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Passarella D, Ciampi S, Di Liberto V, Zuccarini M, Ronci M, Medoro A, Foderà E, Frinchi M, Mignogna D, Russo C, Porcile C. Low-Density Lipoprotein Receptor-Related Protein 8 at the Crossroad between Cancer and Neurodegeneration. Int J Mol Sci 2022; 23:ijms23168921. [PMID: 36012187 PMCID: PMC9408729 DOI: 10.3390/ijms23168921] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
The low-density-lipoprotein receptors represent a family of pleiotropic cell surface receptors involved in lipid homeostasis, cell migration, proliferation and differentiation. The family shares common structural features but also has significant differences mainly due to tissue-specific interactors and to peculiar proteolytic processing. Among the receptors in the family, recent studies place low-density lipoprotein receptor-related protein 8 (LRP8) at the center of both neurodegenerative and cancer-related pathways. From one side, its overexpression has been highlighted in many types of cancer including breast, gastric, prostate, lung and melanoma; from the other side, LRP8 has a potential role in neurodegeneration as apolipoprotein E (ApoE) and reelin receptor, which are, respectively, the major risk factor for developing Alzheimer’s disease (AD) and the main driver of neuronal migration, and as a γ-secretase substrate, the main enzyme responsible for amyloid formation in AD. The present review analyzes the contributions of LDL receptors, specifically of LRP8, in both cancer and neurodegeneration, pointing out that depending on various interactions and peculiar processing, the receptor can contribute to both proliferative and neurodegenerative processes.
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Affiliation(s)
- Daniela Passarella
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy
| | - Silvia Ciampi
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy
| | - Valentina Di Liberto
- Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, 90133 Palermo, Italy
| | - Mariachiara Zuccarini
- Department of Medical Oral and Biotechnological Sciences, University of Chieti-Pescara, 66100 Chieti, Italy
| | - Maurizio Ronci
- Department of Pharmacy, University of Chieti-Pescara, 66100 Chieti, Italy
| | - Alessandro Medoro
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy
| | - Emanuele Foderà
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy
| | - Monica Frinchi
- Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, 90133 Palermo, Italy
| | - Donatella Mignogna
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy
| | - Claudio Russo
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy
- Correspondence: ; Tel.: +39-0874404897
| | - Carola Porcile
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy
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2
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Benetatos L, Benetatou A, Vartholomatos G. Epialleles and epiallelic heterogeneity in hematological malignancies. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:139. [PMID: 35834015 DOI: 10.1007/s12032-022-01737-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/22/2022] [Indexed: 10/17/2022]
Abstract
DNA methylation has a well-established role in the pathogenesis, prognosis, and response to treatment in all the spectra of hematological malignancies. However, most of the data reported involve average DNA methylation observed in a sample. The emergence of bisulfite sequencing methods such as enhanced reduced representation that permit analyze adjacent CpGs led to exciting findings. Among these are the epialleles shift and the resulting epigenetic heterogeneity observed in leukemias and lymphomas. Epialleles seem to have an influential role as the cause of mutations that characterize leukemias, may stratify groups with different prognosis and response to treatment, and may be redistributed in the genome at different time points of the disease promoting activation of alternate transcriptional networks. Epiallelic shift may be responsible for the intratumor heterogeneity observed within the cells of the same tumor which increases with disease aggressiveness. It may also responsible for the interpatient heterogeneity explaining why blood cancers exhibit different behavior among different patients. Understanding better epiallelic conformation and the consequent chromatin conformational changes and the pathways that may be affected will permit deeper understanding of hematological malignancies pathogenesis and treatment.
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Affiliation(s)
- Leonidas Benetatos
- Blood Bank, Preveza General Hospital, Selefkias 2, 48100, Preveza, Greece.
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3
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Poppova L, Pavlova S, Gonzalez B, Kotaskova J, Plevova K, Dumbovic G, Janovska P, Bystry V, Panovska A, Bezdekova L, Maslejova S, Brychtova Y, Doubek M, Krzyzankova M, Borsky M, Mayer J, Bryja V, Alonso S, Pospisilova S. Memory B-cell like chronic lymphocytic leukaemia is associated with specific methylation profile of WNT5A promoter and undetectable expression of WNT5A gene. Epigenetics 2022; 17:1628-1635. [PMID: 35333703 PMCID: PMC9621079 DOI: 10.1080/15592294.2022.2050004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Genome methylation profiles define naïve-like (n-CLL), memory-like (m-CLL), and intermediate (i-CLL) subsets of chronic lymphocytic leukaemia (CLL). The profiles can be easily determined by the analysis of the five-CpG signature. m-CLL, i-CLL, and n-CLL with the good, intermediate, and poor prognoses, respectively, differ by the somatic hypermutation status of the immunoglobulin heavy chain variable gene (IGHV), a widely used prognostic predictor in CLL. We have previously shown that the expression of WNT5A, encoding a ROR1 ligand, distinguishes patients with the worse outcome within the prognostically favourable IGHV-mutated subgroup. To analyse the mechanisms controlling WNT5A expression, we investigated the methylation status of 54 CpG sites within the WNT5A promoter and its relation to the WNT5A gene expression. In a cohort of 59 CLL patients balanced for combinations of IGHV and WNT5A statuses, we identified three promoter CpG sites whose methylation level correlated with the WNT5A expression within the IGHV-mutated subgroup. Further, we complemented our data with the methylation status of the five-CpG signature. IGHV-mutated/WNT5A-negative and IGHV-mutated/WNT5A-positive cases overlapped with m‑CLL and i‑CLL methylation subgroups, respectively, while most IGHV‑unmutated samples were assigned to n-CLL. Median methylation levels of all the three CpG sites in the WNT5A promoter were lowest in i-CLL. Finally, a detailed analysis of m-CLL and i-CLL showed that undetectable WNT5A expression predicts longer treatment-free survival with higher statistical significance than the classification according to the five-CpG signature. To conclude, a favourable m-CLL subgroup is associated with mutated IGHV and undetectable WNT5A expression due to its promoter methylation.
