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Ornos ED, Cando LF, Catral CD, Quebral EP, Tantengco OA, Arevalo MVP, Dee EC. Molecular basis of sex differences in cancer: Perspective from Asia. iScience 2023; 26:107101. [PMID: 37404373 PMCID: PMC10316661 DOI: 10.1016/j.isci.2023.107101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023] Open
Abstract
Cancer is a leading cause of mortality and morbidity globally. Sex differences in cancer are evident in death rates and treatment responses in several cancers. Asian patients have unique cancer epidemiology influenced by their genetic ancestry and sociocultural factors in the region. In this review, we show molecular associations that potentially mediate sex disparities observed in cancer in Asian populations. Differences in sex characteristics are evident at the cytogenetic, genetic, and epigenetic levels mediating processes that include cell cycle, oncogenesis, and metastasis. Larger clinical and in vitro studies that explore mechanisms can confirm the associations of these molecular markers. In-depth studies of these markers can reveal their importance as diagnostics, prognostics, and therapeutic efficacy markers. Sex differences should be considered in designing novel cancer therapeutics in this era of precision medicine.
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Affiliation(s)
- Eric David Ornos
- Department of Medical Microbiology, College of Public Health, University of the Philippines Manila, Manila 1000, Philippines
- College of Medicine, University of the Philippines Manila, Manila, 1000, Philippines
| | - Leslie Faye Cando
- College of Medicine, University of the Philippines Manila, Manila, 1000, Philippines
| | | | - Elgin Paul Quebral
- College of Medicine, University of the Philippines Manila, Manila, 1000, Philippines
- Virology Laboratory, Department of Medical Microbiology, College of Public Health, University of the Philippines Manila, Manila 1000, Philippines
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Ourlad Alzeus Tantengco
- College of Medicine, University of the Philippines Manila, Manila, 1000, Philippines
- Department of Physiology, College of Medicine, University of the Philippines Manila, Manila 1000, Philippines
- Department of Biology, College of Science, De La Salle University, Manila 0922, Philippines
| | | | - Edward Christopher Dee
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10028, USA
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Merkle FT, Ghosh S, Genovese G, Handsaker RE, Kashin S, Meyer D, Karczewski KJ, O'Dushlaine C, Pato C, Pato M, MacArthur DG, McCarroll SA, Eggan K. Whole-genome analysis of human embryonic stem cells enables rational line selection based on genetic variation. Cell Stem Cell 2022; 29:472-486.e7. [PMID: 35176222 PMCID: PMC8900618 DOI: 10.1016/j.stem.2022.01.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 10/29/2021] [Accepted: 01/24/2022] [Indexed: 02/02/2023]
Abstract
Despite their widespread use in research, there has not yet been a systematic genomic analysis of human embryonic stem cell (hESC) lines at a single-nucleotide resolution. We therefore performed whole-genome sequencing (WGS) of 143 hESC lines and annotated their single-nucleotide and structural genetic variants. We found that while a substantial fraction of hESC lines contained large deleterious structural variants, finer-scale structural and single-nucleotide variants (SNVs) that are ascertainable only through WGS analyses were present in hESC genomes and human blood-derived genomes at similar frequencies. Moreover, WGS allowed us to identify SNVs associated with cancer and other diseases that could alter cellular phenotypes and compromise the safety of hESC-derived cellular products transplanted into humans. As a resource to enable reproducible hESC research and safer translation, we provide a user-friendly WGS data portal and a data-driven scheme for cell line maintenance and selection.
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Affiliation(s)
- Florian T Merkle
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wellcome - MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK.
| | - Sulagna Ghosh
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert E Handsaker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Seva Kashin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Colm O'Dushlaine
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carlos Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA; Department of Psychiatry, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Michele Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA; Department of Psychiatry, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Daniel G MacArthur
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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A novel form of Deleted in breast cancer 1 (DBC1) lacking the N-terminal domain does not bind SIRT1 and is dynamically regulated in vivo. Sci Rep 2019; 9:14381. [PMID: 31591441 PMCID: PMC6779753 DOI: 10.1038/s41598-019-50789-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 09/19/2019] [Indexed: 12/24/2022] Open
Abstract
The protein Deleted in Breast Cancer-1 is a regulator of several transcription factors and epigenetic regulators, including HDAC3, Rev-erb-alpha, PARP1 and SIRT1. It is well known that DBC1 regulates its targets, including SIRT1, by protein-protein interaction. However, little is known about how DBC1 biological activity is regulated. In this work, we show that in quiescent cells DBC1 is proteolytically cleaved, producing a protein (DN-DBC1) that misses the S1-like domain and no longer binds to SIRT1. DN-DBC1 is also found in vivo in mouse and human tissues. Interestingly, DN-DBC1 is cleared once quiescent cells re-enter to the cell cycle. Using a model of liver regeneration after partial hepatectomy, we found that DN-DBC1 is down-regulated in vivo during regeneration. In fact, WT mice show a decrease in SIRT1 activity during liver regeneration, coincidentally with DN-DBC1 downregulation and the appearance of full length DBC1. This effect on SIRT1 activity was not observed in DBC1 KO mice. Finally, we found that DBC1 KO mice have altered cell cycle progression and liver regeneration after partial hepatectomy, suggesting that DBC1/DN-DBC1 transitions play a role in normal cell cycle progression in vivo after cells leave quiescence. We propose that quiescent cells express DN-DBC1, which either replaces or coexist with the full-length protein, and that restoring of DBC1 is required for normal cell cycle progression in vitro and in vivo. Our results describe for the first time in vivo a naturally occurring form of DBC1, which does not bind SIRT1 and is dynamically regulated, thus contributing to redefine the knowledge about its function.
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Schulten HJ, Hussein D. Array expression meta-analysis of cancer stem cell genes identifies upregulation of PODXL especially in DCC low expression meningiomas. PLoS One 2019; 14:e0215452. [PMID: 31083655 PMCID: PMC6513070 DOI: 10.1371/journal.pone.0215452] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 04/02/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Meningiomas are the most common intracranial tumors, with a subset of cases bearing a progressive phenotype. The DCC netrin 1 receptor (DCC) is a candidate gene for early meningioma progression. Cancer stem cell (CSC) genes are emerging as cancer therapeutic targets, as their expression is frequently associated with aggressive tumor phenotypes. The main objective of the study was to identify deregulated CSC genes in meningiomas. MATERIALS AND METHODS Interrogating two expression data repositories, significantly differentially expressed genes (DEGs) were determined using DCC low vs. DCC high expression groups and WHO grade I (GI) vs. grade II + grade III (GII + GIII) comparison groups. Human stem cell (SC) genes were compiled from two published data sets and were extracted from the DEG lists. Biofunctional analysis was performed to assess associations between genes or molecules. RESULTS In the DCC low vs. DCC high expression groups, we assessed seven studies representing each between seven and 58 samples. The type I transmembrane protein podocalyxin like (PODXL) was markedly upregulated in DCC low expression meningiomas in six studies. Other CSC genes repeatedly deregulated included, e.g., BMP/retinoic acid inducible neural specific 1 (BRINP1), prominin 1 (PROM1), solute carrier family 24 member 3 (SLC24A3), rRho GTPase activating protein 28 (ARHGAP28), Kruppel like factor 5 (KLF5), and leucine rich repeat containing G protein-coupled receptor 4 (LGR4). In the GI vs. GII + GIII comparison groups, we assessed six studies representing each between nine and 68 samples. DNA topoisomerase 2-alpha (TOP2A) was markedly upregulated in GII + GIII meningiomas in four studies. Other CSC genes repeatedly deregulated included, e.g., ARHGAP28 and PODXL. Network analysis revealed associations of molecules with, e.g., cellular development and movement; nervous system development and function; and cancer. CONCLUSIONS This meta-analysis on meningiomas identified a comprehensive list of deregulated CSC genes across different array expression studies. Especially, PODXL is of interest for functional assessment in progressive meningiomas.
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Affiliation(s)
- Hans-Juergen Schulten
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Deema Hussein
- King Fahad Medical Research Center, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Zhang W, Cui Q, Qu W, Ding X, Jiang D, Liu H. TRIM58/cg26157385 methylation is associated with eight prognostic genes in lung squamous cell carcinoma. Oncol Rep 2018; 40:206-216. [PMID: 29749538 PMCID: PMC6059744 DOI: 10.3892/or.2018.6426] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/30/2018] [Indexed: 12/17/2022] Open
Abstract
The present study aimed to analyze the differentially expressed genes related to the tripartite motif containing 58 (TRIM58)/cg26157385 methylation sites, and consequently to provide theoretical basis for elucidating the influence of TRIM58/cg26157385 methylation on lung cancer prognosis. Methylation-sequencing information, mRNA expression profiling data and clinical data were downloaded from cBioPortal database to screen out candidate genes related to the methylation of TRIM58/cg26157385 in squamous cell lung carcinoma. The differentially expressed genes related to TRIM58 methylation were extracted form both training dataset and validation dataset. Cox regression analysis, risk scoring system construction, correlation analysis between the expression value of genes and clinical information were conducted to reveal TRIM58 methylation-related factors. Additionally, GO function analysis and KEGG pathway enrichment analysis were performed. Based on their expression level and the corresponding survival information for 347 out of 370 samples with squamous cell lung carcinoma, 183 genes significantly associated with prognosis were gained, and the top 8 ones, including alpha-2-macroglobulin-like 1 (A2ML1), cyclin-E1 (CCNE1), COBL, establishment of sister chromatid cohesion N-acetyltransferase 2 (ESCO2), G protein-coupled receptor 115 (GPR115), matrix metalloproteinases 10 (MMP10), OVO homologue-like 1 (OVOL1) and secretoglobin family 1A member 1 (SCGB1A1), were candidate signature genes significantly correlated with TRIM58 methylation. Furthermore, targeted therapy was significantly correlated with prognosis. Functional enrichment analysis demonstrated that the proliferation and differentiation of epidermal cells in lung squamous cell carcinoma patients were abnormal and the homeostasis was disturbed. Eight genes, including A2ML1, CCNE1, COBL, ESCO2, GPR115, MMP10, OVOL1 and SCGB1A1, were significantly related to TRIM58 methylation and treatment of lung squamous cell carcinoma, and may be used as potential prognostic biomarkers. The present study would help to elucidate the influence of TRIM58/cg26157385 methylation on lung cancer prognosis.
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Affiliation(s)
- Weimin Zhang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Nantong University, Wuxi, Jiangsu 214000, P.R. China
| | - Qichen Cui
- Department of Thoracic Surgery, The Third Affiliated Hospital of Nantong University, Wuxi, Jiangsu 214000, P.R. China
| | - Weifeng Qu
- Department of Thoracic Surgery, The Third Affiliated Hospital of Nantong University, Wuxi, Jiangsu 214000, P.R. China
| | - Xiaoyun Ding
- Department of Thoracic Surgery, The Third Affiliated Hospital of Nantong University, Wuxi, Jiangsu 214000, P.R. China
| | - Donglin Jiang
- Department of Central Laboratory, The Third Affiliated Hospital of Nantong University, Wuxi, Jiangsu 214000, P.R. China
| | - Hongcheng Liu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Shanghai 200000, P.R. China
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Daifuku R, Grimes S, Stackhouse M. NUC041, a Prodrug of the DNA Methytransferase Inhibitor 5-aza-2',2'-Difluorodeoxycytidine (NUC013), Leads to Tumor Regression in a Model of Non-Small Cell Lung Cancer. Pharmaceuticals (Basel) 2018; 11:ph11020036. [PMID: 29690576 PMCID: PMC6027359 DOI: 10.3390/ph11020036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 01/10/2023] Open
Abstract
5-aza-2′,2′-difluorodeoxycytidine (NUC013) has been shown to be significantly safer and more effective than decitabine in xenograft models of human leukemia and colon cancer. However, it suffers from a similar short half-life as other DNA methyltransferase inhibitors with a 5-azacytosine base, which is problematic for nucleosides that primarily target tumor cells in S phase. Because of the relative instability of 5-azanucleosides, a prodrug approach was developed to improve the pharmacology of NUC013. NUC013 was conjugated with trimethylsilanol (TMS) at the 3′ and 5′ position of the sugar, rendering the molecule hydrophobic and producing 3′,5′-di-trimethylsilyl-2′,2′-difluoro-5-azadeoxycytidine (NUC041). NUC041 was designed to be formulated in a hydrophobic vehicle, protecting it from deamination and hydrolysis. In contact with blood, the TMS moieties are readily hydrolyzed to release NUC013. The half-life of NUC013 administered intravenously in mice is 20.1 min, while that of NUC013 derived from intramuscular NUC041 formulated in a pegylated-phospholipid depot is 3.4 h. In a NCI-H460 xenograft of non-small cell lung cancer, NUC013 was shown to significantly inhibit tumor growth and improve survival. Treatment with NUC041 also led to significant tumor growth inhibition. However, NUC041-treated mice had significantly more tumors ulcerate than either NUC013 treated mice or saline control mice, and such ulceration occurred at significantly lower tumor volumes. In these nude mice, tumor regression was likely mediated by the derepression of the tumor suppressor gene p53 and resultant activation of natural killer (NK) cells.
