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Pacholewska A, Grimm C, Herling CD, Lienhard M, Königs A, Timmermann B, Altmüller J, Mücke O, Reinhardt HC, Plass C, Herwig R, Hallek M, Schweiger MR. Altered DNA Methylation Profiles in SF3B1 Mutated CLL Patients. Int J Mol Sci 2021; 22:ijms22179337. [PMID: 34502260 PMCID: PMC8431484 DOI: 10.3390/ijms22179337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022] Open
Abstract
Mutations in splicing factor genes have a severe impact on the survival of cancer patients. Splicing factor 3b subunit 1 (SF3B1) is one of the most frequently mutated genes in chronic lymphocytic leukemia (CLL); patients carrying these mutations have a poor prognosis. Since the splicing machinery and the epigenome are closely interconnected, we investigated whether these alterations may affect the epigenomes of CLL patients. While an overall hypomethylation during CLL carcinogenesis has been observed, the interplay between the epigenetic stage of the originating B cells and SF3B1 mutations, and the subsequent effect of the mutations on methylation alterations in CLL, have not been investigated. We profiled the genome-wide DNA methylation patterns of 27 CLL patients with and without SF3B1 mutations and identified local decreases in methylation levels in SF3B1mut CLL patients at 67 genomic regions, mostly in proximity to telomeric regions. These differentially methylated regions (DMRs) were enriched in gene bodies of cancer-related signaling genes, e.g., NOTCH1, HTRA3, and BCL9L. In our study, SF3B1 mutations exclusively emerged in two out of three epigenetic stages of the originating B cells. However, not all the DMRs could be associated with the methylation programming of B cells during development, suggesting that mutations in SF3B1 cause additional epigenetic aberrations during carcinogenesis.
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Affiliation(s)
- Alicja Pacholewska
- Institute for Translational Epigenetics, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (A.P.); (C.G.); (A.K.)
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Christina Grimm
- Institute for Translational Epigenetics, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (A.P.); (C.G.); (A.K.)
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Carmen D. Herling
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German CLL Study Group, Department I of Internal Medicine, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (C.D.H.); (H.C.R.); (M.H.)
| | - Matthias Lienhard
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; (M.L.); (R.H.)
| | - Anja Königs
- Institute for Translational Epigenetics, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (A.P.); (C.G.); (A.K.)
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany;
| | - Oliver Mücke
- German Cancer Research Center, Cancer Epigenomics, 69120 Heidelberg, Germany; (O.M.); (C.P.)
| | - Hans Christian Reinhardt
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German CLL Study Group, Department I of Internal Medicine, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (C.D.H.); (H.C.R.); (M.H.)
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- West German Cancer Center Essen, Department of Hematology and Stem Cell Transplantation, University Hospital Essen, 45147 Essen, Germany
| | - Christoph Plass
- German Cancer Research Center, Cancer Epigenomics, 69120 Heidelberg, Germany; (O.M.); (C.P.)
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; (M.L.); (R.H.)
| | - Michael Hallek
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German CLL Study Group, Department I of Internal Medicine, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (C.D.H.); (H.C.R.); (M.H.)
| | - Michal R. Schweiger
- Institute for Translational Epigenetics, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (A.P.); (C.G.); (A.K.)
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Correspondence:
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Mandhair HK, Novak U, Radpour R. Epigenetic regulation of autophagy: A key modification in cancer cells and cancer stem cells. World J Stem Cells 2021; 13:542-567. [PMID: 34249227 PMCID: PMC8246247 DOI: 10.4252/wjsc.v13.i6.542] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/02/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
Aberrant epigenetic alterations play a decisive role in cancer initiation and propagation via the regulation of key tumor suppressor genes and oncogenes or by modulation of essential signaling pathways. Autophagy is a highly regulated mechanism required for the recycling and degradation of surplus and damaged cytoplasmic constituents in a lysosome dependent manner. In cancer, autophagy has a divergent role. For instance, autophagy elicits tumor promoting functions by facilitating metabolic adaption and plasticity in cancer stem cells (CSCs) and cancer cells. Moreover, autophagy exerts pro-survival mechanisms to these cancerous cells by influencing survival, dormancy, immunosurveillance, invasion, metastasis, and resistance to anti-cancer therapies. In addition, recent studies have demonstrated that various tumor suppressor genes and oncogenes involved in autophagy, are tightly regulated via different epigenetic modifications, such as DNA methylation, histone modifications and non-coding RNAs. The impact of epigenetic regulation of autophagy in cancer cells and CSCs is not well-understood. Therefore, uncovering the complex mechanism of epigenetic regulation of autophagy provides an opportunity to improve and discover novel cancer therapeutics. Subsequently, this would aid in improving clinical outcome for cancer patients. In this review, we provide a comprehensive overview of the existing knowledge available on epigenetic regulation of autophagy and its importance in the maintenance and homeostasis of CSCs and cancer cells.
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Affiliation(s)
- Harpreet K Mandhair
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3008, Switzerland
| | - Urban Novak
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3008, Switzerland
| | - Ramin Radpour
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3008, Switzerland
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Sumei S, Xiangyun K, Fenrong C, Xueguang S, Sijun H, Bin B, Xiaolei S, Yongjiu T, Kaichun W, Qingchuan Z, Yongzhan N, Bin X. Hypermethylation of DHRS3 as a Novel Tumor Suppressor Involved in Tumor Growth and Prognosis in Gastric Cancer. Front Cell Dev Biol 2021; 9:624871. [PMID: 33553182 PMCID: PMC7859350 DOI: 10.3389/fcell.2021.624871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022] Open
Abstract
Background/Aims The role of DHRS3 in human cancer remains unclear. Our study explored the role of DHRS3 in gastric cancer (GC) and its clinicopathological significance and associated mechanisms. Materials Bisulfite-assisted genomic sequencing PCR and a Mass-Array system were used to evaluate and quantify the methylation levels of the promoter. The expression levels and biological function of DHRS3 was examined by both in vitro and in vivo assays. A two-way hierarchical cluster analysis was used to classify the methylation profiles, and the correlation between the methylation status of the DHRS3 promoter and the clinicopathological characteristics of GC were then assessed. Results The DHRS3 promoter was hypermethylated in GC samples, while the mRNA and protein levels of DHRS3 were significantly downregulated. Ectopic expression of DHRS3 in GC cells inhibited cell proliferation and migration in vitro, decreased tumor growth in vivo. DHRS3 methylation was correlated with histological type and poor differentiation of tumors. GC patients with high degrees of CpG 9.10 methylation had shorter survival times than those with lower methylation. Conclusion DHRS3 was hypermethylated and downregulated in GC patients. Reduced expression of DHRS3 is implicated in gastric carcinogenesis, which suggests DHRS3 is a tumor suppressor.
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Affiliation(s)
- Sha Sumei
- The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Kong Xiangyun
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China.,Xi'an No.1 Hospital, Xi'an, China
| | - Chen Fenrong
- The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Sun Xueguang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Hu Sijun
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Bai Bin
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Shi Xiaolei
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China.,Dongfang Hospital of Xiamen University, Fuzhou, China
| | - Tu Yongjiu
- The General Surgery Department of Chenggong Hospital of Xiamen University (Central Hospital of the 73th Chinese People's Liberation Army), Xiamen, China
| | - Wu Kaichun
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Zhao Qingchuan
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Nie Yongzhan
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China
| | - Xu Bin
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases of the Air Force Medical University, Xi'an, China.,The General Surgery Department of Chenggong Hospital of Xiamen University (Central Hospital of the 73th Chinese People's Liberation Army), Xiamen, China
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Radpour R, Forouharkhou F. Single-cell analysis of tumors: Creating new value for molecular biomarker discovery of cancer stem cells and tumor-infiltrating immune cells. World J Stem Cells 2018; 10:160-171. [PMID: 30631391 PMCID: PMC6325074 DOI: 10.4252/wjsc.v10.i11.160] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/18/2018] [Accepted: 10/23/2018] [Indexed: 02/06/2023] Open
Abstract
Biomarker-driven individualized treatment in oncology has made tremendous progress through technological developments, new therapeutic modalities and a deeper understanding of the molecular biology for tumors, cancer stem cells and tumor-infiltrating immune cells. Recent technical developments have led to the establishment of a variety of cancer-related diagnostic, prognostic and predictive biomarkers. In this regard, different modern OMICs approaches were assessed in order to categorize and classify prognostically different forms of neoplasia. Despite those technical advancements, the extent of molecular heterogeneity at the individual cell level in human tumors remains largely uncharacterized. Each tumor consists of a mixture of heterogeneous cell types. Therefore, it is important to quantify the dynamic cellular variations in order to predict clinical parameters, such as a response to treatment and or potential for disease recurrence. Recently, single-cell based methods have been developed to characterize the heterogeneity in seemingly homogenous cancer cell populations prior to and during treatment. In this review, we highlight the recent advances for single-cell analysis and discuss the challenges and prospects for molecular characterization of cancer cells, cancer stem cells and tumor-infiltrating immune cells.