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Affiliation(s)
- Lucie Poppova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Sarka Pavlova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Beatriz Gonzalez
- IGTP-PMPPC: Program of Predictive and Personalized Medicine of Cancer, Germans Trias I Pujol Research Institute, Badalona, Spain
| | - Jana Kotaskova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Institute of Medical Genetics and Genomics, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Gabrijela Dumbovic
- IGTP-PMPPC: Program of Predictive and Personalized Medicine of Cancer, Germans Trias I Pujol Research Institute, Badalona, Spain.,Institute for Cardiovascular Regeneration, Center for Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Pavlina Janovska
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Vojtech Bystry
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Anna Panovska
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lucie Bezdekova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Stanislava Maslejova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Yvona Brychtova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michael Doubek
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Institute of Medical Genetics and Genomics, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marcela Krzyzankova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Marek Borsky
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jiri Mayer
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Vitezslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Sergio Alonso
- IGTP-PMPPC: Program of Predictive and Personalized Medicine of Cancer, Germans Trias I Pujol Research Institute, Badalona, Spain
| | - Sarka Pospisilova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Institute of Medical Genetics and Genomics, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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4
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Calvier L, Herz J, Hansmann G. Interplay of Low-Density Lipoprotein Receptors, LRPs, and Lipoproteins in Pulmonary Hypertension. JACC Basic Transl Sci 2022; 7:164-180. [PMID: 35257044 PMCID: PMC8897182 DOI: 10.1016/j.jacbts.2021.09.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 12/21/2022]
Abstract
LDLR regulates oxidized LDL level, which is increased in lung and blood from PAH patients. LRP1 preserving vascular homeostasis is decreased in PAH patients. LRP5/6 regulating Wnt signaling is upregulated in PH. The LRP8 (aka ApoER2) ligand ApoE protects from PAH.
The low-density lipoprotein receptor (LDLR) gene family includes LDLR, very LDLR, and LDL receptor–related proteins (LRPs) such as LRP1, LRP1b (aka LRP-DIT), LRP2 (aka megalin), LRP4, and LRP5/6, and LRP8 (aka ApoER2). LDLR family members constitute a class of closely related multifunctional, transmembrane receptors, with diverse functions, from embryonic development to cancer, lipid metabolism, and cardiovascular homeostasis. While LDLR family members have been studied extensively in the systemic circulation in the context of atherosclerosis, their roles in pulmonary arterial hypertension (PAH) are understudied and largely unknown. Endothelial dysfunction, tissue infiltration of monocytes, and proliferation of pulmonary artery smooth muscle cells are hallmarks of PAH, leading to vascular remodeling, obliteration, increased pulmonary vascular resistance, heart failure, and death. LDLR family members are entangled with the aforementioned detrimental processes by controlling many pathways that are dysregulated in PAH; these include lipid metabolism and oxidation, but also platelet-derived growth factor, transforming growth factor β1, Wnt, apolipoprotein E, bone morpohogenetic proteins, and peroxisome proliferator-activated receptor gamma. In this paper, we discuss the current knowledge on LDLR family members in PAH. We also review mechanisms and drugs discovered in biological contexts and diseases other than PAH that are likely very relevant in the hypertensive pulmonary vasculature and the future care of patients with PAH or other chronic, progressive, debilitating cardiovascular diseases.
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Key Words
- ApoE, apolipoprotein E
- Apoer2
- BMP
- BMPR, bone morphogenetic protein receptor
- BMPR2
- COPD, chronic obstructive pulmonary disease
- CTGF, connective tissue growth factor
- HDL, high-density lipoprotein
- KO, knockout
- LDL receptor related protein
- LDL, low-density lipoprotein
- LDLR
- LDLR, low-density lipoprotein receptor
- LRP
- LRP, low-density lipoprotein receptor–related protein
- LRP1
- LRP1B
- LRP2
- LRP4
- LRP5
- LRP6
- LRP8
- MEgf7
- Mesd, mesoderm development
- PAH
- PAH, pulmonary arterial hypertension
- PASMC, pulmonary artery smooth muscle cell
- PDGF
- PDGFR-β, platelet-derived growth factor receptor-β
- PH, pulmonary hypertension
- PPARγ
- PPARγ, peroxisome proliferator-activated receptor gamma
- PVD
- RV, right ventricle/ventricular
- RVHF
- RVSP, right ventricular systolic pressure
- TGF-β1
- TGF-β1, transforming growth factor β1
- TGFBR, transforming growth factor β1 receptor
- TNF, tumor necrosis factor receptor
- VLDLR
- VLDLR, very low density lipoprotein receptor
- VSMC, vascular smooth muscle cell
- Wnt
- apolipoprotein E receptor 2
- endothelial cell
- gp330
- low-density lipoprotein receptor
- mRNA, messenger RNA
- megalin
- monocyte
- multiple epidermal growth factor-like domains 7
- pulmonary arterial hypertension
- pulmonary vascular disease
- right ventricle heart failure
- smooth muscle cell
- very low density lipoprotein receptor
- β-catenin
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Affiliation(s)
- Laurent Calvier
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Center for Translational Neurodegeneration Research, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Joachim Herz
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Center for Translational Neurodegeneration Research, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Georg Hansmann
- Department of Pediatric Cardiology and Critical Care, Hannover Medical School, Hannover, Germany.,Pulmonary Vascular Research Center, Hannover Medical School, Hannover, Germany
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5
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Sheng M, Cai H, Yang Q, Li J, Zhang J, Liu L. A Random Walk-Based Method to Identify Candidate Genes Associated With Lymphoma. Front Genet 2021; 12:792754. [PMID: 34899868 PMCID: PMC8655984 DOI: 10.3389/fgene.2021.792754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022] Open
Abstract
Lymphoma is a serious type of cancer, especially for adolescents and elder adults, although this malignancy is quite rare compared with other types of cancer. The cause of this malignancy remains ambiguous. Genetic factor is deemed to be highly associated with the initiation and progression of lymphoma, and several genes have been related to this disease. Determining the pathogeny of lymphoma by identifying the related genes is important. In this study, we presented a random walk-based method to infer the novel lymphoma-associated genes. From the reported 1,458 lymphoma-associated genes and protein–protein interaction network, raw candidate genes were mined by using the random walk with restart algorithm. The determined raw genes were further filtered by using three screening tests (i.e., permutation, linkage, and enrichment tests). These tests could control false-positive genes and screen out essential candidate genes with strong linkages to validate the lymphoma-associated genes. A total of 108 inferred genes were obtained. Analytical results indicated that some inferred genes, such as RAC3, TEC, IRAK2/3/4, PRKCE, SMAD3, BLK, TXK, PRKCQ, were associated with the initiation and progression of lymphoma.