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Affiliation(s)
- Richard Daifuku
- Epigenetics Pharma, 9270 SE 36th Pl, Mercer Island, WA 98040, USA.
| | - Sheila Grimes
- Southern Research, 2000 9th Avenue South, Birmingham, AL 35205, USA.
| | - Murray Stackhouse
- Southern Research, 2000 9th Avenue South, Birmingham, AL 35205, USA.
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Frequent silencing of the candidate tumor suppressor TRIM58 by promoter methylation in early-stage lung adenocarcinoma. Oncotarget 2018; 8:2890-2905. [PMID: 27926516 PMCID: PMC5356850 DOI: 10.18632/oncotarget.13761] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/22/2016] [Indexed: 01/15/2023] Open
Abstract
In this study, we aimed to identify novel drivers that would be epigenetically altered through aberrant methylation in early-stage lung adenocarcinoma (LADC), regardless of the presence or absence of tobacco smoking-induced epigenetic field defects. Through genome-wide screening for aberrantly methylated CpG islands (CGIs) in 12 clinically uniform, stage-I LADC cases affecting six non-smokers and six smokers, we identified candidate tumor-suppressor genes (TSGs) inactivated by hypermethylation. Through systematic expression analyses of those candidates in panels of additional tumor samples and cell lines treated or not treated with 5-aza-deoxycitidine followed by validation analyses of cancer-specific silencing by CGI hypermethylation using a public database, we identified TRIM58 as the most prominent candidate for TSG. TRIM58 was robustly silenced by hypermethylation even in early-stage primary LADC, and the restoration of TRIM58 expression in LADC cell lines inhibited cell growth in vitro and in vivo in anchorage-dependent and -independent manners. Our findings suggest that aberrant inactivation of TRIM58 consequent to CGI hypermethylation might stimulate the early carcinogenesis of LADC regardless of smoking status; furthermore, TRIM58 methylation might be a possible early diagnostic and epigenetic therapeutic target in LADC.
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Wu D, Zhang J, Fan P, Li H, Li D, Pan H, He H, Ren X, Pan Z, Shao R, Pan Z. Methylation in the promoter regions of WT1, NKX6-1 and DBC1 genes in cervical cancer tissues of Uygur women in Xinjiang. Genet Mol Biol 2018; 41:9-17. [PMID: 29658966 PMCID: PMC5901490 DOI: 10.1590/1678-4685-gmb-2016-0146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 06/07/2017] [Indexed: 11/22/2022] Open
Abstract
This study aimed to explore: 1) DNA methylation in the promoter regions of Wilms tumor gene 1 (WT1), NK6 transcription factor related locus 1 gene (NKX6-1) and Deleted in bladder cancer 1 (DBC1) gene in cervical cancer tissues of Uygur women in Xinjiang, and 2) the correlation of gene methylation with the infection of HPV16/18 viruses. We detected HPV16/18 infection in 43 normal cervical tissues, 30 cervical intraepithelial neoplasia lesions (CIN) and 48 cervical cancer tissues with polymerase chain reaction (PCR) method. Methylation in the promoter regions of the WT1, NKX6-1 and DBC1 genes in the above-mentioned tissues was measured by methylation-specific PCR (MSP) and cloning sequencing. The expression level of these three genes was measured by real-time PCR (qPCR) in 10 methylation-positive cervical cancer tissues and 10 methylation-negative normal cervical tissues. We found that the infection of HPV16 in normal cervical tissues, CIN and cervical cancer tissues was 14.0, 36.7 and 66.7%, respectively. The infection of HPV18 was 0, 6.7 and 10.4%, respectively. The methylation rates of WT1, NKX6-1 and DBC1 genes were 7.0, 11.6 and 23.3% in normal cervical tissues, 36.7, 46.7 and 30.0% in CIN tissues, and 89.6, 77.1 and 85.4% in cervical cancer tissues. Furthermore, WT1, NKX6-1 and DBC1 genes were hypermethylated in the high-grade squamous intraepithelial lesion (CIN2, CIN3) and in the cervical cancer tissues with infection of HPV16/18 (both P< 0.05). The expression of WT1, NKX6-1 and DBC1 was significantly lower in the methylation-positive cervical cancer tissues than in methylation-negative normal cervical tissues. Our findings indicated that methylation in the promoter regions of WT1, NKX6-1 and DBC1 is correlated with cervical cancer tumorigenesis in Uygur women. The infection of HPV16/18 might be correlated with methylation in these genes. Gene inactivation caused by methylation might be related to the incidence and development of cervical cancer.
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Affiliation(s)
- Dan Wu
- Department of Biochemistry and Molecular Biology, School of Medicine, Shihezi University, Xinjiang Endemic and Ethnic Disease and Education Ministry Key Laboratory, Shihezi, Xinjiang, China.,Clinical Laboratory, Branch of the First Affiliated Hospital of Xinjiang Medical University, Changji, Xinjiang, China
| | - Jinli Zhang
- Department of Biochemistry and Molecular Biology, School of Medicine, Shihezi University, Xinjiang Endemic and Ethnic Disease and Education Ministry Key Laboratory, Shihezi, Xinjiang, China
| | - Peiwen Fan
- Department of Biochemistry and Molecular Biology, School of Medicine, Shihezi University, Xinjiang Endemic and Ethnic Disease and Education Ministry Key Laboratory, Shihezi, Xinjiang, China
| | - Hongtao Li
- Department of Biochemistry and Molecular Biology, School of Medicine, Shihezi University, Xinjiang Endemic and Ethnic Disease and Education Ministry Key Laboratory, Shihezi, Xinjiang, China
| | - Dongmei Li
- Department of Biochemistry and Molecular Biology, School of Medicine, Shihezi University, Xinjiang Endemic and Ethnic Disease and Education Ministry Key Laboratory, Shihezi, Xinjiang, China
| | - Huan Pan
- Department of Biochemistry and Molecular Biology, School of Medicine, Shihezi University, Xinjiang Endemic and Ethnic Disease and Education Ministry Key Laboratory, Shihezi, Xinjiang, China
| | - Hongchang He
- Department of Biochemistry and Molecular Biology, School of Medicine, Shihezi University, Xinjiang Endemic and Ethnic Disease and Education Ministry Key Laboratory, Shihezi, Xinjiang, China
| | - Xianxian Ren
- Department of Biochemistry and Molecular Biology, School of Medicine, Shihezi University, Xinjiang Endemic and Ethnic Disease and Education Ministry Key Laboratory, Shihezi, Xinjiang, China
| | - Zhenzhen Pan
- Department of Biochemistry and Molecular Biology, School of Medicine, Shihezi University, Xinjiang Endemic and Ethnic Disease and Education Ministry Key Laboratory, Shihezi, Xinjiang, China
| | - Renfu Shao
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Zemin Pan
- Department of Biochemistry and Molecular Biology, School of Medicine, Shihezi University, Xinjiang Endemic and Ethnic Disease and Education Ministry Key Laboratory, Shihezi, Xinjiang, China
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Kajiura K, Takizawa H, Morimoto Y, Masuda K, Tsuboi M, Kishibuchi R, Wusiman N, Sawada T, Kawakita N, Toba H, Yoshida M, Kawakami Y, Naruto T, Imoto I, Tangoku A, Kondo K. Frequent silencing of RASSF1A by DNA methylation in thymic neuroendocrine tumours. Lung Cancer 2017; 111:116-123. [PMID: 28838380 DOI: 10.1016/j.lungcan.2017.05.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/20/2017] [Accepted: 05/20/2017] [Indexed: 01/12/2023]
Abstract
OBJECTIVES Aberrant methylation of promoter CpG islands (CGIs) of tumour suppressor genes is a common epigenetic mechanism underlying cancer pathogenesis. The methylation patterns of thymic tumours have not been studied in detail since such tumours are rare. Herein, we sought to identify genes that could serve as epigenetic targets for thymic neuroendocrine tumour (NET) therapy. MATERIALS AND METHODS Genome-wide screening for aberrantly methylated CGIs was performed in three NET samples, seven thymic carcinoma (TC) samples, and eight type-B3 thymoma samples. The methylation status of thymic epithelial tumours (TETs) samples was validated by pyrosequencing in a larger cohort. The expression status was analysed by quantitative polymerase chain reaction (PCR) and immunohistochemistry. RESULTS We identified a CGI on a novel gene, RASSF1A, which was strongly hypermethylated in NET, but not in thymic carcinoma or B3 thymoma. RASSF1A was identified as a candidate gene statistically and bibliographically, as it showed frequent CGI hypermethylation in NET by genome-wide screening. Pyrosequencing confirmed significant hypermethylation of a RASSF1A CGI in NET. Low-grade NET tissue was more strongly methylated than high-grade NET. Quantitative PCR and immunohistochemical staining revealed that RASSF1A mRNA and protein expression levels were negatively regulated by DNA methylation. CONCLUSIONS RASSF1A is a tumour suppressor gene epigenetically dysregulated in NET. Aberrant methylation of RASSF1A has been reported in various tumours, but this is the first report of RASSF1A hypermethylation in TETs. RASSF1A may represent an epigenetic therapeutic target in thymic NET.
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Affiliation(s)
- Koichiro Kajiura
- Department of Thoracic, Endocrine and Oncological Surgery, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan; Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan.
| | - Hiromitsu Takizawa
- Department of Thoracic, Endocrine and Oncological Surgery, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan.
| | - Yuki Morimoto
- Department of Oncological Medical Services, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan.
| | - Kiyoshi Masuda
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan.
| | - Mitsuhiro Tsuboi
- Department of Thoracic, Endocrine and Oncological Surgery, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan.
| | - Reina Kishibuchi
- Department of Oncological Medical Services, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan.
| | - Nuliamina Wusiman
- Department of Oncological Medical Services, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan.
| | - Toru Sawada
- Department of Thoracic, Endocrine and Oncological Surgery, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan.
| | - Naoya Kawakita
- Department of Thoracic, Endocrine and Oncological Surgery, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan.
| | - Hiroaki Toba
- Department of Thoracic, Endocrine and Oncological Surgery, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan.
| | - Mitsuteru Yoshida
- Department of Thoracic, Endocrine and Oncological Surgery, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan.
| | - Yukikiyo Kawakami
- Department of Thoracic, Endocrine and Oncological Surgery, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan.
| | - Takuya Naruto
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan.
| | - Issei Imoto
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan.
| | - Akira Tangoku
- Department of Thoracic, Endocrine and Oncological Surgery, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan.
| | - Kazuya Kondo
- Department of Oncological Medical Services, Graduate School of Biomedical Sciences, Tokushima University Graduate School, Tokushima city 770-8503, Japan.
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High-definition CpG methylation of novel genes in gastric carcinogenesis identified by next-generation sequencing. Mod Pathol 2016; 29:182-93. [PMID: 26769141 DOI: 10.1038/modpathol.2015.144] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/01/2015] [Indexed: 12/12/2022]
Abstract
Gastric cancers are the most frequent gastric malignancy and usually arise in the sequence of Helicobacter pylori-associated chronic gastritis. CpG methylation is a central mechanism of epigenetic gene regulation affecting cancer-related genes, and occurs early in gastric carcinogenesis. DNA samples from non-metaplastic gastric mucosa with variable levels of gastritis (non-metaplastic mucosa), intestinal metaplasia, or gastric cancer were screened with methylation arrays for CpG methylation of cancer-related genes and 30 gene targets were further characterized by high-definition bisulfite next-generation sequencing. In addition, data from The Cancer Genome Atlas were analyzed for correlation of methylation with gene expression. Overall, 13 genes had significantly increased CpG methylation in gastric cancer vs non-metaplastic mucosa (BRINP1, CDH11, CHFR, EPHA5, EPHA7, FGF2, FLI1, GALR1, HS3ST2, PDGFRA, SEZ6L, SGCE, and SNRPN). Further, most of these genes had corresponding reduced expression levels in gastric cancer compared with intestinal metaplasia, including novel hypermethylated genes in gastric cancer (FLI1, GALR1, SGCE, and SNRPN), suggesting that they may regulate neoplastic transformation from non-malignant intestinal metaplasia to cancer. Our data suggest a tumor-suppressor role for FLI1 in gastric cancer, consistent with recently reported data in breast cancer. For the genes with strongest methylation/expression correlation, namely FLI1, the expression was lowest in microsatellite-unstable tumors compared with other gastric cancer molecular subtypes. Importantly, reduced expression of hypermethylated BRINP1 and SGCE was significantly associated with favorable survival in gastric cancer. In summary, we report novel methylation gene targets that may have functional roles in discrete stages of gastric carcinogenesis and may serve as biomarkers for diagnosis and prognosis of gastric cancer.