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Affiliation(s)
- Ramin Radpour
- Tumor Immunology, Department for BioMedical Research (DBMR), University of Bern, Bern 3008, Switzerland
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3008, Switzerland
| | - Farzad Forouharkhou
- Department for Bioinformatics, Persian Bioinformatics System, Tehran 14166, Iran
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5
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Liu J, Ding Z, Li G, Tang L, Xu Y, Luo H, Yi J, Lu Y, Mao R, Nan Q, Ren L, Zhang T, Wang K. Identification and validation of colorectal neoplasia-specific methylation biomarkers based on CTCF-binding sites. Oncotarget 2017; 8:114183-114194. [PMID: 29371978 PMCID: PMC5768395 DOI: 10.18632/oncotarget.23172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/22/2017] [Indexed: 12/31/2022] Open
Abstract
To date, the sensitivity of currently available biomarkers based on the methylation of gene promoters is suboptimal for detecting adenomas and early-stage colorectal cancer (CRC). We aimed to develop biomarkers with methylated DNA binding sites of the multifunctional transcriptional factor CTCF for early detection of CRC. Using combined analyses of genome-wide occupation and the methylation profile of CTCF-binding sites, we identified candidate CTCF-binding sites. Then, we applied methylation-sensitive high-resolution melting (MS-HRM) and mass spectrometry analysis to screen and validate these candidate sites in diverse sample sets. We identified a set of colorectal neoplasia-specific biomarkers with robust performance. The top five biomarkers were selected and recommended for early detection of colorectal neoplasia. All of the five novel biomarkers exhibited a more robust discriminatory performance than that by BMP3 and NDRG4, two currently acknowledged robust methylation biomarkers. When the five new biomarkers were considered as a marker panel and tumor-positive was defined as having two or more (of the five) positive biomarkers, the marker panel could achieve a sensitivity of 91.67% for adenomas, 97.44% for Stage I CRC, 94.06% for Stage II CRC, 93.62% for Stage III CRC, and 93.54% for total colorectal tumors with a specificity of 94.05%. To our knowledge, this is the first study for colorectal neoplasia-specific methylation biomarkers based on CTCF-binding sites. Using a similar strategy, CTCF-binding sites could be potentially developed into biomarkers for other tumors. In summary, this study opens a new area in developing biomarkers for tumor prevention and treatment.
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Affiliation(s)
- Jiang Liu
- Department of Reproduction and Genetics, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, China
| | - Zhaoli Ding
- Public Technical Service Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650032, Yunnan, China.,Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Chinese Academy of Sciences, Kunming 650032, Yunnan, China
| | - Guimei Li
- Public Technical Service Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650032, Yunnan, China.,Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Chinese Academy of Sciences, Kunming 650032, Yunnan, China
| | - Li Tang
- Department of Reproduction and Genetics, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, China
| | - Yu Xu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming 650032, Yunnan, China
| | - Huayou Luo
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming 650032, Yunnan, China
| | - Jinhua Yi
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming 650032, Yunnan, China
| | - Youwang Lu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming 650032, Yunnan, China
| | - Rui Mao
- School of Stomatology, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Qiong Nan
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming 650032, Yunnan, China
| | - Li Ren
- The First People's Hospital of Yunnan Province, Kunming 650031, Yunnan, China
| | - Tong Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming 650032, Yunnan, China
| | - Kunhua Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming 650032, Yunnan, China
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Radpour R. Tracing and targeting cancer stem cells: New venture for personalized molecular cancer therapy. World J Stem Cells 2017; 9:169-178. [PMID: 29104735 PMCID: PMC5661129 DOI: 10.4252/wjsc.v9.i10.169] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/14/2017] [Accepted: 09/03/2017] [Indexed: 02/06/2023] Open
Abstract
Tumors consist of a mixture of heterogeneous cell types. Cancer stem cells (CSCs) are a minor sub-population within the bulk cancer fraction which has been found to reconstitute and propagate the disease and to be frequently resistant to chemotherapy, irradiation, cytotoxic drugs and probably also against immune attack. CSCs are considered as the seeds of tumor recurrence, driving force of tumorigenesis and metastases. This underlines the urgent need for innovative methods to identify and target CSCs. However, the role and existence of CSCs in therapy resistance and cancer recurrence remains a topic of intense debate. The underlying biological properties of the tumor stem cells are extremely dependent on numerous signals, and the targeted inhibition of these stem cell signaling pathways is one of the promising approaches of the new antitumor therapy approaches. This perspective review article summarizes the novel methods of tracing CSCs and discusses the hallmarks of CSC identification influenced by the microenvironment or by having imperfect detection markers. In addition, explains the known molecular mechanisms of therapy resistance in CSCs as reliable and clinically predictive markers that could enable the use of new targeted antitumor therapy in the sense of personalized medicine.
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Affiliation(s)
- Ramin Radpour
- Tumor Immunology and Cancer Stem Cells, Inselspital, Bern University Hospital, Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland.
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7
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Whole genome DNA methylation profiling of oral cancer in ethnic population of Meghalaya, North East India reveals novel genes. Genomics 2017; 110:112-123. [PMID: 28890207 DOI: 10.1016/j.ygeno.2017.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 12/22/2022]
Abstract
Oral Squamous Cell Carcinoma (OSCC) is a serious and one of the most common and highly aggressive malignancies. Epigenetic factors such as DNA methylation have been known to be implicated in a number of cancer etiologies. The main objective of this study was to investigate physiognomies of Promoter DNA methylation patterns associated with oral cancer epigenome with special reference to the ethnic population of Meghalaya, North East India. The present study identifies 27,205 CpG sites and 3811 regions that are differentially methylated in oral cancer when compared to matched normal. 45 genes were found to be differentially methylated within the promoter region, of which 38 were hypermethylated and 7 hypomethylated. 14 of the hypermethylated genes were found to be similar to that of the TCGA-HNSCC study some of which are TSGs and few novel genes which may serve as candidate methylation biomarkers for OSCC in this poorly characterized ethnic group.
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Llorca-Cardeñosa MJ, Fleitas T, Ibarrola-Villava M, Peña-Chilet M, Mongort C, Martinez-Ciarpaglini C, Navarro L, Gambardella V, Castillo J, Roselló S, Navarro S, Ribas G, Cervantes A. Epigenetic changes in localized gastric cancer: the role of RUNX3 in tumor progression and the immune microenvironment. Oncotarget 2016; 7:63424-63436. [PMID: 27566570 PMCID: PMC5325374 DOI: 10.18632/oncotarget.11520] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/15/2016] [Indexed: 02/07/2023] Open
Abstract
Gastric cancer (GC) pathogenesis involves genetic, epigenetic and environmental factors. Epigenetic alterations, such as DNA methylation are considered pivotal in the inactivation of tumor-related genes. We assessed a methylation panel of 5 genes to study their association to GC progression and microsatellite instability (MSI), and studied the role of RUNX3 in GC pathogenesis and the tumor immune microenvironment.The methylation status of 47 promoter-CpG islands was studied through MALDI-TOF mass spectrometry analysis in 35 Microsatellite stable (MSS) GC, 26 MSI, and 18 cancer-free samples (CFS), and 6 MSS GC and 4 MSI GC cell lines. We also studied RUNX3 expression by immunohistochemistry (IHC) in 40 samples, and validated differences in methylation levels between tumor, normal, and immune tissue in 14 additional samples.Unsupervised hierarchical clustering of methylation levels revealed no distinct subgroups between MSI and MSS samples or cell lines. CFSs clustered together showing higher levels of RUNX3 methylation compared to GC samples. RUNX3 showed protein silencing in cancer and normal mucosa, compared to inflammatory peritumoural infiltrate in almost all cases, showing a non-lymphocytic predominant pattern and being correlated with epigenetic silencing.Our results show aberrant promoter's methylation in APC, CDH1, CDKN2A, MLH1 and RUNX3 associated with GC, as well as a non-lymphocytic predominant infiltrate with high expression of RUNX3. Deep study of RUNX3 inflammation signaling could help in understanding inflammation and immune activation in the tumor microenvironment.