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Affiliation(s)
- Minjie Sheng
- Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Haiying Cai
- Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qin Yang
- Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jing Li
- Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jian Zhang
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai, China.,Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China.,National Clinical Research Center for Eye Diseases, Shanghai, China.,Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, China
| | - Lihua Liu
- Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
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6
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Príncipe C, Dionísio de Sousa IJ, Prazeres H, Soares P, Lima RT. LRP1B: A Giant Lost in Cancer Translation. Pharmaceuticals (Basel) 2021; 14:836. [PMID: 34577535 PMCID: PMC8469001 DOI: 10.3390/ph14090836] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/14/2021] [Accepted: 08/16/2021] [Indexed: 12/23/2022] Open
Abstract
Low-density lipoprotein receptor-related protein 1B (LRP1B) is a giant member of the LDLR protein family, which includes several structurally homologous cell surface receptors with a wide range of biological functions from cargo transport to cell signaling. LRP1B is among the most altered genes in human cancer overall. Found frequently inactivated by several genetic and epigenetic mechanisms, it has mostly been regarded as a putative tumor suppressor. Still, limitations in LRP1B studies exist, in particular associated with its huge size. Therefore, LRP1B expression and function in cancer remains to be fully unveiled. This review addresses the current understanding of LRP1B and the studies that shed a light on the LRP1B structure and ligands. It goes further in presenting increasing knowledge brought by technical and methodological advances that allow to better manipulate LRP1B expression in cells and to more thoroughly explore its expression and mutation status. New evidence is pushing towards the increased relevance of LRP1B in cancer as a potential target or translational prognosis and response to therapy biomarker.
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Affiliation(s)
- Catarina Príncipe
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (C.P.); (H.P.); (P.S.)
- Cancer Signalling and Metabolism Group, IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Isabel J. Dionísio de Sousa
- Department of Oncology, Centro Hospitalar Universitário de São João, 4200-450 Porto, Portugal;
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Hugo Prazeres
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (C.P.); (H.P.); (P.S.)
- IPO-Coimbra, Portuguese Oncology Institute of Coimbra, 3000-075 Coimbra, Portugal
| | - Paula Soares
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (C.P.); (H.P.); (P.S.)
- Cancer Signalling and Metabolism Group, IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Raquel T. Lima
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (C.P.); (H.P.); (P.S.)
- Cancer Signalling and Metabolism Group, IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
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7
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Brown LC, Tucker MD, Sedhom R, Schwartz EB, Zhu J, Kao C, Labriola MK, Gupta RT, Marin D, Wu Y, Gupta S, Zhang T, Harrison MR, George DJ, Alva A, Antonarakis ES, Armstrong AJ. LRP1B mutations are associated with favorable outcomes to immune checkpoint inhibitors across multiple cancer types. J Immunother Cancer 2021; 9:e001792. [PMID: 33653800 PMCID: PMC7929846 DOI: 10.1136/jitc-2020-001792] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Low-density lipoprotein receptor-related protein 1b (encoded by LRP1B) is a putative tumor suppressor, and preliminary evidence suggests LRP1B-mutated cancers may have improved outcomes with immune checkpoint inhibitors (ICI). METHODS We conducted a multicenter, retrospective pan-cancer analysis of patients with LRP1B alterations treated with ICI at Duke University, Johns Hopkins University (JHU) and University of Michigan (UM). The primary objective was to assess the association between overall response rate (ORR) to ICI and pathogenic or likely pathogenic (P/LP) LRP1B alterations compared with LRP1B variants of unknown significance (VUS). Secondary outcomes were the associations with progression-free survival (PFS) and overall survival (OS) by LRP1B status. RESULTS We identified 101 patients (44 Duke, 35 JHU, 22 UM) with LRP1B alterations who were treated with ICI. The most common tumor types by alteration (P/LP vs VUS%) were lung (36% vs 49%), prostate (9% vs 7%), sarcoma (5% vs 7%), melanoma (9% vs 0%) and breast cancer (3% vs 7%). The ORR for patients with LRP1B P/LP versus VUS alterations was 54% and 13%, respectively (OR 7.5, 95% CI 2.9 to 22.3, p=0.0009). P/LP LRP1B alterations were associated with longer PFS (HR 0.42, 95% CI 0.26 to 0.68, p=0.0003) and OS (HR 0.62, 95% CI 0.39 to 1.01, p=0.053). These results remained consistent when excluding patients harboring microsatellite instability (MSI) and controlling for tumor mutational burden (TMB). CONCLUSIONS This multicenter study shows significantly better outcomes with ICI therapy in patients harboring P/LP versus VUS LRP1B alterations, independently of TMB/MSI status. Further mechanistic and prospective validation studies are warranted.
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Affiliation(s)
- Landon C Brown
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Matthew D Tucker
- Internal Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ramy Sedhom
- Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Eric B Schwartz
- Division of Hematology Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason Zhu
- Levine Cancer Institute, Charlotte, North Carolina, USA
| | - Chester Kao
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Matthew K Labriola
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Rajan T Gupta
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Daniele Marin
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Yuan Wu
- Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, USA
| | - Santosh Gupta
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Tian Zhang
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Michael R Harrison
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Daniel J George
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Ajjai Alva
- Division of Hematology Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Emmanuel S Antonarakis
- Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Andrew J Armstrong
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
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8
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Rosén A, Bergh AC, Gogok P, Evaldsson C, Myhrinder AL, Hellqvist E, Rasul A, Björkholm M, Jansson M, Mansouri L, Liu A, Teh BT, Rosenquist R, Klein E. Lymphoblastoid cell line with B1 cell characteristics established from a chronic lymphocytic leukemia clone by in vitro EBV infection. Oncoimmunology 2021; 1:18-27. [PMID: 22720208 PMCID: PMC3376971 DOI: 10.4161/onci.1.1.18400] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) cells express the receptor for Epstein-Barr virus (EBV) and can be infected in vitro. Infected cells do not express the growth-promoting set of EBV-encoded genes and therefore they do not yield LCLs, in most experiments. With exceptional clones, lines were obtained however. We describe a new line, HG3, established by in vitro EBV-infection from an IGHV1–2 unmutated CLL patient clone. All cells expressed EBNA-2 and LMP-1, the EBV-encoded genes pivotal for transformation. The karyotype, FISH cytogenetics and SNP-array profile of the line and the patient's ex vivo clone showed biallelic 13q14 deletions with genomic loss of DLEU7, miR15a/miR16–1, the two micro-RNAs that are deleted in 50% of CLL cases. Further features of CLL cells were: expression of CD5/CD20/CD27/CD43 and release of IgM natural antibodies reacting with oxLDL-like epitopes on apoptotic cells (cf. stereotyped subset-1). Comparison with two LCLs established from normal B cells showed 32 genes expressed at higher levels (> 2-fold). Among these were LHX2 and LILRA. These genes may play a role in the development of the disease. LHX2 expression was shown in self-renewing multipotent hematopoietic stem cells, and LILRA4 codes for a receptor for bone marrow stromal cell antigen-2 that contributes to B cell development. Twenty-four genes were expressed at lower levels, among these PARD3 that is essential for asymmetric cell division. These genes may contribute to establish precursors of CLL clones by regulation of cellular phenotype in the hematopoietic compartment. Expression of CD5/CD20/CD27/CD43 and spontaneous production of natural antibodies may identify the CLL cell as a self-renewing B1 lymphocyte.