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Cloning and characterization of the porcine DBC1 gene encoding deleted in bladder cancer. Mol Biol Rep 2014; 42:383-91. [PMID: 25258124 DOI: 10.1007/s11033-014-3779-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/23/2014] [Indexed: 01/12/2023]
Abstract
Deleted in bladder cancer 1 (DBC1) is a tumour suppressor which is involved in the regulation of cell growth and programmed cell death. In this study we report the cloning and characterization of porcine DBC1 cDNA. RT-PCR cloning produced a cDNA with an open reading frame of 2,283 bp encoding a polypeptide of 761 amino acids with a predicted molecular mass of 88.6 kDa and estimated isoelectric point of 9.1. The encoded pig DBC1 protein shows a very high amino acid similarity to human (99 %) and to mouse (98 %) DBC1. The porcine DBC1 gene was mapped to chromosome 1. The nucleotide sequence of the promoter displayed a high degree of conservation of elements responsible for neuron-specific expression. The porcine DBC1 gene was found to be highly expressed in brain tissues. The methylation status of the porcine DBC1 gene was examined in brain and liver by bisulfite sequencing. Methylation percentages of 53-61 were observed for the gene body whereas significantly lower values (1-4 %) were found in exon 1 and the promoter sequence of DBC1. The sequences of the porcine DBC1 cDNA and the DBC1 promoter and exon 1 sequence have been submitted to DDBJ/EMBL/GenBank under the accession numbers KF733442 and KJ396193, respectively.
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Shim UJ, Lee IS, Kang HW, Kim J, Kim WT, Kim IY, Ryu KH, Choi YH, Moon SK, Kim YJ, Yun SJ, Lee SC, Kim WJ. Decreased DBC1 Expression Is Associated With Poor Prognosis in Patients With Non-Muscle-Invasive Bladder Cancer. Korean J Urol 2013; 54:631-7. [PMID: 24044099 PMCID: PMC3773595 DOI: 10.4111/kju.2013.54.9.631] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 07/22/2013] [Indexed: 11/25/2022] Open
Abstract
Purpose The deleted in bladder cancer 1 (DBC1) gene is located within chromosome 9 (9q32-33), a chromosomal region that frequently shows loss of heterozygosity in bladder cancer (BC). It is suspected that it acts as a tumor suppressor gene, but its prognostic value remains unclear. The aim of the present study was to investigate the value of DBC1 as a prognostic marker in BC. Materials and Methods The expression of DBC1 was determined by real-time polymerase chain reaction analysis in 344 patients with BC (220 non-muscle-invasive BC [NMIBC] and 124 muscle-invasive BC [MIBC]) and in 34 patients with normal bladder mucosa. The results were compared with clinicopathologic parameters, and the prognostic value of DBC1 was evaluated by Kaplan-Meier analysis and a multivariate Cox regression model. Results DBC1 expression was significantly decreased in patients with MIBC compared with those diagnosed with NMIBC (p=0.010). Patients with aggressive tumor characteristics had lower DBC1 expression levels in NMIBC (each, p<0.05). By multivariate Cox regression analysis, low DBC1 expression was a predictor of progression to MIBC (hazard ratio, 7.104; p=0.013). Kaplan-Meier estimates revealed a significant difference in tumor recurrence, progression to MIBC, and cancer-specific survival depending on the level of DBC1 expression in NMIBC (log-rank test, each, p<0.05). Conclusions The expression of DBC1 was associated with tumor aggressiveness, progression to MIBC, and survival in NMIBC. Our results suggest that DBC1 expression can be a useful prognostic marker for patients with NMIBC.
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Affiliation(s)
- Ui Jae Shim
- Department of Urology, Chungbuk National University College of Medicine, Cheongju, Korea
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Grimm C, Chavez L, Vilardell M, Farrall AL, Tierling S, Böhm JW, Grote P, Lienhard M, Dietrich J, Timmermann B, Walter J, Schweiger MR, Lehrach H, Herwig R, Herrmann BG, Morkel M. DNA-methylome analysis of mouse intestinal adenoma identifies a tumour-specific signature that is partly conserved in human colon cancer. PLoS Genet 2013; 9:e1003250. [PMID: 23408899 PMCID: PMC3567140 DOI: 10.1371/journal.pgen.1003250] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 12/02/2012] [Indexed: 12/31/2022] Open
Abstract
Aberrant CpG methylation is a universal epigenetic trait of cancer cell genomes. However, human cancer samples or cell lines preclude the investigation of epigenetic changes occurring early during tumour development. Here, we have used MeDIP-seq to analyse the DNA methylome of APCMin adenoma as a model for intestinal cancer initiation, and we present a list of more than 13,000 recurring differentially methylated regions (DMRs) characterizing intestinal adenoma of the mouse. We show that Polycomb Repressive Complex (PRC) targets are strongly enriched among hypermethylated DMRs, and several PRC2 components and DNA methyltransferases were up-regulated in adenoma. We further demonstrate by bisulfite pyrosequencing of purified cell populations that the DMR signature arises de novo in adenoma cells rather than by expansion of a pre-existing pattern in intestinal stem cells or undifferentiated crypt cells. We found that epigenetic silencing of tumour suppressors, which occurs frequently in colon cancer, was rare in adenoma. Quite strikingly, we identified a core set of DMRs, which is conserved between mouse adenoma and human colon cancer, thus possibly revealing a global panel of epigenetically modified genes for intestinal tumours. Our data allow a distinction between early conserved epigenetic alterations occurring in intestinal adenoma and late stochastic events promoting colon cancer progression, and may facilitate the selection of more specific clinical epigenetic biomarkers. The formation and progression of tumours to metastatic disease is driven by two major mechanisms, i.e. genetic alterations that activate oncogenes or inactivate tumour suppressor genes, and changes in the epigenome that cause variations in the expression of the genetic information. A deeper understanding of the interaction between the genetic and epigenetic mechanisms is critical for the selection of tumour biomarkers and for the future development of therapies. Human tumour specimens and cell lines contain a plethora of genetic and epigenetic changes, which complicate data analysis. In contrast, mouse tumour models such as the APCMin mouse used in this study arise by a single initiating genetic mutation, yet share key traits with human cancer. Here we show that mouse adenomas acquire a multitude of epigenetic alterations, which are recurring in mouse adenoma and in human colon cancer, representing early and advanced tumours, respectively. The use of a mouse model thus allowed us to uncover a sequence of epigenetic changes occurring in tumours, which may facilitate the identification of novel clinical colon cancer biomarkers.
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Affiliation(s)
- Christina Grimm
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
- Charité Universitätsmedizin Berlin, Department of Rheumatology, Berlin, Germany
| | - Lukas Chavez
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Mireia Vilardell
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Alexandra L. Farrall
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Berlin, Germany
| | - Sascha Tierling
- Universität des Saarlandes, FR 8.3 Biowissenschaften, Genetik/Epigenetik Campus, Saarbrücken, Germany
| | - Julia W. Böhm
- Universität des Saarlandes, FR 8.3 Biowissenschaften, Genetik/Epigenetik Campus, Saarbrücken, Germany
| | - Phillip Grote
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Berlin, Germany
| | - Matthias Lienhard
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Jörn Dietrich
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Next Generation Sequencing Core Facility, Berlin, Germany
| | - Jörn Walter
- Universität des Saarlandes, FR 8.3 Biowissenschaften, Genetik/Epigenetik Campus, Saarbrücken, Germany
| | - Michal R. Schweiger
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Ralf Herwig
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Bernhard G. Herrmann
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Berlin, Germany
- Charité Universitätsmedizin Berlin, Institute for Medical Genetics, Berlin, Germany
| | - Markus Morkel
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Berlin, Germany
- Charité Universitätsmedizin Berlin, Laboratory of Molecular Tumor Pathology, Berlin, Germany
- * E-mail:
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Genomic methylation profiling combined with gene expression microarray reveals the aberrant methylation mechanism involved in nasopharyngeal carcinoma taxol resistance. Anticancer Drugs 2012; 23:856-64. [DOI: 10.1097/cad.0b013e3283548d73] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C, Kharchenko PV, Park PJ, The Cancer Genome Atlas Research Network. Landscape of somatic retrotransposition in human cancers. Science 2012; 337:967-71. [PMID: 22745252 PMCID: PMC3656569 DOI: 10.1126/science.1222077] [Citation(s) in RCA: 555] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Transposable elements (TEs) are abundant in the human genome, and some are capable of generating new insertions through RNA intermediates. In cancer, the disruption of cellular mechanisms that normally suppress TE activity may facilitate mutagenic retrotranspositions. We performed single-nucleotide resolution analysis of TE insertions in 43 high-coverage whole-genome sequencing data sets from five cancer types. We identified 194 high-confidence somatic TE insertions, as well as thousands of polymorphic TE insertions in matched normal genomes. Somatic insertions were present in epithelial tumors but not in blood or brain cancers. Somatic L1 insertions tend to occur in genes that are commonly mutated in cancer, disrupt the expression of the target genes, and are biased toward regions of cancer-specific DNA hypomethylation, highlighting their potential impact in tumorigenesis.
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Affiliation(s)
- Eunjung Lee
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Rebecca Iskow
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA 02115, USA
| | - Lixing Yang
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Omer Gokcumen
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA 02115, USA
| | - Psalm Haseley
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Lovelace J. Luquette
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Jens G. Lohr
- The Eli and Edythe Broad Institute, Cambridge, MA 02412, USA
- Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Christopher C. Harris
- The Genome Institute, Washington University, School of Medicine, St. Louis, MO 63108, USA
| | - Li Ding
- The Genome Institute, Washington University, School of Medicine, St. Louis, MO 63108, USA
| | - Richard K. Wilson
- The Genome Institute, Washington University, School of Medicine, St. Louis, MO 63108, USA
| | - David A. Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Raju Kucherlapati
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Charles Lee
- Department of Pathology, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA 02115, USA
| | - Peter V. Kharchenko
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Informatics Program, Children’s Hospital, Boston, MA 02115, USA
| | - Peter J. Park
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Informatics Program, Children’s Hospital, Boston, MA 02115, USA
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Accumulation of genomic alterations in 2p16, 9q33.1 and 19p13 in lung tumours of asbestos-exposed patients. Mol Oncol 2012; 7:29-40. [PMID: 22901466 DOI: 10.1016/j.molonc.2012.07.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 07/12/2012] [Accepted: 07/31/2012] [Indexed: 11/24/2022] Open
Abstract
We have previously demonstrated an association between genomic alterations in 19p13, 2p16, and 9q33.1 and asbestos exposure in patients' lung tumours. This study detected allelic imbalance (AI) in these regions in asbestos-exposed lung cancer (LC) patients' histologically normal pulmonary epithelium. We extended the analyses of tumour tissue to cover a large LC patient cohort and studied DNA copy number alteration (CNA) and AI in 19p13, 2p16, and 9q33.1 for the first time in combination. We found both CNA and AI in ≥2/3 of the regions to be significantly and dose-dependently (P < 0.001) associated with pulmonary asbestos fibre count. Twenty percent of the exposed patients' LC showed CNA in ≥2/3 of the regions, whereas none of the non-exposed patients' LC showed CNA in more than one region. AI was evident in 89% of the exposed and in only 26% of the non-exposed patients' LC. The genomic alterations in 19p13, 2p16, and 9q33.1 in compilation identified asbestos-exposed patients' lung tumours better than each of the regions alone. These alterations form the basis for the development of a combinatorial molecular assay that could be used to identify asbestos-related LC.