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Affiliation(s)
| | - Tania Fleitas
- Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Maider Ibarrola-Villava
- Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - María Peña-Chilet
- Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Cristina Mongort
- Department of Pathology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | | | - Lara Navarro
- Department of Pathology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Valentina Gambardella
- Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Josefa Castillo
- Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Susana Roselló
- Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Samuel Navarro
- Department of Pathology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Gloria Ribas
- Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | - Andrés Cervantes
- Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
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9
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Aghagolzadeh P, Radpour R. New trends in molecular and cellular biomarker discovery for colorectal cancer. World J Gastroenterol 2016; 22:5678-5693. [PMID: 27433083 PMCID: PMC4932205 DOI: 10.3748/wjg.v22.i25.5678] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/16/2016] [Accepted: 06/15/2016] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the third leading cause of cancer death worldwide, which is consequence of multistep tumorigenesis of several genetic and epigenetic events. Since CRC is mostly asymptomatic until it progresses to advanced stages, the early detection using effective screening approaches, selection of appropriate therapeutic strategies and efficient follow-up programs are essential to reduce CRC mortalities. Biomarker discovery for CRC based on the personalized genotype and clinical information could facilitate the classification of patients with certain types and stages of cancer to tailor preventive and therapeutic approaches. These cancer-related biomarkers should be highly sensitive and specific in a wide range of specimen(s) (including tumor tissues, patients’ fluids or stool). Reliable biomarkers which enable the early detection of CRC, can improve early diagnosis, prognosis, treatment response prediction, and recurrence risk. Advances in our understanding of the natural history of CRC have led to the development of different CRC associated molecular and cellular biomarkers. This review highlights the new trends and approaches in CRC biomarker discovery, which could be potentially used for early diagnosis, development of new therapeutic approaches and follow-up of patients.
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10
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Riether C, Schürch CM, Flury C, Hinterbrandner M, Drück L, Huguenin AL, Baerlocher GM, Radpour R, Ochsenbein AF. Tyrosine kinase inhibitor-induced CD70 expression mediates drug resistance in leukemia stem cells by activating Wnt signaling. Sci Transl Med 2016. [PMID: 26223302 DOI: 10.1126/scitranslmed.aab1740] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In chronic myelogenous leukemia (CML), oncogenic BCR-ABL1 activates the Wnt pathway, which is fundamental for leukemia stem cell (LSC) maintenance. Tyrosine kinase inhibitor (TKI) treatment reduces Wnt signaling in LSCs and often results in molecular remission of CML; however, LSCs persist long term despite BCR-ABL1 inhibition, ultimately causing disease relapse. We demonstrate that TKIs induce the expression of the tumor necrosis factor (TNF) family ligand CD70 in LSCs by down-regulating microRNA-29, resulting in reduced CD70 promoter DNA methylation and up-regulation of the transcription factor specificity protein 1. The resulting increase in CD70 triggered CD27 signaling and compensatory Wnt pathway activation. Combining TKIs with CD70 blockade effectively eliminated human CD34(+) CML stem/progenitor cells in xenografts and LSCs in a murine CML model. Therefore, targeting TKI-induced expression of CD70 and compensatory Wnt signaling resulting from the CD70/CD27 interaction is a promising approach to overcoming treatment resistance in CML LSCs.
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Affiliation(s)
- Carsten Riether
- Tumor Immunology, Department of Clinical Research, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Christian M Schürch
- Tumor Immunology, Department of Clinical Research, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland. Institute of Pathology, University of Bern, Murtenstrasse 31, 3010 Bern, Switzerland
| | - Christoph Flury
- Tumor Immunology, Department of Clinical Research, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Magdalena Hinterbrandner
- Tumor Immunology, Department of Clinical Research, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Linda Drück
- Tumor Immunology, Department of Clinical Research, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Anne-Laure Huguenin
- Tumor Immunology, Department of Clinical Research, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Gabriela M Baerlocher
- Experimental Hematology, Department of Clinical Research, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland. Department of Hematology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
| | - Ramin Radpour
- Tumor Immunology, Department of Clinical Research, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Adrian F Ochsenbein
- Tumor Immunology, Department of Clinical Research, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland. Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland.
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11
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Hu JM, Li L, Chen YZ, Liu C, Cui X, Yin L, Yang L, Zou H, Pang L, Zhao J, Qi Y, Cao Y, Jiang J, Liang W, Li F. HLA-DRB1 and HLA-DQB1 methylation changes promote the occurrence and progression of Kazakh ESCC. Epigenetics 2015; 9:1366-73. [PMID: 25437052 DOI: 10.4161/15592294.2014.969625] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Human leukocyte antigen II (HLA-II) plays an important role in host immune responses to cancer cells. Changes in gene methylation may result in aberrant expression of HLA-II, serving a key role in the pathogenesis of Kazakh esophageal squamous cell carcinoma (ESCC). We analyzed the expression level of HLA-II (HLA-DP, -DQ, and -DR) by immunohistochemistry, as well as the methylation status of HLA-DRB1 and HLA-DQB1 by MassARRAY spectrometry in Xinjiang Kazakh ESCC. Expression of HLA-II in ESCC was significantly higher than that in cancer adjacent normal (ACN) samples (P < 0.05). Decreased HLA-II expression was closely associated with later clinical stages of ESCC (P < 0.05). Hypomethylation of HLA-DRB1 and hypermethylation of HLA-DQB1 was significantly correlated with occurrence of Kazakh ESCC (P < 0.01), and mainly manifested as hypomethylation of CpG9, CpG10-11, and CpG16 in HLA-DRB1 and hypermethylation of CpG6-7 and CpG16-17 in HLA-DQB1 (P < 0.01). Moreover, hypomethylation of HLA-DQB1 CpG6-7 correlated with poor differentiation in ESCCs, whereas hypermethylation of HLA-DRB1 CpG16 and hypomethylation of HLA-DQB1 CpG16-17 were significantly associated with later stages of ESCC (P < 0.05). A significant inverse association between HLA-DRB1 CpG9 methylation and HLA-II expression was found in ESCC (P < 0.05). These findings suggest aberrant HLA-DRB1 and HLA-DQB1 methylation contributes to the aberrant expression of HLA-II. These molecular changes may influence the immune response to specific tumor epitopes, promoting the occurrence and progression of Kazakh ESCC.
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Key Words
- ACN, cancer adjacent normal
- CIITA, class II transactivator
- CpG, CG dinucleotides
- DNA methylation
- EC, Esophageal carcinoma
- ESCC, esophageal squamous cell carcinoma
- Esophageal squamous cell carcinoma
- HLA
- HLA-II, Human leukocyte antigen II
- HPV, human papillomavirus
- IHC, Immunohistochemistry
- Kazakh
- MHC, major histocompatibility complex
- Massarray
- NE, normal esophageal tissues
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Affiliation(s)
- Jian Ming Hu
- a Department of Pathology and Key Laboratory of Xinjiang Endemic and Ethnic Diseases (Ministry of Education) ; Shihezi University School of Medicine ; Shihezi , China
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12
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Dadmehr M, Hosseini M, Hosseinkhani S, Reza Ganjali M, Sheikhnejad R. Label free colorimetric and fluorimetric direct detection of methylated DNA based on silver nanoclusters for cancer early diagnosis. Biosens Bioelectron 2015; 73:108-113. [PMID: 26056954 DOI: 10.1016/j.bios.2015.05.062] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/25/2015] [Accepted: 05/26/2015] [Indexed: 11/28/2022]
Abstract
Epigenetic changes such as DNA methylation of CpG islands located in the promoter region of some tumor suppressor genes are very common in human diseases such as cancer. Detection of aberrant methylation pattern could serve as an excellent diagnostic approach. Recently, the direct detection of methylated DNA sequences without using chemical and enzymatic treatments or antibodies has received great deal of attentions. In this study, we report a colorimetric and fluorimetric technique for direct detection of DNA methylation. Here, the DNA is being used as an effective template for fluorescent silver nanoclusters formation without any chemical modification or DNA labeling. The sensitivity test showed that upon the addition of target methylated DNA, the fluorescence intensity is decreased in a linear range when the concentration of methylated DNA has increased from 2.0×10(-9) to 6.3 ×10(-7) M with the detection limit of 9.4×10(-10) M. The optical and fluorescence spectral behaviors were highly reproducible and clearly discriminated between unmethylated, methylated and even partially methylated DNA in CpG rich sequences. The results were also reproducible when the human plasma was present in our assay system.
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Affiliation(s)
- Mehdi Dadmehr
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Morteza Hosseini
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran.
| | | | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, Tehran, Iran; Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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13
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Haghighi MM, Aghagolzadeh P, Zadeh SM, Molaei M, Zali MR, Radpour R. Telomere shortening: a biological marker of sporadic colorectal cancer with normal expression of p53 and mismatch repair proteins. Genet Test Mol Biomarkers 2014; 18:236-44. [PMID: 24495131 DOI: 10.1089/gtmb.2013.0436] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Uncontrolled growth of cells, a main criterion of cancer, is merged with pathologic telomere length alteration. Thereby, measurement of telomere length could provide important information on cell proliferation and senescence in cancer tissues. Telomere shortening and its potential correlation with clinicopathological predictive markers in sporadic colorectal cancer (CRC) with normal expression of mismatch repair (MMR) proteins (including Mlh1, Msh2, Pms2, and Msh6) and normal p53 expression was completely explored. Relative telomere length (RTL) was quantitatively measured in a cohort of 164 samples (68 patients with sporadic CRC and 96 healthy unrelated controls). Our results demonstrated a significant shortening of RTL in the tumor-derived tissue of patients compared with the control group (p<0.001). Interestingly, significant telomere shortening was observed in tumors from an ascending and sigmoid colon in comparison with tumors located in a descending colon. Additionally, the telomere length was significantly shorter in those with lymph node metastasis (p<0.05). The results suggest that pathological telomere shortening, leading to genome instability and lymphatic transformation, could serve as a potential sensitive detection and also as a classification marker for facilitating diagnosis and management of CRC.