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Affiliation(s)
- Anders Rosén
- Department of Clinical and Experimental Medicine; Division of Cell Biology; Linköping University; Linköping, Sweden
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9
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Chung HH, Lee CT, Hu JM, Chou YC, Lin YW, Shih YL. NKX6.1 Represses Tumorigenesis, Metastasis, and Chemoresistance in Colorectal Cancer. Int J Mol Sci 2020; 21:ijms21145106. [PMID: 32707737 PMCID: PMC7404324 DOI: 10.3390/ijms21145106] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 12/28/2022] Open
Abstract
Accumulating evidence suggests that NKX6.1 (NK homeobox 1) plays a role in various types of cancer. In our previous studies, we identified NKX6.1 hypermethylation as a promising marker and demonstrated that the NKX6.1 gene functions as a metastasis suppressor through the epigenetic regulation of the epithelial-to-mesenchymal transition (EMT) in cervical cancer. More recently, we have demonstrated that NKX6.1 methylation is related to the chemotherapy response in colorectal cancer (CRC). Nevertheless, the biological function of NKX6.1 in the tumorigenesis of CRC remains unclear. In this study, we showed that NKX6.1 suppresses tumorigenic and metastatic ability both in vitro and in vivo. NKX6.1 represses cell invasion partly through the modulation of EMT. The overexpression of NKX6.1 enhances chemosensitivity in CRC cells. To further explore how NKX6.1 exerts its tumor-suppressive function, we used RNA sequencing technology for comprehensive analysis. The results showed that differentially expressed genes (DEGs) were mainly related to cell migration, response to drug, transcription factor activity, and growth factor activity, suggesting that these DEGs are involved in the function of NKX6.1 suppressing cancer invasion and metastasis. Our results demonstrated that NKX6.1 functions as a tumor suppressor partly by repressing EMT and enhancing chemosensitivity in CRC, making it a potential therapeutic target.
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Affiliation(s)
- Hsin-Hua Chung
- Graduate Institute of Medical Sciences, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan; (H.-H.C.); (J.-M.H.); (Y.-W.L.)
| | - Chun-Te Lee
- Division of Urological Surgery, Department of Surgery, Tri-Service General Hospital Songshan Branch, No.131, Jiankang Rd., Songshan District, Taipei 10581, Taiwan;
| | - Je-Ming Hu
- Graduate Institute of Medical Sciences, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan; (H.-H.C.); (J.-M.H.); (Y.-W.L.)
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, No.325, Sec.2, Chenggong Rd., Neihu District, Taipei 11490, Taiwan
| | - Yu-Ching Chou
- School of Public Health, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan;
| | - Ya-Wen Lin
- Graduate Institute of Medical Sciences, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan; (H.-H.C.); (J.-M.H.); (Y.-W.L.)
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan
| | - Yu-Lueng Shih
- Graduate Institute of Medical Sciences, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan; (H.-H.C.); (J.-M.H.); (Y.-W.L.)
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu District, Taipei 11490, Taiwan
- Correspondence: ; Tel./Fax: +886-2-87917654
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10
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Li J, Li X. Comprehensive analysis of prognosis-related methylated sites in breast carcinoma. Mol Genet Genomic Med 2020; 8:e1161. [PMID: 32037691 PMCID: PMC7196449 DOI: 10.1002/mgg3.1161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/20/2019] [Accepted: 01/23/2020] [Indexed: 12/26/2022] Open
Abstract
Background Breast carcinoma has become a nonnegligible public health problem in China with its increasing incidence and mortality in woman. As a early event regulating tumorigenesis and development, DNA methylation became one of the focuses of current carcinoma researches on potential diagnostic and therapeutic targets. Methods In this study, we comprehensively analyzed the gene expression data and DNA methylation data of breast carcinoma and adjacent normal tissues samples in the Gene Expression Omnibus database. Influences of tumor stage, adjuvant therapy, hormone therapy, and chemotherapy on CpG methylation level were explored by linear regression analysis. Correlations between methylation and gene expression levels were determined by spearman rank correlation analysis. Log‐rank test was applied for determining significance of associations between CpG sites methylation level and breast cancer patients' Kaplan–Meier survival. Results A total of 229 CpG sites were found to be significantly associated with tumor stage or treatment, and eight of which were potential markers that affect the survival of breast carcinoma and negatively correlated with their genes' expression levels. Conclusions We reported eight CpG sites as potential breast cancer prognosis signatures through comprehensively analyzed gene expression and DNA methylation datasets, and excluding influences of tumor stage and treatment. This should be helpful for breast cancer early diagnosis and treatment.
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Affiliation(s)
- Jia Li
- Department of Breast Surgery, Shanxi Provincial Cancer Hospital, Taiyuan, P.R. China
| | - Xinzheng Li
- Department of Breast Surgery, Shanxi Provincial Cancer Hospital, Taiyuan, P.R. China
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11
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Dunbar F, Xu H, Ryu D, Ghosh S, Shi H, George V. Detection of Differentially Methylated Regions Using Bayes Factor for Ordinal Group Responses. Genes (Basel) 2019; 10:genes10090721. [PMID: 31533352 PMCID: PMC6770971 DOI: 10.3390/genes10090721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/11/2019] [Accepted: 09/15/2019] [Indexed: 11/16/2022] Open
Abstract
Researchers in genomics are increasingly interested in epigenetic factors such as DNA methylation, because they play an important role in regulating gene expression without changes in the DNA sequence. There have been significant advances in developing statistical methods to detect differentially methylated regions (DMRs) associated with binary disease status. Most of these methods are being developed for detecting differential methylation rates between cases and controls. We consider multiple severity levels of disease, and develop a Bayesian statistical method to detect the region with increasing (or decreasing) methylation rates as the disease severity increases. Patients are classified into more than two groups, based on the disease severity (e.g., stages of cancer), and DMRs are detected by using moving windows along the genome. Within each window, the Bayes factor is calculated to test the hypothesis of monotonic increase in methylation rates corresponding to severity of the disease versus no difference. A mixed-effect model is used to incorporate the correlation of methylation rates of nearby CpG sites in the region. Results from extensive simulation indicate that our proposed method is statistically valid and reasonably powerful. We demonstrate our approach on a bisulfite sequencing dataset from a chronic lymphocytic leukemia (CLL) study.