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Huang RL, Chang CC, Su PH, Chen YC, Liao YP, Wang HC, Yo YT, Chao TK, Huang HC, Lin CY, Chu TY, Lai HC. Methylomic analysis identifies frequent DNA methylation of zinc finger protein 582 (ZNF582) in cervical neoplasms. PLoS One 2012; 7:e41060. [PMID: 22815913 PMCID: PMC3397950 DOI: 10.1371/journal.pone.0041060] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 06/16/2012] [Indexed: 12/26/2022] Open
Abstract
Background Despite of the trend that the application of DNA methylation as a biomarker for cancer detection is promising, clinically applicable genes are few. Therefore, we looked for novel hypermethylated genes for cervical cancer screening. Methods and Findings At the discovery phase, we analyzed the methylation profiles of human cervical carcinomas and normal cervixes by methylated DNA immunoprecipitation coupled to promoter tiling arrays (MeDIP-on-chip). Methylation-specific PCR (MSP), quantitative MSP and bisulfite sequencing were used to verify the methylation status in cancer tissues and cervical scrapings from patients with different severities. Immunohistochemical staining of a cervical tissue microarray was used to confirm protein expression. We narrowed to three candidate genes: DBC1, PDE8B, and ZNF582; their methylation frequencies in tumors were 93%, 29%, and 100%, respectively. At the pre-validation phase, the methylation frequency of DBC1 and ZNF582 in cervical scraping correlated significantly with disease severity in an independent cohort (n = 330, both P<0.001). For the detection of cervical intraepithelial neoplasia 3 (CIN3) and worse, the area under the receiver operating characteristic curve (AUC) of ZNF582 was 0.82 (95% confidence interval = 0.76–0.87). Conclusions Our study shows ZNF582 is frequently methylated in CIN3 and worse lesions, and it is demonstrated as a potential biomarker for the molecular screening of cervical cancer.
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Affiliation(s)
- Rui-Lan Huang
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
- Laboratory of Epigenetics and Cancer Stem Cells, National Defense Medical Centre, Taipei, Taiwan
| | - Cheng-Chang Chang
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan
- Laboratory of Epigenetics and Cancer Stem Cells, National Defense Medical Centre, Taipei, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Po-Hsuan Su
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Yu-Chih Chen
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Yu-Ping Liao
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Hui-Chen Wang
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan
- Laboratory of Epigenetics and Cancer Stem Cells, National Defense Medical Centre, Taipei, Taiwan
| | - Yi-Te Yo
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan
- Laboratory of Epigenetics and Cancer Stem Cells, National Defense Medical Centre, Taipei, Taiwan
| | - Tai-Kuang Chao
- Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Ching-Yu Lin
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Tang-Yuan Chu
- Center for Cervical Cancer Prevention, Department of Obstetrics and Gynecology, Graduate Institute of Clinical Medicine, Tzu Chi Medical Center, Tzu Chi University, Hualien, Taiwan
| | - Hung-Cheng Lai
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan
- Laboratory of Epigenetics and Cancer Stem Cells, National Defense Medical Centre, Taipei, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- * E-mail:
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Nordlund J, Milani L, Lundmark A, Lönnerholm G, Syvänen AC. DNA methylation analysis of bone marrow cells at diagnosis of acute lymphoblastic leukemia and at remission. PLoS One 2012; 7:e34513. [PMID: 22493696 PMCID: PMC3321015 DOI: 10.1371/journal.pone.0034513] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 03/06/2012] [Indexed: 01/17/2023] Open
Abstract
To detect genes with CpG sites that display methylation patterns that are characteristic of acute lymphoblastic leukemia (ALL) cells, we compared the methylation patterns of cells taken at diagnosis from 20 patients with pediatric ALL to the methylation patterns in mononuclear cells from bone marrow of the same patients during remission and in non-leukemic control cells from bone marrow or blood. Using a custom-designed assay, we measured the methylation levels of 1,320 CpG sites in regulatory regions of 413 genes that were analyzed because they display allele-specific gene expression (ASE) in ALL cells. The rationale for our selection of CpG sites was that ASE could be the result of allele-specific methylation in the promoter regions of the genes. We found that the ALL cells had methylation profiles that allowed distinction between ALL cells and control cells. Using stringent criteria for calling differential methylation, we identified 28 CpG sites in 24 genes with recurrent differences in their methylation levels between ALL cells and control cells. Twenty of the differentially methylated genes were hypermethylated in the ALL cells, and as many as nine of them (AMICA1, CPNE7, CR1, DBC1, EYA4, LGALS8, RYR3, UQCRFS1, WDR35) have functions in cell signaling and/or apoptosis. The methylation levels of a subset of the genes were consistent with an inverse relationship with the mRNA expression levels in a large number of ALL cells from published data sets, supporting a potential biological effect of the methylation signatures and their application for diagnostic purposes.
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Affiliation(s)
- Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine, Uppsala University, Uppsala, Sweden
| | - Lili Milani
- Department of Medical Sciences, Molecular Medicine, Uppsala University, Uppsala, Sweden
| | - Anders Lundmark
- Department of Medical Sciences, Molecular Medicine, Uppsala University, Uppsala, Sweden
| | - Gudmar Lönnerholm
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine, Uppsala University, Uppsala, Sweden
- * E-mail:
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States JC, Barchowsky A, Cartwright IL, Reichard JF, Futscher BW, Lantz RC. Arsenic toxicology: translating between experimental models and human pathology. ENVIRONMENTAL HEALTH PERSPECTIVES 2011; 119:1356-63. [PMID: 21684831 PMCID: PMC3230447 DOI: 10.1289/ehp.1103441] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 06/17/2011] [Indexed: 05/21/2023]
Abstract
BACKGROUND Chronic arsenic exposure is a worldwide health problem. How arsenic exposure promotes a variety of diseases is poorly understood, and specific relationships between experimental and human exposures are not established. We propose phenotypic anchoring as a means to unify experimental observations and disease outcomes. OBJECTIVES We examined the use of phenotypic anchors to translate experimental data to human pathology and investigated research needs for which phenotypic anchors need to be developed. METHODS During a workshop, we discussed experimental systems investigating arsenic dose/exposure and phenotypic expression relationships and human disease responses to chronic arsenic exposure and identified knowledge gaps. In a literature review, we identified areas where data exist to support phenotypic anchoring of experimental results to pathologies from specific human exposures. DISCUSSION Disease outcome is likely dependent on cell-type-specific responses and interaction with individual genetics, other toxicants, and infectious agents. Potential phenotypic anchors include target tissue dosimetry, gene expression and epigenetic profiles, and tissue biomarkers. CONCLUSIONS Translation to human populations requires more extensive profiling of human samples along with high-quality dosimetry. Anchoring results by gene expression and epigenetic profiling has great promise for data unification. Genetic predisposition of individuals affects disease outcome. Interactions with infectious agents, particularly viruses, may explain some species-specific differences between human pathologies and experimental animal pathologies. Invertebrate systems amenable to genetic manipulation offer potential for elaborating impacts of specific biochemical pathways. Anchoring experimental results to specific human exposures will accelerate understanding of mechanisms of arsenic-induced human disease.
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Affiliation(s)
- J Christopher States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA.
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Frequent and simultaneous epigenetic inactivation of TP53 pathway genes in acute lymphoblastic leukemia. PLoS One 2011; 6:e17012. [PMID: 21386967 PMCID: PMC3046174 DOI: 10.1371/journal.pone.0017012] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 01/18/2011] [Indexed: 02/08/2023] Open
Abstract
Aberrant DNA methylation is one of the most frequent alterations in patients with Acute Lymphoblastic Leukemia (ALL). Using methylation bead arrays we analyzed the methylation status of 807 genes implicated in cancer in a group of ALL samples at diagnosis (n = 48). We found that 154 genes were methylated in more than 10% of ALL samples. Interestingly, the expression of 13 genes implicated in the TP53 pathway was downregulated by hypermethylation. Direct or indirect activation of TP53 pathway with 5-aza-2′-deoxycitidine, Curcumin or Nutlin-3 induced an increase in apoptosis of ALL cells. The results obtained with the initial group of 48 patients was validated retrospectively in a second cohort of 200 newly diagnosed ALL patients. Methylation of at least 1 of the 13 genes implicated in the TP53 pathway was observed in 78% of the patients, which significantly correlated with a higher relapse (p = 0.001) and mortality (p<0.001) rate being an independent prognostic factor for disease-free survival (DFS) (p = 0.006) and overall survival (OS) (p = 0.005) in the multivariate analysis. All these findings indicate that TP53 pathway is altered by epigenetic mechanisms in the majority of ALL patients and correlates with prognosis. Treatments with compounds that may reverse the epigenetic abnormalities or activate directly the p53 pathway represent a new therapeutic alternative for patients with ALL.
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DNA methylation profiles and their relationship with cytogenetic status in adult acute myeloid leukemia. PLoS One 2010; 5:e12197. [PMID: 20808941 PMCID: PMC2922373 DOI: 10.1371/journal.pone.0012197] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 07/14/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Aberrant promoter DNA methylation has been shown to play a role in acute myeloid leukemia (AML) pathophysiology. However, further studies to discuss the prognostic value and the relationship of the epigenetic signatures with defined genomic rearrangements in acute myeloid leukemia are required. METHODOLOGY/PRINCIPAL FINDINGS We carried out high-throughput methylation profiling on 116 de novo AML cases and we validated the significant biomarkers in an independent cohort of 244 AML cases. Methylation signatures were associated with the presence of a specific cytogenetic status. In normal karyotype cases, aberrant methylation of the promoter of DBC1 was validated as a predictor of the disease-free and overall survival. Furthermore, DBC1 expression was significantly silenced in the aberrantly methylated samples. Patients with chromosome rearrangements showed distinct methylation signatures. To establish the role of fusion proteins in the epigenetic profiles, 20 additional samples of human hematopoietic stem/progenitor cells (HSPC) transduced with common fusion genes were studied and compared with patient samples carrying the same rearrangements. The presence of MLL rearrangements in HSPC induced the methylation profile observed in the MLL-positive primary samples. In contrast, fusion genes such as AML1/ETO or CBFB/MYH11 failed to reproduce the epigenetic signature observed in the patients. CONCLUSIONS/SIGNIFICANCE Our study provides a comprehensive epigenetic profiling of AML, identifies new clinical markers for cases with a normal karyotype, and reveals relevant biological information related to the role of fusion proteins on the methylation signature.
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Yi J, Luo J. SIRT1 and p53, effect on cancer, senescence and beyond. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1804:1684-9. [PMID: 20471503 PMCID: PMC2989880 DOI: 10.1016/j.bbapap.2010.05.002] [Citation(s) in RCA: 247] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 04/01/2010] [Accepted: 05/01/2010] [Indexed: 12/21/2022]
Abstract
NAD(+)-dependent Class III histone deacetylase SIRT1 is a multiple function protein critically involved in stress responses, cellular metabolism and aging through deacetylating a variety of substrates including p53, forkhead-box transcription factors, PGC-1alpha, NF-kappaB, Ku70 and histones. The first discovered non-histone target of SIRT1, p53, is suggested to play a central role in SIRT1-mediated functions in tumorigenesis and senescence. SIRT1 was originally considered to be a potential tumor promoter since it negatively regulates the tumor suppressor p53 and other tumor suppressors. There is new evidence that SIRT1 acts as a tumor suppressor based on its role in negatively regulating beta-catenin and survivin. This review provides an overview of current knowledge of SIRT1-p53 signaling and controversies regarding the functions of SIRT1 in tumorigenesis.
