of tumors and for determining the prognosis. Because DNA methylation is reversible, drugs like 5'-azacytidine, decitabine, and histone deacetylase inhibitors are being used to treat a variety of tumors. Novel demethylating agents such as antisense DNA methyl transferase and small interference RNA are being developed, making the field of DNA methylation wider and more exciting.
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Affiliation(s)
- Partha M Das
- Department of Medicine, Miami VA Medical Center, Miami, FL, USA
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Bello MJ, Amiñoso C, Lopez-Marin I, Arjona D, Gonzalez-Gomez P, Alonso ME, Lomas J, de Campos JM, Kusak ME, Vaquero J, Isla A, Gutierrez M, Sarasa JL, Rey JA. DNA methylation of multiple promoter-associated CpG islands in meningiomas: relationship with the allelic status at 1p and 22q. Acta Neuropathol 2004; 108:413-21. [PMID: 15365725 DOI: 10.1007/s00401-004-0911-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2004] [Revised: 06/22/2004] [Accepted: 06/22/2004] [Indexed: 11/30/2022]
Abstract
The purpose of this research was to examine the DNA methylation profile of meningiomas. Accordingly, we examined the DNA methylation status of ten tumor-related genes (RB1, p16(INK4a), p73, MGMT, ER, DAPK, TIMP-3, p14(ARF), THBS1, and Caspase-8) in 98 meningiomas (68 grade I; 27 grade II; and 3 grade III samples) using methylation-specific PCR and sequencing. The most frequently methylated genes were THBS1 (30%), TIMP-3 (24%), p16(INK4a) (17%), MGMT (16%), p73 (15%), ER (15%), and p14(ARF) (13%), whereas methylation was relatively rare in the other genes (<10%). Methylation occurred in at least one gene in 77.5% of the cases and in three or more genes in 25.5%. Methylation was tumor specific since it was absent in the controls: two non-neoplastic meningeal samples and two non-neoplastic brain samples. The frequency of aberrant gene methylation in grade I versus grade II-III tumors showed some differences for TIMP-3, THBS1, MGMT, p16(INK4a) and p73; these differences reached statistical significance for TIMP-3: 18% in grade I versus 40% in grade II-III (P < 0.02). Our previous loss of heterozygosity studies provided the allelic constitution at 1p and 22q for 60 of the 98 meningiomas included in this report. The level of aberrant promoter methylation increased in tumors (30 samples) displaying 1p loss (either isolated or as concurrent deletion at 1p/22q; P = 0.014). These meningiomas primarily accumulated the epigenetic changes of THBS1 (14/30; 47%; P < 0.005), TIMP-3 (12/30; 40%; P < 0.05), p73 (10/30; 26%; P < 0.02) and p14(ARF) /p16(INK4a)(7/30 each one; 23%; not significant). Our findings indicate that aberrant DNA methylation of promoter-associated CpG islands in meningiomas contributes to the development of these tumors.
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Affiliation(s)
- M Josefa Bello
- Department of C. Experimental, Laboratorio Oncogenetica Molecular, Hospital Universitario La Paz, Paseo Castellana 261, 28046 Madrid, Spain
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Yu J, Zhang H, Gu J, Lin S, Li J, Lu W, Wang Y, Zhu J. Methylation profiles of thirty four promoter-CpG islands and concordant methylation behaviours of sixteen genes that may contribute to carcinogenesis of astrocytoma. BMC Cancer 2004; 4:65. [PMID: 15367334 PMCID: PMC520749 DOI: 10.1186/1471-2407-4-65] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2004] [Accepted: 09/14/2004] [Indexed: 01/04/2023] Open
Abstract
Background Astrocytoma is a common aggressive intracranial tumor and presents a formidable challenge in the clinic. Association of altered DNA methylation patterns of the promoter CpG islands with the expression profile of cancer-related genes, has been found in many human tumors. Therefore, DNA methylation status as such may serve as an epigenetic biomarker for both diagnosis and prognosis of human tumors, including astrocytoma. Methods We used the methylation specific PCR in conjunction with sequencing verification to establish the methylation profile of the promoter CpG island of thirty four genes in astrocytoma tissues from fifty three patients (The WHO grading:. I: 14, II: 15, III: 12 and IV: 12 cases, respectively). In addition, compatible tissues (normal tissues distant from lesion) from three non-astrocytoma patients were included as the control. Results Seventeen genes (ABL, APC, APAF1, BRCA1, CSPG2, DAPK1, hMLH1, LKB1, PTEN, p14ARF, p15INK4b, p27KIP1, p57KIP2, RASSF1C, RB1, SURVIVIN, and VHL) displayed