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Affiliation(s)
- Fengjiao Dunbar
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA.
| | - Hongyan Xu
- Department of Population Health Sciences, Augusta University, Augusta, GA 30912, USA.
| | - Duchwan Ryu
- Department of Statistics and Actuarial Science, Northern Illinois University, DeKalb, IL 60178, USA.
| | - Santu Ghosh
- Department of Population Health Sciences, Augusta University, Augusta, GA 30912, USA.
| | - Huidong Shi
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA.
| | - Varghese George
- Department of Population Health Sciences, Augusta University, Augusta, GA 30912, USA.
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12
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Sun J, Zhang J, Wang Y, Li Y, Zhang R. A Pilot Study of Aberrant CpG Island Hypermethylation of SPRED1 in Acute Myeloloid Leukemia. Int J Med Sci 2019; 16:324-330. [PMID: 30745814 PMCID: PMC6367533 DOI: 10.7150/ijms.27757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/13/2018] [Indexed: 12/15/2022] Open
Abstract
Background: Epigenetic silencing of tumor suppressor genes plays important role in acute myeloid leukemia (AML). Recently, SPRED1, a negative regulator of the RAS MAPK pathway, is identified as a tumour suppressor downregulated in AML. However, little is known regarding its underlying dysregulation in AML. In this study, we investigated methylation status of SPRED1 promoters and their association with mRNA levels in AML. Methods: Methylation level were measured in four regions of SPRED1 (#1: 310 bp ~ 723 bp, #2: 810 bp ~ 1299 bp, #3: 1280 bp ~ 1742 bp and #4: 1715 bp ~ 2059 bp) in a total of 16 patients with de novonon-acute promyelocytic leukemia (non-APL) and three patients who got complete remission after induction treatment using the Sequenom MassARRAY platform. Quantitative real-time polymerase chain reaction (q-RT PCR) was used to analyze SPRED1 mRNA levels. Results: AML patients had a significantly higher average methylation level than controls at regions of #1_CpG_1 (p= 0.04) and #1_CpG_11 (p =0.002). The methylation values for #1_CpG_11 were negatively correlated with mRNA levels (r= -0.558, p=0.013) but there was no significant association between #1_CpG_1 methylation status and mRNA levels (r=-0.103, p=0.675) in AML patients. There was no significant difference in the methylation level when comparing with clinical biochemical parameters and treatment response (p>0.05). Mutations of epigenetic regulation genes such as DNMT3A, TET2 and IDH1/2 were most frequently observed in patients with higher methylation levels. Decreased methylation levels were revealed in three patients who got complete remission. Conclusions: Aberrant methylation statuses of the SPRED1 promoter regions are associated with the downregulation of gene transcription in AML. The methylation level is probably associated with the treatment response of AML. Mutations of epigenetic regulation genes might be involved in the epigenetic aberration of SPRED1.
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Affiliation(s)
- Jingwen Sun
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, 110001, China
| | - Jinjing Zhang
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, 110001, China
| | - Yue Wang
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, 110001, China
| | - Yan Li
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, 110001, China
| | - Rui Zhang
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, 110001, China
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13
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Expression of a recombinant full-length LRP1B receptor in human non-small cell lung cancer cells confirms the postulated growth-suppressing function of this large LDL receptor family member. Oncotarget 2018; 7:68721-68733. [PMID: 27626682 PMCID: PMC5356585 DOI: 10.18632/oncotarget.11897] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 08/13/2016] [Indexed: 12/26/2022] Open
Abstract
Low-density lipoprotein (LDL) receptor-related protein 1B (LRP1B), a member of the LDL receptor family, is frequently inactivated in multiple malignancies including lung cancer. LRP1B is therefore considered as a putative tumor suppressor. Due to its large size (4599 amino acids), until now only minireceptors or receptor fragments have been successfully cloned. To assess the effect of LRP1B on the proliferation of non-small cell lung cancer cells, we constructed and expressed a transfection vector containing the 13.800 bp full-length murine Lrp1b cDNA using a PCR-based cloning strategy. Expression of LRP1B was analyzed by quantitative RT-PCR (qRT-PCR) using primers specific for human LRP1B or mouse Lrp1b. Effective expression of the full length receptor was demonstrated by the appearance of a single 600 kDa band on Western Blots of HEK 293 cells. Overexpression of Lrp1b in non-small cell lung cancer cells with low or absent endogenous LRP1B expression significantly reduced cellular proliferation compared to empty vector-transfected control cells. Conversely, in Calu-1 cells, which express higher endogenous levels of the receptor, siRNA-mediated LRP1B knockdown significantly enhanced cellular proliferation. Taken together, these findings demonstrate that, consistent with the postulated tumor suppressor function, overexpression of full-length Lrp1b leads to impaired cellular proliferation, while LRP1B knockdown has the opposite effect. The recombinant Lrp1b construct represents a valuable tool to unravel the largely unknown physiological role of LRP1B and its potential functions in cancer pathogenesis.