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Affiliation(s)
- Mahdi Montazer Haghighi
- 1 Department of Biology, Science Faculty, Islamic Azad University , East Tehran Branch, Tehran, Iran
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Swift-Scanlan T, Smith CT, Bardowell SA, Boettiger CA. Comprehensive interrogation of CpG island methylation in the gene encoding COMT, a key estrogen and catecholamine regulator. BMC Med Genomics 2014; 7:5. [PMID: 24460628 PMCID: PMC3910242 DOI: 10.1186/1755-8794-7-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 01/14/2014] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The catechol-O-methyltransferase (COMT) enzyme has been widely studied due to its multiple roles in neurological functioning, estrogen biology, and methylation metabolic pathways. Numerous studies have investigated variation in the large COMT gene, with the majority focusing on single nucleotide polymorphisms (SNPs). This body of work has linked COMT genetic variation with a vast array of conditions, including several neurobehavioral disorders, pain sensitivity, and multiple human cancers. Based on COMT's numerous biological roles and recent studies suggesting that methylation of the COMT gene impacts COMT gene expression, we comprehensively interrogated methylation in over 200 CpG dinucleotide sequences spanning the length of the COMT gene. METHODS Using saliva-derived DNA from a non-clinical sample of human subjects, we tested for associations between COMT CpG methylation and factors reported to interact with COMT genetic effects, including demographic factors and alcohol use. Finally, we tested associations between COMT CpG methylation state and COMT gene expression in breast cancer cell lines. We interrogated >200 CpGs in 13 amplicons spanning the 5' UTR to the last exon of the CpG dinucleotide-rich COMT gene in n = 48 subjects, n = 11 cell lines and 1 endogenous 18S rRNA control. RESULTS With the exception of the CpG island in the 5'UTR and 1st exon, all other CpG islands were strongly methylated with typical dynamic ranges between 50-90%. In the saliva samples, methylation of multiple COMT loci was associated with socioeconomic status or ethnicity. We found associations between methylation at numerous loci and genotype at the functional Val158Met SNP (rs4680), and most of the correlations between methylation and demographic and alcohol use factors were Val158Met allele-specific. Methylation at several of these loci also associated with COMT gene expression in breast cancer cell lines. CONCLUSIONS We report the first comprehensive interrogation of COMT methylation. We corroborate previous findings of variation in COMT methylation with gene expression and the Val158Met genotype, and also report novel associations with socioeconomic status (SES) and ethnicity at several methylated loci. These results point to novel mechanisms for COMT regulation, which may have broad therapeutic implications.
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Affiliation(s)
- Theresa Swift-Scanlan
- School of Nursing, University of North Carolina, Carrington Hall, CB #7460, Chapel Hill, NC, USA,Lineberger Comprehensive Cancer Center, University of North Carolina, 450 West Drive, Chapel Hill, NC, USA
| | - Christopher T Smith
- Department of Psychology, University of North Carolina, Davie Hall, CB #3270, Chapel Hill, NC, USA
| | - Sabrina A Bardowell
- School of Nursing, University of North Carolina, Carrington Hall, CB #7460, Chapel Hill, NC, USA
| | - Charlotte A Boettiger
- Department of Psychology, University of North Carolina, Davie Hall, CB #3270, Chapel Hill, NC, USA,Department of Psychology, Biomedical Research Imaging Center, and Bowles Center for Alcohol Studies, University of North Carolina, Davie Hall, CB #3270, Chapel Hill, NC, USA
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15
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Kwon M, Lee SJ, Reddy S, Rybak Y, Adem A, Libutti SK. Down-regulation of Filamin A interacting protein 1-like Is associated with promoter methylation and an invasive phenotype in breast, colon, lung and pancreatic cancers [corrected]. PLoS One 2013; 8:e82620. [PMID: 24340050 PMCID: PMC3855469 DOI: 10.1371/journal.pone.0082620] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/25/2013] [Indexed: 12/12/2022] Open
Abstract
Identifying key mediators of cancer cell invasion and metastasis is critical to the development of more effective cancer therapies. We previously identified Filamin A interacting protein 1-like (FILIP1L) as an important inhibitor of cell migration and invasion in ovarian cancer. FILIP1L expression was inversely correlated with the invasive potential of ovarian cancer cell lines and ovarian cancer specimens. We also demonstrated that DNA methylation in the FILIP1L promoter was a mechanism by which FILIP1L was down-regulated in ovarian cancer. In our present study, we tested this observation in other cancer histologies: breast, colon, lung and pancreatic cancers. Both mRNA and protein expression of FILIP1L were down-regulated in these cancer cells compared with their normal epithelial cells. As in ovarian cancer, DNA methylation is a mechanism by which FILIP1L is down-regulated in these cancer histologies. Methylation status of the FILIP1L promoter was inversely correlated with FILIP1L expression. Reduced methylation in the FILIP1L promoter following treatment with a DNA demethylating agent was associated with restoration of FILIP1L expression in these cancer cells. Further, FILIP1L expression was inversely correlated with the invasive potential of these cancer cells. Re-expression of FILIP1L in FILIP1L-low expressing, highly-invasive cancer cell lines resulted in inhibition of cell invasion. Correspondingly, knockdown of FILIP1L in FILIP1L-high expressing, low-invasive cancer cell lines resulted in increase of cell invasion. Overall, these findings suggest that down-regulation of FILIP1L associated with DNA methylation is related with the invasive phenotype in various cancers. Thus, modulation of FILIP1L expression has the potential to be a target for cancer therapy.
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Affiliation(s)
- Mijung Kwon
- Department of Surgery, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Soo Jin Lee
- Department of Surgery, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Srilakshmi Reddy
- Department of Surgery, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Yevangelina Rybak
- Department of Surgery, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Asha Adem
- Department of Surgery, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Steven K. Libutti
- Department of Surgery, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
- * E-mail:
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16
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Yin L, Cai WJ, Liu CX, Chen YZ, Hu JM, Jiang JF, Li HA, Cui XB, Chang XY, Zhang WJ, Sun K, Li F. Analysis of PTEN methylation patterns in soft tissue sarcomas by MassARRAY spectrometry. PLoS One 2013; 8:e62971. [PMID: 23690972 PMCID: PMC3656904 DOI: 10.1371/journal.pone.0062971] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 03/27/2013] [Indexed: 12/29/2022] Open
Abstract
Soft tissue sarcomas (STSs) are a rare and fascinating group of diseases that can be subdivided into specific reciprocal translocations in STSs (SRTSs) and nonspecific reciprocal translocations in STSs (NRTSs). PTEN mutations are rare in STSs, suggesting that PTEN expression may be lost by alternative mechanisms such as methylation. In order to reveal whether aberrant PTEN methylation occurs in STSs, MassARRAY Spectrometry was carried to detect methylation patterns of PTEN in STSs. We evaluated methylation levels in 41 CpG sites from −2,515 to −2,186 bp (amplicon A) and −1,786 to −1,416 bp (amplicon B) relative to the translation initiation site in 110 different cases (46 cases of SRTSs, 40 cases of NRTSs, and 24 cases of normal controls). In addition, immunohistochemistry (IHC) was used to detect the loss of PTEN to determine whether PTEN alterations were responsible for decreased PTEN expression. Our data showed that expression of PTEN was diminished in 49 (57%) STSs, whereas the remaining cases (43%) were classified as high expression. Our previous results found that only 2 of 86 cases (2.3%) had a PTEN mutation suggesting that PTEN may be mainly downregulated in STSs by methylation, but not by mutation of PTEN itself. We observed that amplicon A was hypermethylated in STSs with low PTEN expression, whereas normal controls had low methylation levels (P<0.0001), which was not present in amplicon B (P>0.05), nor were there significant differences in the methylation levels in PTEN between SRTS and NRTS cases. The majority of individual CpG units within two amplicons was demonstrated to be hypermethylated. These findings indicate that PTEN hypermethylation is a common event in STSs suggesting that the inactivation of PTEN may be due to hypermethylation in the promoter of PTEN. The aberrant methylation of the CpG sites within PTEN promoter may serve as a potential candidate biomarker for STSs.