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Affiliation(s)
- Jingjie Yi
- Department of Cancer Biology and the Cancer Center, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, 01605, USA
- School of Life sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Jianyuan Luo
- Department of Cancer Biology and the Cancer Center, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, 01605, USA
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23
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Wnek SM, Jensen TJ, Severson PL, Futscher BW, Gandolfi AJ. Monomethylarsonous acid produces irreversible events resulting in malignant transformation of a human bladder cell line following 12 weeks of low-level exposure. Toxicol Sci 2010; 116:44-57. [PMID: 20375083 DOI: 10.1093/toxsci/kfq106] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Arsenic is a known human bladder carcinogen; however, the mechanisms underlying arsenical-induced bladder carcinogenesis are not understood. Previous research has demonstrated that exposure of a nontumorigenic human urothelial cell line, UROtsa, to 50 nM monomethylarsonous acid (MMA(III)) for 52 weeks resulted in malignant transformation. To focus research on the early mechanistic events leading to MMA(III)-induced malignancy, the goal of this research was to resolve the critical period in which continuous MMA(III) exposure (50 nM) induces the irreversible malignant transformation of UROtsa cells. An increased growth rate of UROtsa cells results after 12 weeks of MMA(III) exposure. Anchorage-independent growth occurred after 12 weeks with a continued increase in colony formation when 12-week exposed cells were cultured for an additional 12 or 24 weeks without MMA(III) exposure. UROtsa cells as early as 12 weeks MMA(III) exposure were tumorigenic in severe combined immunodeficiency mice with tumorigenicity increasing when 12-week exposed cells were cultured for an additional 12 or 24 weeks in the absence of MMA(III) exposure. To assess potential underlying mechanisms associated with the early changes that occur during MMA(III)-induced malignancy, DNA methylation was assessed in known target gene promoter regions. Although DNA methylation remains relatively unchanged after 12 weeks of exposure, aberrant DNA methylation begins to emerge after an additional 12 weeks in culture and continues to increase through 24 weeks in culture without MMA(III) exposure, coincident with the progression of a tumorigenic phenotype. Overall, these data demonstrate that 50 nM MMA(III) is capable of causing irreversible malignant transformation in UROtsa cells after 12 weeks of exposure. Having resolved an earlier timeline in which MMA(III)-induced malignant transformation occurs in UROtsa cells will allow for mechanistic studies focused on the critical biological changes taking place within these cells prior to 12 weeks of exposure, providing further evidence about potential mechanisms of MMA(III)-induced carcinogenesis.
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Affiliation(s)
- Shawn M Wnek
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, USA.
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Saitoh Y, Martínez Bruyn VJ, Uota S, Hasegawa A, Yamamoto N, Imoto I, Inazawa J, Yamaoka S. Overexpression of NF-κB inducing kinase underlies constitutive NF-κB activation in lung cancer cells. Lung Cancer 2010; 70:263-70. [PMID: 20338663 DOI: 10.1016/j.lungcan.2010.03.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 02/17/2010] [Accepted: 03/01/2010] [Indexed: 01/22/2023]
Abstract
The present study investigates roles for NF-κB inducing kinase (NIK) in constitutive NF-κB activation in lung cancer cells. A wealth of evidence showed that NF-κB is often constitutively activated in human cancer cells, including non-small cell lung cancer tissue specimens and cell lines, which may lead to deregulated apoptosis and enhanced resistance of tumor cells to chemotherapy. However, the mechanisms of NF-κB activation in lung cancer cells remain largely unknown. We report here that NF-κB inducing kinase (NIK) is aberrantly expressed at the pre-translational level in non-small cell lung cancer (NSCLC) cell lines. Depletion of NIK by RNA interference remarkably diminished nuclear NF-κB DNA binding activity and reporter gene expression. NIK depletion induced apoptosis in A549 cells, reduced the matrix metalloproteinase 9 (MMP-9) and survivin mRNA expression and affected efficiency of anchorage-independent H1299 cell growth, suggesting a role for NIK in the manifestation of oncogenic phenotype. These results indicate that NIK plays a key role in constitutive NF-κB activation in NSCLC cells and implicate NIK as a molecular target for lung cancer therapy.
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Affiliation(s)
- Yasunori Saitoh
- Department of Molecular Virology, Bio Response, Graduate School of Medicine, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
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25
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Kusakabe M, Kutomi T, Watanabe K, Emoto N, Aki N, Kage H, Hamano E, Kitagawa H, Nagase T, Sano A, Yoshida Y, Fukami T, Murakawa T, Nakajima J, Takamoto S, Ota S, Fukayama M, Yatomi Y, Ohishi N, Takai D. Identification of G0S2 as a gene frequently methylated in squamous lung cancer by combination of in silico and experimental approaches. Int J Cancer 2010; 126:1895-1902. [PMID: 19816938 DOI: 10.1002/ijc.24947] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Epigenetic changes can lead to abnormal expression of genes in cancer, and several genes have been reported to have aberrant promoter DNA methylation in non-small-cell lung cancer (NSCLC). We identified aberrantly methylated genes in NSCLC by combination of in silico and experimental approaches. We first applied bioinformatics, and from microarray datasets, we selected genes with low expression and having functions related to cancer. Next, combined bisulfite restriction analysis was carried out in 10 pooled resected lung cancer tissues to screen for genes that were aberrantly methylated, and the methylation ratio (the fraction of methylated DNA in extracted DNA from a cancer tissue sample) was quantified using quantitative analysis of methylated alleles. We identified 8 methylated genes (ARPC1B, DNAH9, FLRT2, G0S2, IRS2, PKP1, SPOCK1 and UCHL1) previously unreported in NSCLC. Analyses of methylation profiles of 101 resected lung cancer tissue samples revealed quantitatively low methylation in whole, methylation ratios were almost less than 30% even in the methylated samples, and no significant correlation to prognosis after 2 years of follow-up using hierarchical clustering. DNA methylation of G0S2 gene was significantly more frequent in squamous lung cancer (n = 18, mean of methylation ratios: 15%) compared with nonsquamous lung cancer (n = 83, mean of methylation ratios: 2.6%) (Mann-Whitney U test, p < 0.001). DNA methylation of G0S2 can be an important biomarker for squamous lung cancer.
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Affiliation(s)
- Masashi Kusakabe
- Department of General Thoracic Surgery, The University of Tokyo Hospital, Tokyo, Japan
| | - Tomoko Kutomi
- Department of Respiratory Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - Kousuke Watanabe
- Department of Respiratory Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - Noriko Emoto
- Department of Respiratory Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - Naomi Aki
- Department of Respiratory Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - Hidenori Kage
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Emi Hamano
- Department of Respiratory Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - Hiroshi Kitagawa
- Department of Respiratory Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - Takahide Nagase
- Department of Respiratory Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - Atsushi Sano
- Department of General Thoracic Surgery, The University of Tokyo Hospital, Tokyo, Japan
| | - Yukihiro Yoshida
- Department of General Thoracic Surgery, The University of Tokyo Hospital, Tokyo, Japan
| | - Takeshi Fukami
- Department of General Thoracic Surgery, The University of Tokyo Hospital, Tokyo, Japan
| | - Tomohiro Murakawa
- Department of General Thoracic Surgery, The University of Tokyo Hospital, Tokyo, Japan
| | - Jun Nakajima
- Department of General Thoracic Surgery, The University of Tokyo Hospital, Tokyo, Japan
| | - Shinichi Takamoto
- Department of General Thoracic Surgery, The University of Tokyo Hospital, Tokyo, Japan
| | - Satoshi Ota
- Department of Pathology, The University of Tokyo Hospital, Tokyo, Japan
| | - Masashi Fukayama
- Department of Pathology, The University of Tokyo Hospital, Tokyo, Japan
| | - Yutaka Yatomi
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Nobuya Ohishi
- Department of Respiratory Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - Daiya Takai
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
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26
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Hill VK, Hesson LB, Dansranjavin T, Dallol A, Bieche I, Vacher S, Tommasi S, Dobbins T, Gentle D, Euhus D, Lewis C, Dammann R, Ward RL, Minna J, Maher ER, Pfeifer GP, Latif F. Identification of 5 novel genes methylated in breast and other epithelial cancers. Mol Cancer 2010; 9:51. [PMID: 20205715 PMCID: PMC2841122 DOI: 10.1186/1476-4598-9-51] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 03/05/2010] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND There are several high throughput approaches to identify methylated genes in cancer. We utilized one such recently developed approach, MIRA (methylated-CpG island recovery assay) combined with CpG island arrays to identify novel genes that are epigenetically inactivated in breast cancer. RESULTS Using this approach we identified numerous CpG islands that demonstrated aberrant DNA methylation in breast cancer cell lines. Using a combination of COBRA and sequencing of bisulphite modified DNA, we confirmed 5 novel genes frequently methylated in breast tumours; EMILIN2, SALL1, DBC1, FBLN2 and CIDE-A. Methylation frequencies ranged from between 25% and 63% in primary breast tumours, whilst matched normal breast tissue DNA was either unmethylated or demonstrated a much lower frequency of methylation compared to malignant breast tissue DNA. Furthermore expression of the above 5 genes was shown to be restored following treatment with a demethylating agent in methylated breast cancer cell lines. We have expanded this analysis across three other common epithelial cancers (lung, colorectal, prostate). We demonstrate that the above genes show varying levels of methylation in these cancers. Lastly and most importantly methylation of EMILIN2 was associated with poorer clinical outcome in breast cancer and was strongly associated with estrogen receptor as well as progesterone receptor positive breast cancers. CONCLUSION The combination of the MIRA assay with CpG island arrays is a very useful technique for identifying epigenetically inactivated genes in cancer genomes and can provide molecular markers for early cancer diagnosis, prognosis and epigenetic therapy.
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Affiliation(s)
- Victoria K Hill
- Department of Medical and Molecular Genetics, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Luke B Hesson
- Department of Medical and Molecular Genetics, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, NSW2052, Australia
| | - Temuujin Dansranjavin
- Institute for Genetics, Justus Liebig University Giessen, Heinrich-Buff-Ring 58-62, D-35392 Giessen, Germany
| | - Ashraf Dallol
- Department of Medical and Molecular Genetics, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ivan Bieche
- Oncogenetic Laboratory, INSERM U 735, Centre René Huguenin, Saint Cloud, France
| | - Sophie Vacher
- Oncogenetic Laboratory, INSERM U 735, Centre René Huguenin, Saint Cloud, France
| | - Stella Tommasi
- Beckman Research Institute, City of Hope, 1500 E Duarte Road, Duarte, CA 91010. USA
| | - Timothy Dobbins
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, NSW2052, Australia
| | - Dean Gentle
- Department of Medical and Molecular Genetics, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - David Euhus
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Cheryl Lewis
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Reinhard Dammann
- Institute for Genetics, Justus Liebig University Giessen, Heinrich-Buff-Ring 58-62, D-35392 Giessen, Germany
| | - Robyn L Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, NSW2052, Australia
| | - John Minna
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Eammon R Maher
- Department of Medical and Molecular Genetics, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Gerd P Pfeifer
- Beckman Research Institute, City of Hope, 1500 E Duarte Road, Duarte, CA 91010. USA
| | - Farida Latif
- Department of Medical and Molecular Genetics, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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Yuferov V, Levran O, Proudnikov D, Nielsen DA, Kreek MJ. Search for genetic markers and functional variants involved in the development of opiate and cocaine addiction and treatment. Ann N Y Acad Sci 2010; 1187:184-207. [PMID: 20201854 PMCID: PMC3769182 DOI: 10.1111/j.1749-6632.2009.05275.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Addiction to opiates and illicit use of psychostimulants is a chronic, relapsing brain disease that, if left untreated, can cause major medical, social, and economic problems. This article reviews recent progress in studies of association of gene variants with vulnerability to develop opiate and cocaine addictions, focusing primarily on genes of the opioid and monoaminergic systems. In addition, we provide the first evidence of a cis-acting polymorphism and a functional haplotype in the PDYN gene, of significantly higher DNA methylation rate of the OPRM1 gene in the lymphocytes of heroin addicts, and significant differences in genotype frequencies of three single-nucleotide polymorphisms of the P-glycoprotein gene (ABCB1) between "higher" and "lower" methadone doses in methadone-maintained patients. In genomewide and multigene association studies, we found association of several new genes and new variants of known genes with heroin addiction. Finally, we describe the development and application of a novel technique: molecular haplotyping for studies in genetics of drug addiction.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B
- ATP Binding Cassette Transporter, Subfamily B, Member 1/genetics
- Catechol O-Methyltransferase/genetics
- Cocaine-Related Disorders/genetics
- Cocaine-Related Disorders/therapy
- Enkephalins/genetics
- Epigenesis, Genetic
- Genetic Markers
- Genetic Variation
- Genome-Wide Association Study
- Haplotypes
- Humans
- Methadone/metabolism
- Methadone/therapeutic use
- Opioid-Related Disorders/genetics
- Opioid-Related Disorders/therapy
- Pharmacogenetics
- Protein Precursors/genetics
- Receptor, Melanocortin, Type 2/genetics
- Receptor, Serotonin, 5-HT1B/genetics
- Receptors, Opioid, kappa/genetics
- Receptors, Opioid, mu/genetics
- Tryptophan Hydroxylase/genetics
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Affiliation(s)
- Vadim Yuferov
- The Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, New York
| | - Orna Levran
- The Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, New York
| | - Dmitri Proudnikov
- The Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, New York
| | - David A. Nielsen
- The Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, New York
| | - Mary Jeanne Kreek
- The Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, New York
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28
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Huang HY, Li SH, Yu SC, Chou FF, Tzeng CC, Hu TH, Uen YH, Tian YF, Wang YH, Fang FM, Huang WW, Wei YC, Wu JM, Li CF. Homozygous deletion of MTAP gene as a poor prognosticator in gastrointestinal stromal tumors. Clin Cancer Res 2009; 15:6963-6972. [PMID: 19887491 DOI: 10.1158/1078-0432.ccr-09-1511] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Chromosome 9 is frequently deleted in high-risk gastrointestinal stromal tumors (GISTs), whereas its specific tumor suppressor genes (TSGs) are less understood. We did an integrative study of MTAP gene at 9p21 to analyze its implication in GISTs. EXPERIMENTAL DESIGN To search TSGs on chromosome 9, we used ultrahigh-resolution array comparative genomic hybridization to profile DNA copy number alterations of 22 GISTs, with special attention to MTAP gene. MTAP immunoexpression was assessable for 306 independent GISTs on tissue microarrays, with 146 cases analyzed for MTAP homozygous deletion, 181 for mutations of KIT and PDGFRA receptor tyrosine kinase genes, and 7 for MTAP hypermethylation. RESULTS Array comparative genomic hybridization identified 11 candidate TSGs on 9p and six on 9q. MTAP and/or CDKN2A/CDKN2B at 9p21.3 were deleted in one intermediate-risk (11%) and seven high-risk (70%) GISTs with two cases homozygously codeleted at both loci. MTAP homozygous deletion, present in 25 of 146 cases, was highly associated with larger size and higher mitotic rate, Ki-67 index, and risk level (all P < 0.01) but not with receptor tyrosine kinase genotypes. Whereas MTAP homozygous deletion correlated with MTAP protein loss (P < 0.001), 7 of 30 GISTs without MTAP expression did not show homozygous deletion, including three MTAP-hypermethylated cases. MTAP homozygous deletion was univariately predictive of decreased disease-free survival (P < 0.0001) and remained multivariately independent (P = 0.0369, hazard ratio = 2.166), together with high-risk category (P < 0.0001), Ki-67 index >5% (P = 0.0106), and nongastric location (P = 0.0416). CONCLUSIONS MTAP homozygous deletion, the predominant mechanism to deplete protein expression, is present in 17% of GISTs. It correlates with important prognosticators and independently predicts worse outcomes, highlighting the role in disease progression.