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14
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Chang SY, Kuo CC, Wu CC, Hsiao CW, Hu JM, Hsu CH, Chou YC, Shih YL, Lin YW. NKX6.1 hypermethylation predicts the outcome of stage II colorectal cancer patients undergoing chemotherapy. Genes Chromosomes Cancer 2018; 57:268-277. [PMID: 29363224 DOI: 10.1002/gcc.22529] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 12/16/2022] Open
Abstract
Colorectal cancer (CRC) is a common malignancy worldwide. CRC patients in the same stage often present with dramatically different clinical scenarios. Thus, robust prognostic biomarkers are urgently needed to guide therapies and improve treatment outcomes. The NKX6.1 gene has been identified as a hypermethylation marker in cervical cancer, functioning as a metastasis suppressor by regulating epithelial-mesenchymal transition. Here, we investigated whether hypermethylation of NKX6.1 might be a prognostic biomarker for CRC. By analyzing the methylation and expression of NKX6.1 in CRC tissues and CRC cell lines. We quantitatively examined the NKX6.1 methylation levels in 151 pairs of CRC tissues by using methylation-specific polymerase chain reaction analysis and found that NKX6.1 was hypermethylated in 35 of 151 CRC tissues (23%). NKX6.1 gene expression was inversely correlated with the DNA methylation level in CRC cell lines in vitro. Then, we analyzed the association of NKX6.1 methylation with clinical characteristics of these CRC patients. Our data demonstrated that patients with NKX6.1 methylation presented poorer 5-year overall survival (P = 0.0167) and disease-free survival (P = 0.0083) than patients without NKX6.1 methylation after receiving adjuvant chemotherapy. Most importantly, these data revealed that stage II CRC patients with NKX6.1 methylation had poorer 5-year disease-free survival (P = 0.0322) than patients without NKX6.1 methylation after adjuvant chemotherapy. Our results demonstrate that methylation of NKX6.1 is a novel prognostic biomarker in CRC and that it may be used as a predictor of the response to chemotherapy.
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Affiliation(s)
- Sou-Yi Chang
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,Division of Hematology & Oncology, Department of Internal Medicine, Taipei Tzu Chi Hospital, Taipei, Taiwan, Republic of China
| | - Chih-Chi Kuo
- Teaching and Research Office, Tri-Service General Hospital Songshan Branch, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Chang-Chieh Wu
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Cheng-Wen Hsiao
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Je-Ming Hu
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Chih-Hsiung Hsu
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,School of Medicine, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Yu-Ching Chou
- School of Public Health, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Yu-Lueng Shih
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Ya-Wen Lin
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan, Republic of China
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15
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Soozangar N, Sadeghi MR, Jeddi F, Somi MH, Shirmohamadi M, Samadi N. Comparison of genome‐wide analysis techniques to DNA methylation analysis in human cancer. J Cell Physiol 2017; 233:3968-3981. [DOI: 10.1002/jcp.26176] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/24/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Narges Soozangar
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
- Molecular Medicine Research CenterTabriz University of Medical SciencesTabrizIran
| | - Mohammad R. Sadeghi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Farhad Jeddi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Mohammad H. Somi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Masoud Shirmohamadi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
| | - Nasser Samadi
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
- Department of Biochemistry, Faculty of MedicineTabriz University of Medical SciencesTabrizIran
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16
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Queirós AC, Beekman R, Vilarrasa-Blasi R, Duran-Ferrer M, Clot G, Merkel A, Raineri E, Russiñol N, Castellano G, Beà S, Navarro A, Kulis M, Verdaguer-Dot N, Jares P, Enjuanes A, Calasanz MJ, Bergmann A, Vater I, Salaverría I, van de Werken HJG, Wilson WH, Datta A, Flicek P, Royo R, Martens J, Giné E, Lopez-Guillermo A, Stunnenberg HG, Klapper W, Pott C, Heath S, Gut IG, Siebert R, Campo E, Martín-Subero JI. Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage. Cancer Cell 2016; 30:806-821. [PMID: 27846393 PMCID: PMC5805090 DOI: 10.1016/j.ccell.2016.09.014] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 07/18/2016] [Accepted: 09/19/2016] [Indexed: 01/17/2023]
Abstract
We analyzed the in silico purified DNA methylation signatures of 82 mantle cell lymphomas (MCL) in comparison with cell subpopulations spanning the entire B cell lineage. We identified two MCL subgroups, respectively carrying epigenetic imprints of germinal-center-inexperienced and germinal-center-experienced B cells, and we found that DNA methylation profiles during lymphomagenesis are largely influenced by the methylation dynamics in normal B cells. An integrative epigenomic approach revealed 10,504 differentially methylated regions in regulatory elements marked by H3K27ac in MCL primary cases, including a distant enhancer showing de novo looping to the MCL oncogene SOX11. Finally, we observed that the magnitude of DNA methylation changes per case is highly variable and serves as an independent prognostic factor for MCL outcome.
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Affiliation(s)
- Ana C Queirós
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Renée Beekman
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Roser Vilarrasa-Blasi
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Martí Duran-Ferrer
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Guillem Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Angelika Merkel
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Emanuele Raineri
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Nuria Russiñol
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Giancarlo Castellano
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Alba Navarro
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Marta Kulis
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain
| | - Núria Verdaguer-Dot
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Pedro Jares
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Unidad de Genómica, IDIBAPS, Barcelona 08036, Spain
| | | | | | - Anke Bergmann
- Institute of Human Genetics, Christian-Albrechts University, Kiel 24105, Germany; Department of Pediatrics, Christian-Albrechts University & University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Inga Vater
- Institute of Human Genetics, Christian-Albrechts University, Kiel 24105, Germany
| | - Itziar Salaverría
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
| | - Harmen J G van de Werken
- Department of Cell Biology, Erasmus MC, Rotterdam 3015 CN, the Netherlands; Cancer Computational Biology Center, Erasmus MC, Rotterdam 3015 CN, the Netherlands; Department of Urology, Erasmus MC, Rotterdam 3015 CN, the Netherlands
| | - Wyndham H Wilson
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Avik Datta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Romina Royo
- Joint Program on Computational Biology, Barcelona Supercomputing Center (BSC) and Institute of Research in Biomedicine (IRB), Barcelona Science Park, Barcelona 08034, Spain
| | - Joost Martens
- Molecular Biology, NCMLS, FNWI, Radboud University, Nijmegen 6500 HB, the Netherlands
| | - Eva Giné
- Servicio de Hematología, Hospital Clínic, IDIBAPS, Barcelona 08036, Spain
| | | | - Hendrik G Stunnenberg
- Molecular Biology, NCMLS, FNWI, Radboud University, Nijmegen 6500 HB, the Netherlands
| | - Wolfram Klapper
- Hematopathology Section and Lymph Node Registry, Christian-Albrecht University, Kiel 24105, Germany
| | - Christiane Pott
- Second Medical Department, University Hospital Schleswig-Holstein, Kiel 24116, Germany
| | - Simon Heath
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts University, Kiel 24105, Germany
| | - Elías Campo
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain; Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Barcelona 08036, Spain
| | - José I Martín-Subero
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain.