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Affiliation(s)
- Liang Yin
- Department of Pathology and Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
- Department of Endocrinology and Metabolism, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Wei-Juan Cai
- Department of Clinical Laboratory, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Chun-Xia Liu
- Department of Pathology and Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Yun-Zhao Chen
- Department of Pathology and Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Jian-Ming Hu
- Department of Pathology and Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Jin-Fang Jiang
- Department of Pathology and Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Hong-An Li
- Department of Pathology and Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Xiao-Bin Cui
- Department of Pathology and Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Xiang-Yun Chang
- Department of Endocrinology and Metabolism, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Wen Jie Zhang
- Department of Pathology and Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
| | - Kan Sun
- Department of Endocrinology and Metabolism, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
- * E-mail: (KS); (FL)
| | - Feng Li
- Department of Pathology and Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi, Xinjiang, P.R. China
- * E-mail: (KS); (FL)
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17
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Ulirsch J, Fan C, Knafl G, Wu MJ, Coleman B, Perou CM, Swift-Scanlan T. Vimentin DNA methylation predicts survival in breast cancer. Breast Cancer Res Treat 2012; 137:383-96. [PMID: 23239149 DOI: 10.1007/s10549-012-2353-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 11/21/2012] [Indexed: 11/30/2022]
Abstract
The Vimentin gene plays a pivotal role in epithelial-to-mesenchymal transition and is known to be overexpressed in the prognostically poor basal-like breast cancer subtype. Recent studies have reported Vimentin DNA methylation in association with poor clinical outcomes in other solid tumors, but not in breast cancer. We therefore quantified Vimentin DNA methylation using MALDI-TOF mass spectrometry in breast tumors and matched normal pairs in association with gene expression and survival in a hospital-based study of breast cancer patients. Gene expression data via qRT-PCR in cell lines and oligomicroarray data from breast tissues were correlated with percent methylation in the Vimentin promoter. A threshold of 20 percent average methylation compared with matched normal pairs was set for bivariate and multivariate tests of association between methylation and tumor subtype, tumor histopathology, and survival. Vimentin was differentially methylated in luminal breast cancer cell lines, and in luminal A, luminal B, and HER2-enriched breast tumor subtypes, but was rare in basal-like cell lines and tumors. Increased methylation was strongly correlated with decreased mRNA expression in cell lines, and had a moderate inverse correlation in breast tumors. Vimentin methylation predicted poor overall survival independent of race, subtype, stage, nodal status, or metastatic disease and holds promise as a new prognostic biomarker for breast cancer patients.
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Affiliation(s)
- Jacob Ulirsch
- The University of North Carolina at Chapel Hill School of Nursing, Lab 013, Carrington Hall, CB #7460, Chapel Hill, NC 27599-7460, USA
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18
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Sang Q, Zhang S, Zou S, Wang H, Feng R, Li Q, Jin L, He L, Xing Q, Wang L. Quantitative analysis of follistatin (FST) promoter methylation in peripheral blood of patients with polycystic ovary syndrome. Reprod Biomed Online 2012; 26:157-63. [PMID: 23265961 DOI: 10.1016/j.rbmo.2012.10.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 10/11/2012] [Accepted: 10/11/2012] [Indexed: 11/29/2022]
Abstract
Epigenetic mechanisms may contribute to polycystic ovary syndrome (PCOS). To date, however, no studies have associated CpG methylation levels of any candidate gene with PCOS susceptibility. Follistatin (FST), an activin-binding protein, is expressed in numerous tissues and is shown to have linkage with PCOS. However, results from case-control association analyses between this gene and PCOS are inconsistent. Thus, this study investigated possible association of methylation levels in the promoter and 5'-untranscribed region (UTR) of the FST gene with PCOS incidence in peripheral blood leukocytes and endometrial tissue. Using mass array quantitative methylation analysis, first the 5'-UTR methylation in FST was analysed in 130 PCOS patients and 120 controls. The methylation level of the FST gene was further studied in endometrium from 24 controls and 24 PCOS patients. This study demonstrates that methylation levels of CpG sites in the FST promoter and 5'-UTR are not associated with PCOS. Nonetheless, this was the first study to quantitatively evaluate the methylation levels of a candidate gene in association with PCOS. Further studies should be performed to examine methylation in other candidate genes. Understanding the epigenetic mechanisms involved in PCOS may yield new insights into the pathophysiology of the disorder. Animal models demonstrate that epigenetic reprogramming may contribute to polycystic ovary syndrome (PCOS). To date, however, no studies have associated CpG methylation levels of any candidate gene with PCOS susceptibility. Follistatin (FST), an activin-binding protein, is expressed in numerous tissues and is a PCOS candidate gene. However, results from association analyses between this gene and PCOS are inconsistent. Thus, we investigated possible association of methylation levels in the promoter and 5'-UTR of the FST gene with PCOS incidence in peripheral blood leukocytes and endometrial tissue. Using mass array quantitative methylation analysis, we firstly analysed 5'-UTR methylation in 40 PCOS patients and 40 controls. We then validated results in a second sample consisting of 90 PCOS patients and 80 controls. The methylation level of the FST gene was further studied in endometrium from 24 controls and 24 PCOS patients. Finally, we quantitatively analysed FST expression in the endometrium using real-time PCR. Our study demonstrated that methylation levels of CpG sites in the FST promoter and 5'-UTR are not associated with PCOS. Nonetheless, as far as is known, this is the first study to quantitatively evaluate the methylation levels of a candidate gene in association with PCOS. Further studies should be performed to examine methylation in other candidate genes. Understanding the epigenetic mechanisms involved in PCOS may yield new insights into the pathophysiology of the disorder.
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Affiliation(s)
- Qing Sang
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
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19
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Gao X, Sugrue RJ, Tan BH, Tang K. Screening of influenza mutations using base-specific cleavage and MALDI mass spectrometry. Clin Chim Acta 2012; 420:89-93. [PMID: 23078853 DOI: 10.1016/j.cca.2012.10.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 10/09/2012] [Indexed: 11/15/2022]
Abstract
BACKGROUND The hemagglutinin (HA) and neuraminidase (NA) genes encode surface glycoproteins of influenza virus. These two proteins are involved in pathogenicity and are the primary targets of the immune system. Mutations in the HA and NA genes can result in antigenic drift in an influenza viral strain. A comparative sequencing method using MALDI MS combined with base-specific cleavage has been applied for the surveillance of these viral mutations. This approach shows advantages in high throughput and efficiency than the traditional direct sequencing methods in targeted sequence analysis. METHODS Base-specific cleavage assay with RNAse A was combined with MALDI-MS for the analysis of the HA and NA genes of 2 influenza viral strains. The mass peak patterns from the spectra were compared with the in silico digest result of reference gene sequences from the database to achieve comparative sequencing and screening of novel mutations. RESULTS The HA and NA genes of two influenza lab strains were comparatively sequenced using the base-specific cleavage and MALDI-MS approach. Mutations could be exactly identified if more than one observation (mass peak changes) were detected in the spectrum. Mutations with only one observation could be located in a small area for further validation. CONCLUSIONS We showed a proof of a principle that base-specific combined with MALDI-MS comparative sequencing approach can be utilized for targeted sequence analysis and potentially rapid and cost effective screening of emerging viral mutations.
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Affiliation(s)
- Xiang Gao
- Division of Chemical Biology and Biotechnology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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20
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Van De Voorde L, Speeckaert R, Van Gestel D, Bracke M, De Neve W, Delanghe J, Speeckaert M. DNA methylation-based biomarkers in serum of patients with breast cancer. Mutat Res 2012; 751:304-325. [PMID: 22698615 DOI: 10.1016/j.mrrev.2012.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 06/03/2012] [Accepted: 06/05/2012] [Indexed: 12/18/2022]
Abstract
Alterations of genetic and epigenetic features can provide important insights into the natural history of breast cancer. Although DNA methylation analysis is a rapidly developing field, a reproducible epigenetic blood-based assay for diagnosis and follow-up of breast cancer has yet to be successfully developed into a routine clinical test. The aim of this study was to review multiple serum DNA methylation assays and to highlight the value of those novel biomarkers in diagnosis, prognosis and prediction of therapeutic outcome. Serum is readily accessible for molecular diagnosis in all individuals from a peripheral blood sample. The list of hypermethylated genes in breast cancer is heterogeneous and no single gene is methylated in all breast cancer types. There is increasing evidence that a panel of epigenetic markers is essential to achieve a higher sensitivity and specificity in breast cancer detection. However, the reported percentages of methylation are highly variable, which can be partly explained by the different sensitivities and the different intra-/inter-assay coefficients of variability of the analysis methods. Moreover, there is a striking lack of receiver operating characteristic (ROC) curves of the proposed biomarkers. Another point of criticism is the fact that 'normal' patterns of DNA methylation of some tumor suppressor and other cancer-related genes are influenced by several factors and are often poorly characterized. A relatively frequent methylation of those genes has been observed in high-risk asymptomatic women. Finally, there is a call for larger prospective cohort studies to determine methylation patterns during treatment and follow-up. Identification of patterns specific for a differential response to therapeutic interventions should be useful. Only in this way, it will be possible to evaluate the predictive and prognostic characteristics of those novel promising biomarkers.
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Affiliation(s)
- Lien Van De Voorde
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | | | - Dirk Van Gestel
- Department of Radiation Oncology, Antwerp University Hospital, Antwerp, Belgium
| | - Marc Bracke
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Wilfried De Neve
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Joris Delanghe
- Department of Clinical Chemistry, Ghent University Hospital, Ghent, Belgium
| | - Marijn Speeckaert
- Department of Clinical Chemistry, Ghent University Hospital, Ghent, Belgium; Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium.