a uniformly unmethylated pattern in all the astrocytoma and non-astrocytoma tissues examined. However, the MAGEA1 gene that was inactivated and hypermethylated in non-astrocytoma tissues, was partially demethylated in 24.5% of the astrocytoma tissues (co-existence of the hypermethylated and demethylated alleles). Of the astrocytoma associated hypermethylated genes, the methylation pattern of the CDH13, cyclin a1, DBCCR1, EPO, MYOD1, and p16INK4a genes changed in no more than 5.66% (3/53) of astrocytoma tissues compared to non-astrocytoma controls, while the RASSF1A, p73, AR, MGMT, CDH1, OCT6,, MT1A, WT1, and IRF7 genes were more frequently hypermethylated in 69.8%, 47.2%, 41.5%, 35.8%, 32%, 30.2%, 30.2%, 30.2% and 26.4% of astrocytoma tissues, respectively. Demethylation mediated inducible expression of the CDH13, MAGEA1, MGMT, p73 and RASSF1A genes was established in an astrocytoma cell line (U251), demonstrating that expression of these genes is likely regulated by DNA methylation. AR gene hypermethylation was found exclusively in female patients (22/27, 81%, 0/26, 0%, P < 0.001), while the IRF7 gene hypermethylation preferentially occurred in the male counterparts (11/26, 42.3% to 3/27, 11%, P < 0.05). Applying the mathematic method "the Discovery of Association Rules", we have identified groups consisting of up to three genes that more likely display the altered methylation patterns in concert in astrocytoma. Conclusions Of the thirty four genes examined, sixteen genes exhibited astrocytoma associated changes in the methylation profile. In addition to the possible pathological significance, the established concordant methylation profiles of the subsets consisting of two to three target genes may provide useful clues to the development of the useful prognostic as well as diagnostic assays for astrocytoma.
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Affiliation(s)
- Jian Yu
- Cancer Epigenetics and Gene Therapy, State-Key Laboratory for Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, LN 2200/25, Xie-Tu Road, Shanghai 200032, China
| | - Hongyu Zhang
- Cancer Epigenetics and Gene Therapy, State-Key Laboratory for Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, LN 2200/25, Xie-Tu Road, Shanghai 200032, China
| | - Jun Gu
- Cancer Epigenetics and Gene Therapy, State-Key Laboratory for Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, LN 2200/25, Xie-Tu Road, Shanghai 200032, China
| | - Song Lin
- Department of Neurosurgery, Tiantan Hospital of Capital University of Medical Sciences, Beijing Neurosurgical Institute, Beijing 100050, China
| | - Junhua Li
- Department of Neurosurgery, Tiantan Hospital of Capital University of Medical Sciences, Beijing Neurosurgical Institute, Beijing 100050, China
| | - Wei Lu
- Department of Mathematics, Shanghai University, No. 99, Shangda Road, Shanghai 200436, P. R. China
| | - Yifei Wang
- Department of Mathematics, Shanghai University, No. 99, Shangda Road, Shanghai 200436, P. R. China
| | - Jingde Zhu
- Cancer Epigenetics and Gene Therapy, State-Key Laboratory for Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, LN 2200/25, Xie-Tu Road, Shanghai 200032, China
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Semczuk A, Jakowicki JA. Alterations of pRb1-cyclin D1-cdk4/6-p16(INK4A) pathway in endometrial carcinogenesis. Cancer Lett 2004; 203:1-12. [PMID: 14670612 DOI: 10.1016/j.canlet.2003.09.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The retinoblastoma protein pathway (pRb1-cyclin D1-cdk4/6-p16(INK4A)) participates in the regulation of the cellular processes at the transition of G1/S phases of the cell-cycle. Derailments of this pathway, caused either by lack of pRb1 or p16(INK4A) expression or overexpression of cyclin D1 and/or cdk4/6, are implicated in the deregulation of the cell-cycle machinery, resulting in uncontrolled cell proliferation, tumor heterogeneity, invasion and metastasis. Several studies conducted so far have assessed the deregulation of the pRb1-pathway components in various human tumors and cell-lines, provided these pathway alterations play an obligatory role in tumorigenesis. This review briefly summarizes the current information on the pRb1-cyclin D1-cdk4/6-p16(INK4A) alterations in sporadic uterine cancer, placing emphasis on the influence on the dualistic model of endometrial carcinogenesis.
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Affiliation(s)
- Andrzej Semczuk
- Department of Gynecology, Lublin University School of Medicine, 8 Jaczewski str, 20-954 Lublin, Poland.