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17
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Lin H, Ma Y, Wei Y, Shang H. Genome-wide analysis of aberrant gene expression and methylation profiles reveals susceptibility genes and underlying mechanism of cervical cancer. Eur J Obstet Gynecol Reprod Biol 2016; 207:147-152. [PMID: 27863272 DOI: 10.1016/j.ejogrb.2016.10.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 09/09/2016] [Accepted: 10/18/2016] [Indexed: 01/11/2023]
Abstract
BACKGROUND This study aimed to explore the molecular mechanism of cervical cancer (CC) by integrated bioinformatic analyses of gene expression and methylation profiles. METHODS The gene expression and methylation microarrays in CC samples and normal controls were respectively downloaded from the GEO database. After screening the differentially expressed genes (DEGs) with Limma package and the CC-related methylation sites with CpGassoc package in R language, DEGs with CC-related methylation sites were identified from the intersection of the above two groups of results with 50kb upstream and downstream of a gene as the gene region. Then GO enrichment was performed by GenCLIP2.0 software. Sequentially, analysis of metabolic sub-pathways with pathogenic risk was predicted by iSubpathwayMiner package in R language. RESULTS A total of 1357 DEGs including 721 up-regulated and 636 down-regulated, as well as 666 CC-related methylation sites were screened out. After being analyzed, 26 DEGs with 35 CC-related methylation sites were identified. EDN3 and EDNRB were significantly involved in a function cluster in GO terms of vein smooth muscle contraction, vascular smooth muscle contraction and phasic smooth muscle contraction. LHX2 and PAX6 were significantly involved in a function cluster in GO terms of telencephalon regionalization and forebrain regionalization. ACOX3, CYP39A1 and DPYS were significantly enriched in 25 sub-pathways of 6 major pathways. CONCLUSIONS EDN3 and EDNRB might play important roles in the molecular mechanism of CC, and LHX2, ACOX3, CYP39A1 and DPYS might be susceptibility genes and potential risk markers in CC.
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Affiliation(s)
- Hongmei Lin
- Department of Gynaecology and Obstetrics, Shandong University Affiliated Jinan Center Hospital, Jinan 250013, Shandong, China
| | - Yifei Ma
- Department of Gynaecology and Obstetrics, Shandong University Affiliated Jinan Center Hospital, Jinan 250013, Shandong, China.
| | - Yongqing Wei
- Department of Gynaecology and Obstetrics, Shandong University Affiliated Jinan Center Hospital, Jinan 250013, Shandong, China
| | - Hui Shang
- Department of Gynaecology and Obstetrics, Shandong University Affiliated Jinan Center Hospital, Jinan 250013, Shandong, China
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18
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Huang LL, Zhang Y, Zhang JX, He LJ, Lai YR, Liao YJ, Tian XP, Deng HX, Liang YJ, Kung HF, Xie D, Zhu SL. Overexpression of NKX6.1 is closely associated with progressive features and predicts unfavorable prognosis in human primary hepatocellular carcinoma. Tumour Biol 2015; 36:4405-15. [PMID: 25596704 DOI: 10.1007/s13277-015-3080-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/08/2015] [Indexed: 12/24/2022] Open
Abstract
The homeobox gene NKX6.1 was recently identified in cervical tumors. This study was designed to explore the clinical and prognostic significance of NKX6.1 further in patients with primary hepatocellular carcinoma (HCC). The expression levels of NKX6.1 were examined using real-time PCR, Western blotting, and immunohistochemistry in HCC cell lines and HCC tissues. The invasion capability of cell lines following silencing or overexpression of NKX6.1 was investigated by Transwell assay. Cells proliferation was tested by MTT assays. Epithelial-mesenchymal transition (EMT) marker expression levels were detected in relation to NKX6.1 expression. Correlation between NKX6.1 immunohistochemical staining, clinicopathologic parameters, and follow-up data of HCC patients was analyzed statistically. NKX6.1 expression was higher in HCC tissues compared to the adjacent noncancerous tissue. NKX6.1 overexpression was significantly correlated with tumor size, tumor differentiation, clinical stage, metastasis, and relapse. Kaplan-Meier analysis revealed that NKX6.1 overexpression was related to unfavorable 5-year disease-free survival and overall survival. Importantly, multivariate analysis indicated that NKX6.1 overexpression was an independent unfavorable marker for overall survival. Moreover, a significant relationship was observed between NKX6.1 and EMT marker expression levels, and NKX6.1 knockdown inhibited cell invasion, and overexpression of NKX6.1 promotes cell proliferation in vitro. NKX6.1 is upregulated in HCC and is a reliable prognostic marker for patients with HCC.
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Affiliation(s)
- Lin-Lin Huang
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, China
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19
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Functional linc-POU3F3 is overexpressed and contributes to tumorigenesis in glioma. Gene 2014; 554:114-9. [PMID: 25445282 DOI: 10.1016/j.gene.2014.10.038] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 10/15/2014] [Accepted: 10/23/2014] [Indexed: 12/11/2022]
Abstract
Growing number of long intergenic noncoding RNAs (lincRNAs) have recently been identified in mammals as new modulators in cancer origination and progression involved in a broad range of biological processes. Long intergenic noncoding RNA POU3F3 (linc-POU3F3) has been characterized as a highly conserved functional transcription regulator in esophageal squamous cell carcinoma. The contributions of this lincRNA to glioblastoma remain unknown. In this present study, we investigated the expression pattern and functional role of linc-POU3F3 in glioma by using real-time PCR and gain-/loss-of-function studies. The results revealed that linc-POU3F3 levels were extraordinarily associated with the tumor WHO grade. In related biochemical assays, overexpression of linc-POU3F3 promotes cell viability and proliferation in glioma cells, whereas knockdown of linc-POU3F3 showed the opposite effect. As expected, we also found that linc-POU3F3 expression was negatively correlated with the mRNA level of POU3F3 (the evolutionarily conserved neighbor gene of linc-POU3F3). Our results indicate that linc-POU3F3 might affect glioma development via altering expression level of POU3F3, and lead us to believe that linc-POU3F3 may also have a crucial regulatory role in glioma progression.