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García-Giménez JL, Sanchis-Gomar F, Lippi G, Mena S, Ivars D, Gomez-Cabrera MC, Viña J, Pallardó FV. Epigenetic biomarkers: A new perspective in laboratory diagnostics. Clin Chim Acta 2012; 413:1576-82. [PMID: 22664147 DOI: 10.1016/j.cca.2012.05.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 05/23/2012] [Accepted: 05/25/2012] [Indexed: 02/08/2023]
Abstract
Epigenetics comprises the study of chemical modifications in the DNA and histones that regulates the gene expression or cellular phenotype. However, during the last decade this term has evolved after the elucidation of different mechanisms (microRNAs and nuclear organization of the chromosomes) involved in regulating gene expression. Epigenetics and the new designed technologies capable to analyze epigenetic changes (e.g., methylated DNA, miRNAs expression, post-translational modifications on histones among others) have disclosed an appealing scenario that will offer for the biomedical sciences new biomarkers for the study of neurodegenerative diseases, multifactorial complex diseases, rare diseases and cancer. Moreover, new technologies adapted for epigenetic studies will offer promising applications that in the next years will be common technologies in clinical laboratories. In this review we discuss epigenetic modifications used as possible biomarkers in several diseases. We also present the potential of methodologies to purify histones, and high throughput technologies as candidates to be set in clinical laboratories for their high potential analyzing epigenetic processes.
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Affiliation(s)
- J L García-Giménez
- CIBERER, The Biomedical Network Research Centre on Rare Diseases. Valencia, Spain.
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22
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Hoshimoto S, Kuo CT, Chong KK, Takeshima TL, Takei Y, Li MW, Huang SK, Sim MS, Morton DL, Hoon DSB. AIM1 and LINE-1 epigenetic aberrations in tumor and serum relate to melanoma progression and disease outcome. J Invest Dermatol 2012; 132:1689-97. [PMID: 22402438 PMCID: PMC3352986 DOI: 10.1038/jid.2012.36] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aberrations in the methylation status of non-coding genomic repeat DNA sequences and specific gene promoter region are important epigenetic events in melanoma progression. Promoter methylation status in LINE-1 and Absent in melanoma-1(AIM1;6q21) associated with melanoma progression and disease outcome was assessed. LINE-1 and AIM1 methylation status was assessed in paraffin-embedded archival tissues(PEAT)(n=133) and melanoma patients’ serum(n=56). LINE-1 U-Index(hypomethylation) and AIM1 were analyzed in microdissected melanoma PEAT sections. The LINE-1 U-Index of melanoma(n=100) was significantly higher than that of normal skin(n=14) and nevi(n=12)(P=0.0004). LINE-1 U-Index level was elevated with increasing AJCC stage(P<0.0001). AIM1 promoter hypermethylation was found in higher frequency(P=0.005) in metastatic melanoma(65%) than in primary melanomas(38%). When analyzed, high LINE-1 U-Index and/or AIM1 methylation in melanomas were associated with disease-free survival(DFS) and overall survival(OS) in Stage I/II patients (P=0.017, 0.027; respectively). In multivariate analysis, melanoma AIM1 methylation status was a significant prognostic factor of OS(P=0.032). Furthermore, serum unmethylated LINE-1 was at higher levels in both stage III(n=20) and stage IV(n=36) patients compared to healthy donors(n=14)(P=0.022). Circulating methylated AIM1 was detected in patients’ serum and was predictive of OS in Stage IV patients (P=0.009). LINE-1 hypomethylation and AIM1 hypermethylation have prognostic utility in both melanoma patients’ tumors and serum.
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Affiliation(s)
- Sojun Hoshimoto
- Department of Molecular Oncology, John Wayne Cancer Institute at Saint John's Health Center, Santa Monica, California 90404, USA
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Pietanza MC, Kadota K, Huberman K, Sima CS, Fiore JJ, Sumner DK, Travis WD, Heguy A, Ginsberg MS, Holodny AI, Chan TA, Rizvi NA, Azzoli CG, Riely GJ, Kris MG, Krug LM. Phase II Trial of Temozolomide in Patients with Relapsed Sensitive or Refractory Small Cell Lung Cancer, with Assessment of Methylguanine-DNA Methyltransferase as a Potential Biomarker. Clin Cancer Res 2012; 18:1138-45. [DOI: 10.1158/1078-0432.ccr-11-2059] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Burton ER, Gaffar A, Lee SJ, Adeshuko F, Whitney KD, Chung JY, Hewitt SM, Huang GS, Goldberg GL, Libutti SK, Kwon M. Downregulation of Filamin A interacting protein 1-like is associated with promoter methylation and induces an invasive phenotype in ovarian cancer. Mol Cancer Res 2011; 9:1126-38. [PMID: 21693594 DOI: 10.1158/1541-7786.mcr-11-0162] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ovarian cancer is the most lethal gynecologic malignancy with a five-year survival rate below 25% for patients with stages III and IV disease. Identifying key mediators of ovarian cancer invasion and metastasis is critical to the development of more effective therapeutic interventions. We previously identified Filamin A interacting protein 1-like (FILIP1L) as an important mediator of cell proliferation and migration. In addition, targeted expression of FILIP1L in tumors inhibited tumor growth in vivo. In our present study, we confirmed that both mRNA and protein expression of FILIP1L were downregulated in ovarian cancer cells compared with normal ovarian epithelial cells. FILIP1L expression was inversely correlated with the invasive potential of ovarian cancer cell lines and clinical ovarian cancer specimens. We also provide evidence that DNA methylation is a mechanism by which FILIP1L is downregulated in ovarian cancer. The CpG island in the FILIP1L promoter was heavily methylated in ovarian cancer cells. Methylation status of the FILIP1L promoter was inversely correlated with FILIP1L expression in ovarian cell lines and clinical ovarian specimens. Reduced methylation in the FILIP1L promoter following treatment with a DNA demethylating agent was associated with restoration of FILIP1L expression in ovarian cancer cells. A transcription activator, cAMP-responsive element binding protein (CREB) was shown to bind to the CREB/ATF site in the CpG island of the FILIP1L promoter. Overall, these findings suggest that downregulation of FILIP1L associated with DNA methylation is related with the invasive phenotype in ovarian cancer and that modulation of FILIP1L expression has the potential to be a target for ovarian cancer therapy.
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Affiliation(s)
- Elizabeth R Burton
- Department of Surgery, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
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Radpour R, Barekati Z, Kohler C, Lv Q, Bürki N, Diesch C, Bitzer J, Zheng H, Schmid S, Zhong XY. Hypermethylation of tumor suppressor genes involved in critical regulatory pathways for developing a blood-based test in breast cancer. PLoS One 2011; 6:e16080. [PMID: 21283676 PMCID: PMC3025923 DOI: 10.1371/journal.pone.0016080] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Accepted: 12/06/2010] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Aberrant DNA methylation patterns might be used as a biomarker for diagnosis and management of cancer patients. METHODS AND FINDINGS To achieve a gene panel for developing a breast cancer blood-based test we quantitatively assessed the DNA methylation proportion of 248 CpG sites per sample (total of 31,248 sites in all analyzed samples) on 10 candidate genes (APC, BIN1, BMP6, BRCA1, CST6, ESR-b, GSTP1, P16, P21 and TIMP3). The number of 126 samples consisting of two different cohorts was used (first cohort: plasma samples from breast cancer patients and normal controls; second cohort: triple matched samples including cancerous tissue, matched normal tissue and serum samples). In the first cohort, circulating cell free methylated DNA of the 8 tumor suppressor genes (TSGs) was significantly higher in patients with breast cancer compared to normal controls (P<0.01). In the second cohort containing triple matched samples, seven genes showed concordant hypermethylated profile in tumor tissue and serum samples compared to normal tissue (P<0.05). Using eight genes as a panel to develop a blood-based test for breast cancer, a sensitivity and specificity of more than 90% could be achieved in distinguishing between tumor and normal samples. CONCLUSIONS Our study suggests that the selected TSG panel combined with the high-throughput technology might be a useful tool to develop epigenetic based predictive and prognostic biomarker for breast cancer relying on pathologic methylation changes in tumor tissue, as well as in circulation.