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Josefa Bello M, González-Gómez P, Rey J. Metástasis en el sistema nervioso central: biología molecular. Neurocirugia (Astur) 2004. [DOI: 10.1016/s1130-1473(04)70451-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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40
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Alonso ME, Bello MJ, Gonzalez-Gomez P, Arjona D, Lomas J, de Campos JM, Isla A, Sarasa JL, Rey JA. Aberrant promoter methylation of multiple genes in oligodendrogliomas and ependymomas. CANCER GENETICS AND CYTOGENETICS 2003; 144:134-42. [PMID: 12850376 DOI: 10.1016/s0165-4608(02)00928-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Promoter hypermethylation represents a primary mechanism in the inactivation of tumor suppressor genes during tumorigenesis. To determine the frequency and timing of hypermethylation during carcinogenesis of nonastrocytic tumors, we analyzed promoter methylation status of 10 tumor-associated genes in a series of 41 oligodendrogliomas (22 World Health Organization [WHO] grade II; 13 WHO grade III; 6 WHO grade II-III oligoastrocytomas) and 7 WHO grade II-III ependymomas, as well as 2 nonneoplastic brain samples, by a methylation-specific polymerase chain reaction. Aberrant CpG island methylation was detected in 9 of 10 genes analyzed, and all but one sample displayed anomalies in at least one gene. The frequencies of hypermethylation for the 10 genes were as follows, in oligodendrogliomas and ependymomas, respectively: 80% and 28% for MGMT; 70% and 28% for GSTP1; 66% and 57% for DAPK; 44% and 28% for TP14(ARF); 39% and 0% for THBS1; 24% and 28% for TIMP3; 24% and 14% for TP73; 22% and 0% for TP16(INK4A); 3% and 14% for RB1; and 0% in both neoplasms for TP53. No methylation of these genes was detected in normal brain tissue samples. We conclude that a high frequency of aberrant methylation of the 5' CpG island of the MGMT, GSTP1, TP14(ARF), THBS1, TIMP3, and TP73 genes is observed in nonastrocytic neoplasms. This aberration seems to occur early in the carcinogenesis process (it is already present in the low-grade forms), although in some instances (DAPK, THBS1, and TP73) it appears also associated with the genesis of anaplastic forms.
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Affiliation(s)
- M Eva Alonso
- Departmento de Cirurgía Experimental, Laboratorio de Oncogenética Molecular, Hospital Universitario La Paz, Madrid, Spain
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Gonzalez-Gomez P, Bello MJ, Lomas J, Arjona D, Alonso ME, Amiñoso C, Lopez-Marin I, Anselmo NP, Sarasa JL, Gutierrez M, Casartelli C, Rey JA. Aberrant methylation of multiple genes in neuroblastic tumours. relationship with MYCN amplification and allelic status at 1p. Eur J Cancer 2003; 39:1478-85. [PMID: 12826052 DOI: 10.1016/s0959-8049(03)00312-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Aberrant hypermethylation occurs in tumour cell CpG islands and is an important pathway for the repression of gene transcription in cancers. We investigated aberrant hypermethylation of 11 genes by methylation-specific polymerase chain reaction (PCR), after treatment of the DNA with bisulphite, and correlated the findings with MYCN amplification and allelic status at 1p in a series of 44 neuroblastic tumours. This tumour series includes five ganglioneuromas (G), one ganglioneuroblastoma (GN) and 38 neuroblastomas (six stage 1 tumours; five stage 2 tumours; six stage 3 cases; 19 stage 4 tumours, and two stage 4S cases). Aberrant methylation of at least one of the 11 genes studied was detected in 95% (42 of 44) of the cases. The frequencies of aberrant methylation were: 64% for thrombospondin-1 (THBS1); 30% for tissue inhibitor of metalloproteinase 3 (TIMP-3); 27% for O6-methylguanine-DNA methyltransferase (MGMT); 25% for p73; 18% for RB1; 14% for death-associated protein kinase (DAPK), p14ARF, p16INK4a and caspase 8, and 0% for TP53 and glutathione S-transferase P1 (GSTP1). No aberrant methylation was observed in four control normal tissue samples (brain and adrenal medulla). MYCN amplification was found in 11 cases (all stage 4 neuroblastomas), whereas allelic loss at 1p was identified in 16 samples (13 stage 4 and two stage 3 neuroblastomas, and one ganglioneuroma). All but one case with caspase 8 methylation also displayed MYCN amplification. Our results suggest that promoter hypermethylation is a frequent epigenetic event in the tumorigenesis of neuroblastic tumours, but no specific pattern of hypermethylated genes could be demonstrated.
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Affiliation(s)
- P Gonzalez-Gomez
- Laboratorio de Oncogenética Molecular, Dept. C. Experimental, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid Spain
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