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Affiliation(s)
- Hsuan-Ying Huang
- Departments of Pathology, Surgery, and Radiation Oncology, and Divisions of Oncology and Gastroenterology, Department of Internal Medicine, Chang Gung Memorial Hospital-Kaohsiung Medical Center, Chang Gung University College of Medicine, Kaohsiung, Taiwan
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29
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Sredni ST, Gadd S, Huang CC, Breslow N, Grundy P, Green DM, Dome JS, Shamberger RC, Beckwith JB, Perlman EJ. Subsets of very low risk Wilms tumor show distinctive gene expression, histologic, and clinical features. Clin Cancer Res 2009; 15:6800-9. [PMID: 19903788 DOI: 10.1158/1078-0432.ccr-09-0312] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
PURPOSE Recent studies suggest that children <24 months with stage I favorable histology Wilms tumors <550 g [very low risk Wilms tumors (VLRWT)] have an excellent prognosis when treated with nephrectomy only, without adjuvant chemotherapy. The identification of risk categories within VLRWT may enable refinement of their definition and optimization of their therapy. EXPERIMENTAL DESIGN To define biologically distinct subsets, global gene expression analysis was done on 39 VLRWT that passed all quality-control parameters and the clusters identified were validated in an independent set of 11 VLRWT. Validation of select differentially expressed genes was done with immunohistochemistry on a tissue microarray from 20 of 39 tumors. Loss of heterozygosity (LOH) for 11p15, 1p, and 16q was analyzed in 52 tumors using PCR. RESULTS Two distinctive clusters were identified. One cluster included 9 tumors with epithelial differentiated tubular histology, paucity of nephrogenic rests, lack of LOH for 1p, 16q, and 11p, absence of relapse, and a unique gene expression profile consistent with arrest following mesenchymal-to-epithelial transition. The second cluster included 13 tumors with mixed histology, intralobar nephrogenic rests, and decreased expression of WT1. Three of 6 relapses occurred in this cluster. Of 43 informative tumors, 11p LOH was present in 5 of 5 relapses and 11 of 38 nonrelapses. CONCLUSIONS Two subsets comprising a total of 56% of VLRWT are identified that have pathogenetic and molecular differences and apparent differences in risk for relapse. If these predictors can be prospectively validated, this would enable the refinement of clinical stratification and less arbitrary definition of VLRWT.
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Affiliation(s)
- Simone T Sredni
- Departments of Pathology and Preventive Medicine, Northwestern University Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, Illinois, USA
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30
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Martin-Subero JI, Ammerpohl O, Bibikova M, Wickham-Garcia E, Agirre X, Alvarez S, Brüggemann M, Bug S, Calasanz MJ, Deckert M, Dreyling M, Du MQ, Dürig J, Dyer MJS, Fan JB, Gesk S, Hansmann ML, Harder L, Hartmann S, Klapper W, Küppers R, Montesinos-Rongen M, Nagel I, Pott C, Richter J, Román-Gómez J, Seifert M, Stein H, Suela J, Trümper L, Vater I, Prosper F, Haferlach C, Cigudosa JC, Siebert R. A comprehensive microarray-based DNA methylation study of 367 hematological neoplasms. PLoS One 2009; 4:e6986. [PMID: 19750229 PMCID: PMC2737286 DOI: 10.1371/journal.pone.0006986] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Accepted: 08/12/2009] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Alterations in the DNA methylation pattern are a hallmark of leukemias and lymphomas. However, most epigenetic studies in hematologic neoplasms (HNs) have focused either on the analysis of few candidate genes or many genes and few HN entities, and comprehensive studies are required. METHODOLOGY/PRINCIPAL FINDINGS Here, we report for the first time a microarray-based DNA methylation study of 767 genes in 367 HNs diagnosed with 16 of the most representative B-cell (n = 203), T-cell (n = 30), and myeloid (n = 134) neoplasias, as well as 37 samples from different cell types of the hematopoietic system. Using appropriate controls of B-, T-, or myeloid cellular origin, we identified a total of 220 genes hypermethylated in at least one HN entity. In general, promoter hypermethylation was more frequent in lymphoid malignancies than in myeloid malignancies, being germinal center mature B-cell lymphomas as well as B and T precursor lymphoid neoplasias those entities with highest frequency of gene-associated DNA hypermethylation. We also observed a significant correlation between the number of hypermethylated and hypomethylated genes in several mature B-cell neoplasias, but not in precursor B- and T-cell leukemias. Most of the genes becoming hypermethylated contained promoters with high CpG content, and a significant fraction of them are targets of the polycomb repressor complex. Interestingly, T-cell prolymphocytic leukemias show low levels of DNA hypermethylation and a comparatively large number of hypomethylated genes, many of them showing an increased gene expression. CONCLUSIONS/SIGNIFICANCE We have characterized the DNA methylation profile of a wide range of different HNs entities. As well as identifying genes showing aberrant DNA methylation in certain HN subtypes, we also detected six genes--DBC1, DIO3, FZD9, HS3ST2, MOS, and MYOD1--that were significantly hypermethylated in B-cell, T-cell, and myeloid malignancies. These might therefore play an important role in the development of different HNs.
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Affiliation(s)
- Jose I. Martin-Subero
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
- Cancer Epigenetics and Biology Program, Bellvitge Institute for Biomedical Research-Catalan Institute of Oncology, Barcelona, Spain
| | - Ole Ammerpohl
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | - Marina Bibikova
- Illumina, Inc., San Diego, California, United States of America
| | | | - Xabier Agirre
- Division of Cancer and Area of Cell Therapy and Hematology Service, Universidad de Navarra, Pamplona, Spain
| | - Sara Alvarez
- Molecular Cytogenetics Group, Centro Nacional Investigaciones Oncologicas, Madrid, Spain
| | - Monika Brüggemann
- Second Medical Department, Christian-Albrechts University, Kiel, Germany
| | - Stefanie Bug
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | | | - Martina Deckert
- Department of Neuropathology, University Hospital of Cologne, Cologne, Germany
| | - Martin Dreyling
- Department of Medicine III, University Hospital Grosshadern, Munich, Germany
| | - Ming Q. Du
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Jan Dürig
- Department of Hematology, University of Duisburg-Essen, Essen, Germany
| | | | - Jian-Bing Fan
- Illumina, Inc., San Diego, California, United States of America
| | - Stefan Gesk
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | - Martin-Leo Hansmann
- Institute of Pathology, University Hospital of Frankfurt, Frankfurt, Germany
| | - Lana Harder
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | - Sylvia Hartmann
- Institute of Pathology, University Hospital of Frankfurt, Frankfurt, Germany
| | - Wolfram Klapper
- Institute of Pathology, Christian-Albrechts University, Kiel, Germany
| | - Ralf Küppers
- Institute of Cell Biology, University of Duisburg-Essen, Essen, Germany
| | | | - Inga Nagel
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | - Christiane Pott
- Second Medical Department, Christian-Albrechts University, Kiel, Germany
| | - Julia Richter
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | - José Román-Gómez
- Reina Sofia Hospital, Instituto Maimonides de Investigación Biomédica de Córdoba, Cordoba, Spain
| | - Marc Seifert
- Institute of Cell Biology, University of Duisburg-Essen, Essen, Germany
| | - Harald Stein
- Institute of Pathology, Campus Benjamin Franklin, Berlin, Germany
| | - Javier Suela
- Molecular Cytogenetics Group, Centro Nacional Investigaciones Oncologicas, Madrid, Spain
| | - Lorenz Trümper
- Department of Hematology and Oncology, Georg-August University of Göttingen, Göttingen, Germany
| | - Inga Vater
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | - Felipe Prosper
- Division of Cancer and Area of Cell Therapy and Hematology Service, Universidad de Navarra, Pamplona, Spain
| | | | - Juan Cruz Cigudosa
- Molecular Cytogenetics Group, Centro Nacional Investigaciones Oncologicas, Madrid, Spain
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
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31
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Lawless MW, O'Byrne KJ, Gray SG. Oxidative stress induced lung cancer and COPD: opportunities for epigenetic therapy. J Cell Mol Med 2009; 13:2800-21. [PMID: 19602054 PMCID: PMC4498937 DOI: 10.1111/j.1582-4934.2009.00845.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Reactive oxygen species (ROS) form as a natural by-product of the normal metabolism of oxygen and play important roles within the cell. Under normal circumstances the cell is able to maintain an adequate homeostasis between the formation of ROS and its removal through particular enzymatic pathways or via antioxidants. If however, this balance is disturbed a situation called oxidative stress occurs. Critically, oxidative stress plays important roles in the pathogenesis of many diseases, including cancer. Epigenetics is a process where gene expression is regulated by heritable mechanisms that do not cause any direct changes to the DNA sequence itself, and disruption of epigenetic mechanisms has important implications in disease. Evidence is emerging that histone deacetylases (HDACs) play decisive roles in regulating important cellular oxidative stress pathways including those involved with sensing oxidative stress and those involved with regulating the cellular response to oxidative stress. In particular aberrant regulation of these pathways by HDACs may play critical roles in cancer progression. In this review we discuss the current evidence linking epigenetics and oxidative stress and cancer, using chronic obstructive pulmonary disease and non-small cell lung cancer to illustrate the importance of epigenetics on these pathways within these disease settings.