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Affiliation(s)
- Ramin Radpour
- Laboratory for Gynecological Oncology, Department of Biomedicine, Women's Hospital, University of Basel, Basel, Switzerland
| | - Zeinab Barekati
- Laboratory for Gynecological Oncology, Department of Biomedicine, Women's Hospital, University of Basel, Basel, Switzerland
| | - Corina Kohler
- Laboratory for Gynecological Oncology, Department of Biomedicine, Women's Hospital, University of Basel, Basel, Switzerland
| | - Qing Lv
- Department of Breast Surgery, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, China
| | - Nicole Bürki
- Department of Obstetrics and Gynecology, Kantonsspital, Liestal, Switzerland
| | - Claude Diesch
- Department of Obstetrics and Gynecology, Kantonsspital, Liestal, Switzerland
| | - Johannes Bitzer
- Department of Obstetrics and Gynecology, Women's Hospital, University of Basel, Basel, Switzerland
| | - Hong Zheng
- Laboratory of Molecular Diagnosis of Cancer, Department of Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, China
| | - Seraina Schmid
- Department of Obstetrics and Gynecology, Women's Hospital, University of Basel, Basel, Switzerland
- * E-mail: (XYZ); (SS)
| | - Xiao Yan Zhong
- Laboratory for Gynecological Oncology, Department of Biomedicine, Women's Hospital, University of Basel, Basel, Switzerland
- * E-mail: (XYZ); (SS)
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Investigation of DNA damage response and apoptotic gene methylation pattern in sporadic breast tumors using high throughput quantitative DNA methylation analysis technology. Mol Cancer 2010; 9:303. [PMID: 21092294 PMCID: PMC3004830 DOI: 10.1186/1476-4598-9-303] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 11/23/2010] [Indexed: 01/02/2023] Open
Abstract
Background- Sporadic breast cancer like many other cancers is proposed to be a manifestation of abnormal genetic and epigenetic changes. For the past decade our laboratory has identified genes involved in DNA damage response (DDR), apoptosis and immunesurvelliance pathways to influence sporadic breast cancer risk in north Indian population. Further to enhance our knowledge at the epigenetic level, we performed DNA methylation study involving 17 gene promoter regions belonging to DNA damage response (DDR) and death receptor apoptotic pathway in 162 paired normal and cancerous breast tissues from 81 sporadic breast cancer patients, using a high throughput quantitative DNA methylation analysis technology. Results- The study identified five genes with statistically significant difference between normal and tumor tissues. Hypermethylation of DR5 (P = 0.001), DCR1 (P = 0.00001), DCR2 (P = 0.0000000005) and BRCA2 (P = 0.007) and hypomethylation of DR4 (P = 0.011) in sporadic breast tumor tissues suggested a weak/aberrant activation of the DDR/apoptotic pathway in breast tumorigenesis. Negative correlation was observed between methylation status and transcript expression levels for TRAIL, DR4, CASP8, ATM, CHEK2, BRCA1 and BRCA2 CpG sites. Categorization of the gene methylation with respect to the clinicopathological parameters showed an increase in aberrant methylation pattern in advanced tumors. These uncharacteristic methylation patterns corresponded with decreased death receptor apoptosis (P = 0.047) and DNA damage repair potential (P = 0.004) in advanced tumors. The observation of BRCA2 -26 G/A 5'UTR polymorphism concomitant with the presence of methylation in the promoter region was novel and emerged as a strong candidate for susceptibility to sporadic breast tumors. Conclusion- Our study indicates that methylation of DDR-apoptotic gene promoters in sporadic breast cancer is not a random phenomenon. Progressive epigenetic alterations in advancing tumors result in aberrant DDR-apoptotic pathway thereby promoting tumor development. We propose, since pathological epigenetic changes of the DDR-apoptotic genes are reversible modifications, these could further be targeted for therapeutic interventions.
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Wu CQ, Tao KX. Advances in understanding the relationship between aberrant methylation of EDNRB and tumors. Shijie Huaren Xiaohua Zazhi 2010; 18:2448-2452. [DOI: 10.11569/wcjd.v18.i23.2448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is a major epigenetic mechanism and plays an important role in the pathogenesis of tumors. The endothelin receptor B (EDNRB) gene is an important candidate tumor suppressor gene. EDNRB promoter hypermethylation has been detected in several types of tumors and may therefore be used as a useful molecular marker for tumor diagnosis. In addition, EDNRB gene methylation may also be used as a new target for tumor treatment due to the reversibility of DNA methylation.
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Specificity of methylation assays in cancer research: a guideline for designing primers and probes. Obstet Gynecol Int 2010; 2010. [PMID: 20798774 PMCID: PMC2926695 DOI: 10.1155/2010/870865] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2010] [Accepted: 06/21/2010] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is an epigenetic regulation mechanism of genomic function, and aberrant methylation pattern has been found to be a common event in many diseases and human cancers. A large number of cancer studies have been focused on identification of methylation changes as biomarkers (i.e., breast cancer). However, still clinical use of them is very limited because of lack of specificity and sensitivity for diagnostic test. This highlights the critical need for specific primer and probe design to avoid false-positive detection of methylation profiling. The guideline and online web tools that are introduced in this paper might help to perform a successful experiment and to develop specific diagnosis biomarkers by designing right primer pair and probe prior to experimental step.
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Correlation of telomere length shortening with promoter methylation profile of p16/Rb and p53/p21 pathways in breast cancer. Mod Pathol 2010; 23:763-72. [PMID: 20081803 DOI: 10.1038/modpathol.2009.195] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Unregulated cell growth, a major hallmark of cancer, is coupled with telomere shortening. Measurement of telomere length could provide important information on cell replication and proliferation state in cancer tissues. Telomere shortening and its potential correlation with downregulation of cell-cycle regulatory elements were studied by the examination of relative telomere length and methylation status of the TP53, P21 and P16 promoters in tissues from breast cancer patients. Telomere length was measured in 104 samples (52 tumors and paired adjacent normal breast tissues) by quantitative PCR. Methylation profile of selected genes was analyzed in all samples using a matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Our results demonstrated a significant shortening of tumor telomere regions compared with paired adjacent normal tissues (P<0.001). Similarly, telomere lengths were significantly shorter in advanced stage cases and in those with higher histological grades (P<0.05). Telomere shortening in cancer tissues was correlated with a different level of hypermethylation in the TP53, P21 and P16 promoters (r=-0.33, P=0.001; r=-0.70, P<0.0001 and r=-0.71, P<0.0001, respectively). The results suggested that inactivation of p16/Rb and/or p53/p21 pathways by hypermethylation may be linked to critical telomere shortening, leading to genome instability and ultimately to malignant transformation. Thus, telomere shortening and promoter hypermethylation of related genes both might serve as breast cancer biomarkers.
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Radpour R, Sikora M, Grussenmeyer T, Kohler C, Barekati Z, Holzgreve W, Lefkovits I, Zhong XY. Simultaneous isolation of DNA, RNA, and proteins for genetic, epigenetic, transcriptomic, and proteomic analysis. J Proteome Res 2010; 8:5264-74. [PMID: 19780627 DOI: 10.1021/pr900591w] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Analysis of DNA, RNA, and proteins for downstream genetic, epigenetic, transcriptomic, and proteomic analysis holds an important place in the field of medical care and life science. This is often hampered by the limited availability of sample material. For this reason, there exists an increasing interest for simultaneous isolation of DNA, RNA and proteins from a single sample aliquot. Several kit-systems allowing such a procedure have been introduced to the market. We present an approach using the AllPrep method for simultaneous isolation of DNA, RNA and proteins from several human specimens, such as whole blood, buffy coat, serum, plasma and tissue samples. The quantification and qualification of the isolated molecular species were assessed by different downstream methods: NanoDrop for measuring concentration and purity of all molecular species; DNA and RNA LabChip for fractionation analysis of nucleic acids; quantitative PCR for quantification analysis of DNA and RNA; thymidine-specific cleavage mass array on MALDI-TOF silico-chip for epigenetic analysis; Protein LabChip and two-dimensional (2D) gel electrophoresis for proteomic analysis. With our modified method, we can simultaneously isolate DNA, RNA and/or proteins from one single sample aliquot. We could overcome to some method limitations like low quality or DNA fragmentation using reamplification strategy for performing high-throughput downstream assays. Fast and easy performance of the procedure makes this method interesting for all fields of downstream analysis, especially when using limited sample resources. The cost-effectiveness of the procedure when material is abundantly available has not been addressed. This methodological improvement enables to execute such experiments that were not performable with standard procedure, and ensures reproducible outcome.
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Affiliation(s)
- Ramin Radpour
- Laboratory for Prenatal Medicine and Gynecologic Oncology, Women's Hospital/Department of Biomedicine, University of Basel, Switzerland
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Bellido ML, Radpour R, Lapaire O, De Bie I, Hösli I, Bitzer J, Hmadcha A, Zhong XY, Holzgreve W. MALDI-TOF mass array analysis of RASSF1A and SERPINB5 methylation patterns in human placenta and plasma. Biol Reprod 2010; 82:745-50. [PMID: 20075396 DOI: 10.1095/biolreprod.109.082271] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Differences in DNA methylation patterns between placenta and blood cells of pregnant women have been suggested as potential biomarkers for noninvasive prenatal diagnostic strategies, including for common obstetrical complications, such as preeclampsia. New findings in epigenetic origins of fetal or placental disorders may improve our ability for optimal management of these conditions. Using a novel high-throughput mass spectrometry on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass array, we compared the quantitative methylation changes of RASSF1 and SERPINB5 (also known as MASPIN) genes in placenta and plasma samples. We analyzed the methylation status of a total of 3569 CpG dinucleotides on these two genes in 83 different samples: 50 plasma samples (20 from pregnant women and 30 from nonpregnant women) and 33 placenta tissue samples (25 from normal pregnancies and eight from preeclamptic pregnancies). The aim of this study was to assess the utility of epigenetic changes as biomarkers for noninvasive prenatal diagnostic procedures. Using a two-way hierarchical cluster analysis, significantly different methylation levels of the RASSF1 gene were found between placenta (normal and preeclamptic) and plasma samples of pregnant women. Although the SERPINB5 gene was hypomethylated in placenta DNA more than in plasma DNA, it did not demonstrate significant differences between studied groups. The MALDI-TOF mass spectrometry analysis of placenta and plasma DNA methylation patterns may serve as a tool for the study of gender-independent biomarkers in noninvasive prenatal diagnosis.
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Affiliation(s)
- Maria Luz Bellido
- Department of Cell Therapy and Regenerative Medicine, Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), Seville, Spain
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Radpour R, Barekati Z, Kohler C, Holzgreve W, Zhong XY. New trends in molecular biomarker discovery for breast cancer. Genet Test Mol Biomarkers 2010; 13:565-71. [PMID: 19814613 DOI: 10.1089/gtmb.2009.0060] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is one of the most common and leading causes of cancer death in women. Early diagnosis, selection of appropriate therapeutic strategies, and efficient follow-up play an important role in reducing mortality. Recently, HER-2/neu in breast cancer has been routinely used to guide treatment of using Trastuzumab in less than 25-30% of patients. More new biomarkers will be still expected in the future to tailor treatments. However, there are still many obstacles in developing clinically useful biomarker tests for clinical practice. A lack of specificity of tumor markers and lack of sensitivity of testing systems have been noticed, which limit their clinical use. Finding biomarkers for breast cancer could allow physicians to identify individuals who are susceptible to certain types and stages of cancer to tailor preventive and therapeutic modalities based on the genotype and phenotype information. These biomarkers should be cancer specific, and sensitively detectable in a wide range of specimen(s) containing cancer-derived materials, including body fluids (plasma, serum, urine, saliva, etc.), tissues, and cell lines. This review highlights the new trends and approaches in breast cancer biomarker discovery, which could be potentially used for early diagnosis, development of new therapeutic approaches, and follow-up of patients.
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Affiliation(s)
- Ramin Radpour
- Laboratory for Prenatal Medicine and Gynecologic Oncology, Women's Hospital/Department of Biomedicine, University of Basel, Basel, Switzerland
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Zhong XY, Holzgreve W. MALDI-TOF MS in Prenatal Genomics. ACTA ACUST UNITED AC 2009; 36:263-272. [PMID: 21049077 DOI: 10.1159/000223098] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 05/14/2009] [Indexed: 12/23/2022]
Abstract
Prenatal diagnosis aims either to provide the reassurance to the couples at risk of having an affected child by timely appropriate therapy or to give the parents a chance to decide the fate of the unborn babies with health problems. Invasive prenatal diagnosis (IPD) is accurate, however, carrying a risk of miscarriage. Non-invasive prenatal diagnosis (NIPD) has been developed based on the existing of fetal genetic materials in maternal circulation; however, a minority fetal DNA in majority maternal background DNA hinders the detections of fetal traits. Different protocols and assays, such as homogenous MassEXTEND (hME), single allele base extension reaction (SABER), precise measuring copy number variation of each allele, and quantitative methylation and expression analysis using the high-throughput sensitive matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), allow NIPD for single gene disorders, fetal blood group genotyping and fetal aneuploidies as well as the development of fetal gender-independent biomarkers in maternal circulation for management of pathological pregnancies. In this review, we summarise the use of MALDI-TOF MS in prenatal genomics.
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Affiliation(s)
- Xiao Yan Zhong
- Laboratory for Prenatal Medicine and Gynaecological Oncology, University Women's Hospital /Department Research, University of Basel, Switzerland
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35
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Radpour R, Kohler C, Haghighi MM, Fan AXC, Holzgreve W, Zhong XY. Methylation profiles of 22 candidate genes in breast cancer using high-throughput MALDI-TOF mass array. Oncogene 2009; 28:2969-78. [PMID: 19503099 DOI: 10.1038/onc.2009.149] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Alterations of DNA methylation patterns have been suggested as biomarkers for diagnostics and therapy of cancers. Every novel discovery in the epigenetic landscape and every development of an improved approach for accurate analysis of the events may offer new opportunity for the management of patients. Using a novel high-throughput mass spectrometry on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) silico-chips, we determined semiquantitative methylation changes of 22 candidate genes in breast cancer tissues. For the first time we analysed the methylation status of a total of 42 528 CpG dinucleotides on 22 genes in 96 different paraffin-embedded tissues (48 breast cancerous tissues and 48 paired normal tissues). A two-way hierarchical cluster analysis was used to classify methylation profiles. In this study, 10 hypermethylated genes (APC, BIN1, BMP6, BRCA1, CST6, ESRb, GSTP1, P16, P21 and TIMP3) were identified to distinguish between cancerous and normal tissues according to the extent of methylation. Individual assessment of the methylation status for each CpG dinucleotide indicated that cytosine hypermethylation in the cancerous tissue samples was mostly located near the consensus sequences of the transcription factor binding sites. These hypermethylated genes may serve as biomarkers for clinical molecular diagnosis and targeted treatments of patients with breast cancer.
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Affiliation(s)
- R Radpour
- Laboratory for Prenatal Medicine and Gynecologic Oncology, Women's Hospital/Department of Biomedicine, University of Basel, Basel, Switzerland
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Vasilatos SN, Broadwater G, Barry WT, Baker JC, Lem S, Dietze EC, Bean GR, Bryson AD, Pilie PG, Goldenberg V, Skaar D, Paisie C, Torres-Hernandez A, Grant TL, Wilke LG, Ibarra-Drendall C, Ostrander JH, D'Amato NC, Zalles C, Jirtle R, Weaver VM, Seewaldt VL. CpG island tumor suppressor promoter methylation in non-BRCA-associated early mammary carcinogenesis. Cancer Epidemiol Biomarkers Prev 2009; 18:901-14. [PMID: 19258476 DOI: 10.1158/1055-9965.epi-08-0875] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Only 5% of all breast cancers are the result of BRCA1/2 mutations. Methylation silencing of tumor suppressor genes is well described in sporadic breast cancer; however, its role in familial breast cancer is not known. METHODS CpG island promoter methylation was tested in the initial random periareolar fine-needle aspiration sample from 109 asymptomatic women at high risk for breast cancer. Promoter methylation targets included RARB (M3 and M4), ESR1, INK4a/ARF, BRCA1, PRA, PRB, RASSF1A, HIN-1, and CRBP1. RESULTS Although the overall frequency of CpG island promoter methylation events increased with age (P<0.0001), no specific methylation event was associated with age. In contrast, CpG island methylation of RARB M4 (P=0.051), INK4a/ARF (P=0.042), HIN-1 (P=0.044), and PRA (P=0.032), as well as the overall frequency of methylation events (P=0.004), was associated with abnormal Masood cytology. The association between promoter methylation and familial breast cancer was tested in 40 unaffected premenopausal women in our cohort who underwent BRCA1/2 mutation testing. Women with BRCA1/2 mutations had a low frequency of CpG island promoter methylation (15 of 15 women had <or=4 methylation events), whereas women without a mutation showed a high frequency of promoter methylation events (24 of 25 women had 5-8 methylation events; P<0.0001). Of women with a BRCA1/2 mutation, none showed methylation of HIN-1 and only 1 of 15 women showed CpG island methylation of RARB M4, INK4a/ARF, or PRB promoters. CONCLUSIONS This is the first evidence of CpG island methylation of tumor suppressor gene promoters in non-BRCA1/2 familial breast cancer.
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Affiliation(s)
- Shauna N Vasilatos
- Department of Medicine, Duke University Medical Center, Box 2628, Durham, NC 27710, USA
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Dellon AL, Mackinnon SE, Lu Q, Bitzer J, Zheng H, Toniolo P, Lenner P, Zhong XY. Musculoaponeurotic variations along the course of the median nerve in the proximal forearm. BMC Cancer 1988; 12:244. [PMID: 22695536 PMCID: PMC3437205 DOI: 10.1186/1471-2407-12-244] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 05/31/2012] [Indexed: 12/29/2022] Open
Abstract
31 cadaver arms have been dissected to study the variations in the anatomy of the muscles and fibrous arches which might cause compression of the median nerve in the forearm. Pronator teres always had a superficial head and usually a deep head. Flexor digitorum superficialis varied greatly in its site of origin. The median nerve might be crossed by two, one or no fibro-aponeurotic arches. Gantzer's muscle, an accessory head of flexor pollicis longus, was present in 45% of cadavers. No ligament of Struthers was found. Possible sites and causes of nerve compression are discussed.
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Affiliation(s)
- A L Dellon
- Department of Plastic Surgery, Johns Hopkins Hospital, Baltimore, Maryland
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