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Affiliation(s)
- Matthew W Lawless
- Centre for Liver Disease, School of Medicine and Medical Science, Mater Misericordiae University Hospital, University College Dublin, Dublin, Ireland
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Nymark P, Kettunen E, Aavikko M, Ruosaari S, Kuosma E, Vanhala E, Salmenkivi K, Pirinen R, Karjalainen A, Knuutila S, Wikman H, Anttila S. Molecular Alterations at 9q33.1 and Polyploidy in Asbestos-Related Lung Cancer. Clin Cancer Res 2009; 15:468-75. [DOI: 10.1158/1078-0432.ccr-08-1852] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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33
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Suzuki A, Shibata T, Shimada Y, Murakami Y, Horii A, Shiratori K, Hirohashi S, Inazawa J, Imoto I. Identification of SMURF1 as a possible target for 7q21.3-22.1 amplification detected in a pancreatic cancer cell line by in-house array-based comparative genomic hybridization. Cancer Sci 2008; 99:986-94. [PMID: 18380791 PMCID: PMC11158928 DOI: 10.1111/j.1349-7006.2008.00779.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Pancreatic cancer (PC) cell lines provide a useful starting point for the discovery and functional analysis of genes driving the genesis and progression of this lethal cancer. To increase our understanding of the gene copy number changes in pancreatic carcinomas and to identify key amplification and deletion targets, we applied genome-wide array-based comparative genomic hybridization using in-house array (MCG Cancer Array-800) to 24 PC cell lines. Overall, the analyses revealed high genomic complexity, with several copy number changes detected in each line. Homozygous deletions (log(2)ratio < -2) of eight genes (clones) were seen in 14 of the 24 cell lines, whereas high-level amplifications (log(2)ratio > 2) of 10 genes (clones) were detected in seven lines. Among them, we focused on high-level amplification at 7q22.1, because target genes for this alteration remain unknown. Through precise mapping of the altered region by fluorescence in situ hybridization, determination of the expression status of genes located within those regions, and functional analysis using knockdown of the gene expression or the ectopic overexpression approach in PC cell lines, as well as immunohistochemical analyses of candidates in primary tumors of PC, we successfully identified SMURF1 as having the greatest potential as a 7q21.3-22.1 amplification target. SMURF1 may work as a growth-promoting gene in PC through overexpression and might be a good candidate as a therapeutic target. Our results suggest that array-based comparative genomic hybridization analysis combined with further genetic and functional examinations is a useful approach for identifying novel tumor-associated genes involved in the pathogenesis of this lethal disease.
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Affiliation(s)
- Ayako Suzuki
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, 1-5-45 Yushima Bunkyo-ku, Tokyo, Japan
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Abstract
Allelic loss at chromosome 9q31-34 is a frequent event in many lymphoproliferative malignancies. Here, we examined DBC1 at 9q33.1 as a potential target in lymphomagenesis. DBC1 is a putative tumor suppressor that has been shown to be involved in the regulation of cell growth and programmed cell death. The methylation status of the DBC1 promoter CpG island was examined by methylation-specific PCR, bisulfite sequencing, and methylation-specific melting curve analysis. DBC1 was hypermethylated in 5 of 5 B-cell-derived lymphoma cell lines, 41 of 42 diffuse large B-cell lymphomas, 24 of 24 follicular lymphomas, 5 of 5 mantle cell lymphomas, 4 of 4 small lymphocytic lymphomas, 1 of 2 lymphoplasmacytoid lymphomas, and in 12 of 12 acute lymphoblastic leukemias, but was unmethylated in 1 case of splenic marginal zone lymphoma, in 12 of 12 multiple myelomas, in 24 of 24 reactive lymph nodes, and in 12 of 12 samples of blood lymphocytes from random donors. DBC1 hypermethylation was associated with transcriptional silencing in lymphoma cell lines, and reexpression of this gene could be induced by treatment with the demethylating agent, 5-aza-2'-deoxycytidine. Our data suggest that hypermethylation of the DBC1 promoter region is a frequent event during the development of lymphoproliferative malignancies, and that DBC1 hypermethylation may serve as a marker for these cancers.
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Jensen TJ, Novak P, Eblin KE, Gandolfi AJ, Futscher BW. Epigenetic remodeling during arsenical-induced malignant transformation. Carcinogenesis 2008; 29:1500-8. [PMID: 18448484 DOI: 10.1093/carcin/bgn102] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Humans are exposed to arsenicals through many routes with the most common being in drinking water. Exposure to arsenic has been associated with an increase in the incidence of cancer of the skin, lung and bladder. Although the relationship between exposure and carcinogenesis is well documented, the mechanisms by which arsenic participates in tumorigenesis are not fully elucidated. We evaluated the potential epigenetic component of arsenical action by assessing the histone acetylation state of 13 000 human gene promoters in a cell line model of arsenical-mediated malignant transformation. We show changes in histone H3 acetylation occur during arsenical-induced malignant transformation that are linked to the expression state of the associated gene. DNA hypermethylation was detected in hypoacetylated promoters in the select cases analyzed. These epigenetic changes occurred frequently in the same promoters whether the selection was performed with arsenite [As(III)] or with monomethylarsonous acid, suggesting that these promoters were targeted in a non-random fashion, and probably occur in regions important in arsenical-induced malignant transformation. Taken together, these data suggest that arsenicals may participate in tumorigenesis by altering the epigenetic terrain of select genes.
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Affiliation(s)
- Taylor J Jensen
- Department of Pharmacology and Toxicology, College of Pharmacy, Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA
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36
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Nagayama K, Kohno T, Sato M, Arai Y, Minna JD, Yokota J. Homozygous deletion scanning of the lung cancer genome at a 100-kb resolution. Genes Chromosomes Cancer 2007; 46:1000-10. [PMID: 17674361 DOI: 10.1002/gcc.20485] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Whole genome scanning of 43 lung cancer cell lines at a 100-kb resolution led to identification of 51 genomic regions with homozygous deletions (HDs). The regions contained 113 genes, including two known tumor suppressor genes, RBl (RB) and CDKN2A (p16), and eight genes previously reported as being candidate tumor suppressor genes, such as PTPRD and LRP1B. Three miRNA genes, MIRNLET7C (let-7c), MIRN99A (hsa-mir-99a), and MIRN125B2 (hsa-mir-125b-2), were also mapped in a region with HD at 21q11-q21. The present study provides a list of protein- and miRNA-encoding genes whose inactivation is possibly involved in lung carcinogenesis.
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Affiliation(s)
- Kazuhiro Nagayama
- Biology Division, National Cancer Center Research Institute, Tokyo, Japan
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Michels E, De Preter K, Van Roy N, Speleman F. Detection of DNA copy number alterations in cancer by array comparative genomic hybridization. Genet Med 2007; 9:574-84. [PMID: 17873645 DOI: 10.1097/gim.0b013e318145b25b] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Over the past few years, various reliable platforms for high-resolution detection of DNA copy number changes have become widely available. Together with optimized protocols for labeling and hybridization and algorithms for data analysis and representation, this has lead to a rapid increase in the application of this technology in the study of copy number variation in the human genome in normal cells and copy number imbalances in genetic diseases, including cancer. In this review, we briefly discuss specific technical issues relevant for array comparative genomic hybridization analysis in cancer tissues. We specifically focus on recent successes of array comparative genomic hybridization technology in the progress of our understanding of oncogenesis in a variety of cancer types. A third section highlights the potential of sensitive genome-wide detection of patterns of DNA imbalances or molecular portraits for class discovery and therapeutic stratification.
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Affiliation(s)
- Evi Michels
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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Shinoda Y, Kozaki KI, Imoto I, Obara W, Tsuda H, Mizutani Y, Shuin T, Fujioka T, Miki T, Inazawa J. Association of KLK5 overexpression with invasiveness of urinary bladder carcinoma cells. Cancer Sci 2007; 98:1078-86. [PMID: 17459052 PMCID: PMC11158320 DOI: 10.1111/j.1349-7006.2007.00495.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Array-based comparative genomic hybridization (array-CGH) has powerful potential for high-throughput identification of genetic aberrations in cell genomes. We identified high-level amplification of kallikrein (KLK) genes, which are mapped to 19q13.3 and belong to the serine protease family, in the course of a program to screen a panel of urinary bladder carcinoma cell lines for genomic copy number aberrations using our in-house CGH-array. Expression levels of KLK5, -6, -8 and -9 were significantly increased in three cell lines with copy number gains of these KLK genes. Knockdown of these KLK transcripts by specific small interfering RNA significantly inhibited the invasion of a bladder carcinoma cell line through Matrigel in vitro. Reverse transcription-polymerase chain reaction analysis of 42 primary bladder tumor samples showed that increased expression of KLK5 was frequently observed in invasive tumors (pT2-pT4) (14.3%, 6/42) compared with superficial tumors (pTa, pT1) (0%, 0/42; P = 0.0052), and expression levels of KLK5, -6, -8 and -9 mRNA were higher in invasive tumors than in superficial tumors (P < 0.0001, P = 0.0043, P = 0.0790 and P = 0.0037, respectively). These observations indicate that KLK5, -6, -8 and -9 may be the most likely targets of the 19q13.3 amplification, and may play a crucial role in promoting cancer-cell invasion in bladder tumor.
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Affiliation(s)
- Yasuo Shinoda
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
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Kawasaki T, Yokoi S, Tsuda H, Izumi H, Kozaki KI, Aida S, Ozeki Y, Yoshizawa Y, Imoto I, Inazawa J. BCL2L2 is a probable target for novel 14q11.2 amplification detected in a non-small cell lung cancer cell line. Cancer Sci 2007; 98:1070-7. [PMID: 17459056 PMCID: PMC11159300 DOI: 10.1111/j.1349-7006.2007.00491.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Amplification of chromosomal DNA is thought to be one of the mechanisms that activates cancer-related genes in tumors. In a previous genome-wide screening of DNA copy number aberrations in a panel of non-small cell lung cancer (NSCLC) cell lines using an in-house bacterial artificial chromosome-based array, we identified a novel amplification at 14q11.2 in HUT29 cells derived from human lung adenocarcinoma. To identify the most likely target for the 14q11.2 amplification, we determined the extent of the amplicon by fluorescence in situ hybridization and then analyzed NSCLC cell lines for the expression levels of 28 genes present within the 1-Mb amplified region. Significant overexpression in the HUT29 cell line with amplification, relatively frequent overexpression in additional NSCLC cell lines compared with an immortalized normal lung epithelial cell line, and reported information about the function of each candidate gene prompted us to characterize the BCL2-like2 (BCL2L2) gene, a prosurvival member of the BCL2 family, as the most likely target for the 14q11.2 amplicon. Immunohistochemical analysis of 61 primary cases of lung adenocarcinoma demonstrated that BCL2L2 overexpression was significantly associated with tumor stage and differentiation status, and tended to be associated with a poorer prognosis. Downregulation of BCL2L2 expression using small interfering RNA dramatically inhibited the growth of HUT29 cells, but showed no effect on anticancer reagent-induced cell death of the same cell line. These findings demonstrate that overexpressed BCL2L2, through amplification or other mechanisms, promotes the growth of NSCLC, especially the adenocarcinoma subtype, and might be a therapeutic target.
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Affiliation(s)
- Tsutomu Kawasaki
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo, Japan
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Suzuki E, Imoto I, Pimkhaokham A, Nakagawa T, Kamata N, Kozaki KI, Amagasa T, Inazawa J. PRTFDC1, a possible tumor-suppressor gene, is frequently silenced in oral squamous-cell carcinomas by aberrant promoter hypermethylation. Oncogene 2007; 26:7921-32. [PMID: 17599052 DOI: 10.1038/sj.onc.1210589] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Array-based comparative genomic hybridization (array-CGH) has good potential for the high-throughput identification of genetic aberrations in cell genomes. In the course of a program to screen a panel of oral squamous-cell carcinoma (OSCC), cell lines for genomic copy-number aberrations by array-CGH using our in-house arrays, we identified a 3-Mb homozygous deletion at 10p12 in 1 of 18 cell lines (5.6%). Among seven genes located within this region, expression of PRTFDC1 mRNA was not detected in 50% (9/18) or decreased in 5.6% (1/18) of OSCC cell lines, but detected in normal oral epithelia and restored in gene-silenced OSCC cells without its homozygous loss after treatment with 5-aza-2'-deoxycytidine. Among 17 cell lines without a homozygous deletion, the hypermethylation of the PRTFDC1 CpG island, which showed promoter activity, was observed in all nine cell lines with no or reduced PRTFDC1 expression (52.9%). Methylation of this CpG island was also observed in primary OSCC tissues (8/47, 17.0%). In addition, restoration of PRTFDC1 in OSCC cells lacking its expression inhibited cell growth in colony-formation assays, whereas knockdown of PRTFDC1 expression in OSCC cells expressing the gene promoted cell growth. These results suggest that epigenetic silencing of PRTFDC1 by hypermethylation of the CpG island leads to a loss of PRTFDC1 function, which might be involved in squamous cell oral carcinogenesis.
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Affiliation(s)
- E Suzuki
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
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Sano A, Kage H, Sugimoto K, Kitagawa H, Aki N, Goto A, Fukayama M, Nakajima J, Takamoto S, Nagase T, Yatomi Y, Ohishi N, Takai D. A second-generation profiling system for quantitative methylation analysis of multiple gene promoters: application to lung cancer. Oncogene 2007; 26:6518-25. [PMID: 17452971 DOI: 10.1038/sj.onc.1210483] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cancer-specific gene promoter methylation has been described in many types of cancers, and various semi-quantified results have shown their usefulness. Here, we show a more sensitive and specific second-generation system for profiling the DNA methylation status. This method is based on bisulfite reaction of DNA and real-time PCR using two TaqMan MGB probes labeled with different fluorescence, followed by clustering analysis. Primers were designed with CpG-less sequences, and TaqMan MGB probes were designed to contain three or four CpG sites and to be shorter than conventional TaqMan probes. We have added new criteria for primer and probe design for further specificity. We confirmed the reliability of this system and applied it to analysis of lung cancers. Using 10 promoters, 90 primary lung cancers were clustered into six groups consisting of cases having similar smoking status and pathological findings. EGFR mutation and p16 promoter DNA methylation were exclusive, as previously reported; however, DNA methylation in other genes was unrelated to EGFR mutation. This system was also useful to distinguish double primary lung cancers from a single cancer with intrapulmonary metastasis. As above, our system has widespread availability in clinical use and biological research.
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Affiliation(s)
- A Sano
- Department of General Thoracic Surgery, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
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Abstract
Epigenetics is the study of heritable changes in gene expression that occur without changes in DNA sequence. It has a role in determining when and where a gene is expressed during development. Perhaps the most well known epigenetic mechanism is DNA methylation whereby cytosines at position 5 in CpG dinucleotides are methylated. Histone modification is another form of epigenetic control, which is quite complex and diverse. Histones and DNA make up the nucleosome which is the structural unit of chromatin which are involved in packaging DNA. Apart from the crucial role epigenetics plays in embryonic development, transcription, chromatin structure, X chromosome inactivation and genomic imprinting, its role in an increasing number of human diseases is more and more recognized. These diseases include cancer, and lung cancer in particular has been increasingly studied for the potential biological role of epigenetic changes with the promise of better and novel diagnostic and therapeutic tools.
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Ng G, Huang J, Roberts I, Coleman N. Defining ploidy-specific thresholds in array comparative genomic hybridization to improve the sensitivity of detection of single copy alterations in cell lines. J Mol Diagn 2006; 8:449-58. [PMID: 16931585 PMCID: PMC1867620 DOI: 10.2353/jmoldx.2006.060033] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Array comparative genomic hybridization (CGH) is being widely used to screen for recurrent genomic copy number alterations in neoplasms, with imbalances typically detected through the application of gain and loss thresholds. Review of array CGH publications for the year 2005 showed that a wide range of thresholds are used. However, the effect of sample ploidy on the sensitivity of these thresholds for single copy alterations (SCAs) has not been evaluated. Here, we describe a method to evaluate the detection accuracy of thresholds for detecting SCAs in cell line array CGH data. By applying a hidden Markov model-based method, we segmented array CGH data from well-karyotyped cell lines and generated ploidy-specific sensitivity-specificity plots, from which we identified optimum thresholds relevant to sample ploidy. We demonstrate that commonly used nonploidy-specific thresholds are suboptimal in their ability to call SCAs, particularly when applied to hypertriploid or tetraploid cell lines. We conclude that the use of ploidy-specific thresholds improves the sensitivity of thres-hold-based array CGH for detecting SCAs in cell lines. Because polyploidy is a common feature of cancer cells, the application of ploidy-specific thresholds to cell lines (and potentially to clinical samples) may improve the detection sensitivity of SCAs of biological significance.
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Affiliation(s)
- Grace Ng
- Medical Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, Box 197, Hills Rd., Cambridge CB2 2XZ, UK
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Yu W, Imoto I, Inoue J, Onda M, Emi M, Inazawa J. A novel amplification target, DUSP26, promotes anaplastic thyroid cancer cell growth by inhibiting p38 MAPK activity. Oncogene 2006; 26:1178-87. [PMID: 16924234 DOI: 10.1038/sj.onc.1209899] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Anaplastic thyroid cancer (ATC) is one of the most lethal of all human tumors, but cytogenetic information concerning ATC is extremely limited. Using our in-house array-based comparative genomic hybridization and 14 ATC cell lines with further fluorescence in situ hybridization analysis, we demonstrated amplification of the DUSP26 gene, known by another report as MAP kinase phosphatase-8. DUSP26 was overexpressed in ATC cell lines and primary ATC tumor samples. When overexpressed, either exogenously or endogenously, DUSP26 promoted growth of the ATC cells. DUSP26 encodes a protein containing a dual-specificity phosphatase domain that can dephosphorylate itself. DUSP26 effectively dephosphorylates p38 and has a little effect on extracellular signal-regulated kinase in ATC cells. DUSP26 protein formed a physical complex with p38, and promoted survival of ATC cells by inhibiting p38-mediated apoptosis. Our findings suggest that DUSP26 may act as an oncogene in ATC, and might be a useful diagnostic marker and therapeutic target of this disease.
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Affiliation(s)
- W Yu
- Department of Molecular Cytogenetics, Medical Research Institute and Graduate School of Biomedical Science, Tokyo, Japan
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Roman-Gomez J, Jimenez-Velasco A, Agirre X, Castillejo JA, Navarro G, Calasanz MJ, Garate L, San Jose-Eneriz E, Cordeu L, Prosper F, Heiniger A, Torres A. CpG island methylator phenotype redefines the prognostic effect of t(12;21) in childhood acute lymphoblastic leukemia. Clin Cancer Res 2006; 12:4845-50. [PMID: 16914570 DOI: 10.1158/1078-0432.ccr-05-2592] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To examine cancer genes undergoing epigenetic inactivation in a set of ETV6/RUNX1-positive acute lymphoblastic leukemias in order to define the CpG island methylator phenotype (CIMP) in the disease and evaluate its relationship with clinical features and outcome. EXPERIMENTAL DESIGN Methylation-specific PCR was used to analyze the methylation status of 38 genes involved in cell immortalization and transformation in 54 ETV6/RUNX1-positive samples in comparison with 190 ETV6/RUNX1-negative samples. RESULTS ETV6/RUNX1-positive samples had at least one gene methylated in 89% of the cases. According to the number of methylated genes observed in each individual sample, 20 patients (37%) were included in the CIMP- group (0-2 methylated genes) and 34 (67%) in the CIMP+ group (>2 methylated genes). Remission rate did not differ significantly among either group of patients. Estimated disease-free survival and overall survival at 9 years were 92% and 100% for the CIMP- group and 33% and 73% for the CIMP+ group (P = 0.002 and P = 0.04, respectively). Multivariate analysis showed that methylation profile was an independent prognostic factor in predicting disease-free survival (P = 0.01) and overall survival (P = 0.05). A group of four genes (DKK3, sFRP2, PTEN, and P73) showed specificity for ETV6/RUNX1-positive subset of samples. CONCLUSION Our results suggest that methylation profile may be a potential new biomarker of risk prediction in ETV6/RUNX1-positive acute lymphoblastic leukemias.
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San José-Enériz E, Agirre X, Román-Gómez J, Cordeu L, Garate L, Jiménez-Velasco A, Vázquez I, Calasanz MJ, Heiniger A, Torres A, Prósper F. Downregulation of DBC1 expression in acute lymphoblastic leukaemia is mediated by aberrant methylation of its promoter. Br J Haematol 2006; 134:137-44. [PMID: 16846474 DOI: 10.1111/j.1365-2141.2006.06131.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DBC1 gene is a potential tumour suppressor gene that is commonly hypermethylated in epithelial cancers. We studied the role of promoter hypermethylation in the regulation of DBC1 in acute lymphoblastic leukaemia (ALL) cell lines and 170 ALL patients at diagnosis. Abnormal methylation of DBC1 was observed in all ALL cell lines and in 17% of ALL patients. Moreover, DBC1 methylation was associated with decreased DBC1 expression, while treatment of ALL cells with 5-Aza-2'-deoxycytidine resulted in demethylation of the promoter and upregulation of DBC1 expression. Fluorescence in situ hybridisation identified the deletion of one allele of DBC1 in some ALL cell lines, which indicated that the lack of DBC1 expression was due to deletion of one allele and methylation of the other. In conclusion, these results demonstrate, for the first time, that the expression of DBC1 is downregulated in a percentage of patients with ALL due to the hypermethylation of its promoter and/or gene deletion.
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Affiliation(s)
- Edurne San José-Enériz
- Foundation for Applied Medical Research, Division of Cancer and Area of Cell Therapy and Haematology Service, Clínica Universitaria, Universidad de Navarra, Pamplona, Spain
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Imoto I, Izumi H, Yokoi S, Hosoda H, Shibata T, Hosoda F, Ohki M, Hirohashi S, Inazawa J. Frequent silencing of the candidate tumor suppressor PCDH20 by epigenetic mechanism in non-small-cell lung cancers. Cancer Res 2006; 66:4617-26. [PMID: 16651412 DOI: 10.1158/0008-5472.can-05-4437] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Protocadherins are a major subfamily of the cadherin superfamily, but little is known about their functions and intracellular signal transduction. We identified a homozygous loss of protocadherin 20 (PCDH20, 13q21.2) in the course of a program to screen a panel of non-small-cell lung cancer (NSCLC) cell lines (1 of 20 lines) for genomic copy number aberrations using an in-house array-based comparative genomic hybridization. PCDH20 mRNA was expressed in normal lung tissue but was not expressed in the majority of NSCLC cell lines without a homozygous deletion of this gene (10 of 19 lines, 52.6%). Expression of PCDH20 mRNA was restored in gene-silenced NSCLC cells after treatment with 5-aza 2'-deoxycytidine. The DNA methylation status of the PCDH20 CpG-rich region correlated inversely with the expression of the gene and a putative target region for methylation showed clear promoter activity in vitro. Methylation of this PCDH20 promoter was frequently observed in primary NSCLC tissues (32 of 59 tumors, 54.2%). Among our primary NSCLC cases, the methylated PCDH20 seemed to be associated with a shorter overall survival (P = 0.0140 and 0.0211 in all and stage I tumors, respectively; log-rank test), and a multivariate analysis showed that the PCDH20 methylation status was an independent prognosticator. Moreover, restoration of PCDH20 expression in NSCLC cells reduced cell numbers in colony formation and anchorage-independent assays. These results suggest that epigenetic silencing by hypermethylation of the CpG-rich promoter region of PCDH20 leads to loss of PCDH20 function, which may be a factor in the carcinogenesis of NSCLC.
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Affiliation(s)
- Issei Imoto
- Department of Molecular Cytogenetics, Medical Research Institute and Graduate School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
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48
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Saigusa K, Hashimoto N, Tsuda H, Yokoi S, Maruno M, Yoshimine T, Aoyagi M, Ohno K, Imoto I, Inazawa J. Overexpressed Skp2 within 5p amplification detected by array-based comparative genomic hybridization is associated with poor prognosis of glioblastomas. Cancer Sci 2005; 96:676-83. [PMID: 16232199 PMCID: PMC11159392 DOI: 10.1111/j.1349-7006.2005.00099.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
To better understand the pathogenesis of glioblastoma multiforme (GBM) and to increase the accuracy of predicting outcomes for patients with this disease, we performed genome-wide screening for DNA copy-number aberrations in 22 glioma-derived cell lines using a custom-made comparative genomic hybridization-array. Copy-number gains were frequently detected at 3q, 7p, 7q, 20q, Xp and Xq, and losses at 4q, 9p, 10p, 10q, 11q, 13q, 14q, 18q, and 22q. Among several non-random chromosomal aberrations, the gain/amplification of DNA at 5p, which has never been reported before in GBM, was detected with a relatively high ratio (log2 ratio = 0.41-1.19) in four cell lines. Amplification and subsequent overexpression of SKP2, a possible target of amplification within 5p, were detected in four of the 22 cell lines. We also investigated the expression of the gene product in primary GBM by immunohistochemistry, which revealed increased levels of Skp2 in 11 of the 35 tumors examined (31.4%). Heightened expression of Skp2 was associated with shorter overall survival (P = 0.001, logrank test), especially in patients younger than 65 years. These results suggest that overexpression of Skp2 through gene amplification may contribute to the pathogenesis of GBM, and that overabundance of the protein might be a useful prognostic tool in patients with this disease.
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Affiliation(s)
- Kuniyasu Saigusa
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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