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20
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Li W, Zheng J, Deng J, You Y, Wu H, Li N, Lu J, Zhou Y. Increased levels of the long intergenic non-protein coding RNA POU3F3 promote DNA methylation in esophageal squamous cell carcinoma cells. Gastroenterology 2014; 146:1714-26.e5. [PMID: 24631494 DOI: 10.1053/j.gastro.2014.03.002] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 02/25/2014] [Accepted: 03/04/2014] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS Thousands of long intergenic non-protein coding RNAs (lincRNAs) have been identified in mammals via genome-wide sequencing studies. Many are functional, but are expressed aberrantly by cancer cells. We investigated whether levels of lincRNAs are altered during the development of esophageal squamous cell carcinoma (ESCC). METHODS We used quantitative real-time polymerase chain reaction to measure levels of 26 highly conserved lincRNAs in ESCC and surrounding nontumor tissues. A total of 182 ESCC and paired adjacent nontumor tissue samples were collected from patients undergoing tylectomy at The First Affiliate Hospital of Soochow University from 2001 through 2009; another 178 ESCC tissue pairs were collected from Guangzhou Medical University from 2002 through 2009. LincRNAs were expressed from lentiviral vectors or knocked down with small hairpin RNAs in Eca-109 and TE-1 cells. RESULTS Levels of a lincRNA encoded by a gene located next to POU3F3 (linc-POU3F3) were significantly higher in ESCC than neighboring nontumor tissues. In RNA immunoprecipitation assays, linc-POU3F3 was associated with the EZH2 messenger RNA (mRNA). Overexpression of linc-POU3F3 in cell lines increased their proliferation and ability to form colonies, and reduced the expression of POU3F3 mRNA, whereas knockdown of linc-POU3F3 increased the levels of POU3F3 mRNA. CpG islands in POU3F3 were densely hypermethylated in cell lines that overexpressed linc-POU3F3; methylation at these sites was reduced by knockdown of linc-POU3F3. Pharmacologic inhibition of EZH2 increased the levels of POU3F3 mRNA and significantly reduced binding of DNA methyltransferase (DNMT)1, DNMT3A, and DNMT3B to POU3F3. ESCC cells with knockdown of linc-POU3F3 formed xenograft tumors more slowly in mice than control ESCC cells. CONCLUSIONS Levels of linc-POU3F3 are increased in ESCC samples from patients compared with nontumor tissues. This noncoding RNA contributes to the development of ESCC by interacting with EZH2 to promote methylation of POU3F3, which encodes a transcription factor.
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MESH Headings
- Adult
- Animals
- Base Sequence
- Binding Sites
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Carcinoma, Squamous Cell/surgery
- Cell Line, Tumor
- Cell Proliferation
- China
- CpG Islands
- DNA (Cytosine-5-)-Methyltransferase 1
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation/drug effects
- DNA Methyltransferase 3A
- Enhancer of Zeste Homolog 2 Protein
- Enzyme Inhibitors/pharmacology
- Esophageal Neoplasms/genetics
- Esophageal Neoplasms/metabolism
- Esophageal Neoplasms/pathology
- Esophageal Neoplasms/surgery
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Middle Aged
- Molecular Sequence Data
- POU Domain Factors/genetics
- POU Domain Factors/metabolism
- Polycomb Repressive Complex 2/antagonists & inhibitors
- Polycomb Repressive Complex 2/genetics
- Polycomb Repressive Complex 2/metabolism
- RNA, Long Noncoding/metabolism
- RNA, Messenger/metabolism
- Time Factors
- Transfection
- Tumor Burden
- Up-Regulation
- DNA Methyltransferase 3B
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Affiliation(s)
- Wei Li
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Jian Zheng
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Jieqiong Deng
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Yonghe You
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Hongchun Wu
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Na Li
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Jiachun Lu
- The Institute for Chemical Carcinogenesis, The State Key Lab of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Yifeng Zhou
- Department of Genetics, Medical College of Soochow University, Suzhou, China.
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WANG XI, HE CHAO, HU XIAOTONG. LIM homeobox transcription factors, a novel subfamily which plays an important role in cancer (Review). Oncol Rep 2014; 31:1975-85. [DOI: 10.3892/or.2014.3112] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 03/13/2014] [Indexed: 11/06/2022] Open
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22
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Bryan JN, Kumar SR, Jia F, Balkin ER, Lewis MR. Zebularine significantly sensitises MEC1 cells to external irradiation and radiopharmaceutical therapy when administered sequentially in vitro. Cell Biol Int 2014; 38:187-97. [PMID: 24323360 PMCID: PMC3947096 DOI: 10.1002/cbin.10215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/10/2013] [Indexed: 01/13/2023]
Abstract
Zebularine is a cytidine analogue incorporated into DNA during replication, inhibiting DNA methyltransferase 1 (DNMT1), resulting in demethylation and changes in gene expression. Such modification may improve radiosensitivity in resistant lymphoma cells. The hypothesis of this study was that zebularine and radiation would synergistically inhibit cell growth and viability. Human MEC1 malignant B cells were incubated with 0-200 µM zebularine for 48 h. Media containing zebularine was removed, and the cells were irradiated with 0-2 Gy of either external beam irradiation or (177) Lu-DOTA-TATE, a radiolabelled somatostatin analogue. Concentration and viability were measured over 48-72 h. The proportion of apoptotic cells was identified using an active Caspase 3/7 assay. Zebularine inhibited growth of cells in a dose-dependent manner during exposure. No residual growth inhibition occurred following removal of the drug. Zebularine and external irradiation inhibited cell proliferation in a dose-dependent, synergistic interaction, but the effect on viability was additive. Treatment with zebularine and (177) Lu-DOTA-TATE resulted in less inhibition of proliferation (P = 0.0135), but a synergistic decrease in viability. Apoptotic fraction was much higher in cells irradiated with (177) Lu-DOTA-TATE than external irradiation. External irradiation induces growth arrest rather than apoptosis. Apoptosis is the primary effect of radiopharmaceutical therapy on tumour cells. Treatment with the methylation inhibitor, zebularine, appears to synergistically augment these natural effects in vitro, which could be exploited clinically.
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Affiliation(s)
- Jeffrey N. Bryan
- Dept of Veterinary Medicine and Surgery, University of Missouri-Columbia, Columbia, MO 65211
- Research Service, Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65211
- Area of Pathobiology, University of Missouri-Columbia, Columbia MO 65211
| | - Senthil R. Kumar
- Dept of Veterinary Medicine and Surgery, University of Missouri-Columbia, Columbia, MO 65211
- Research Service, Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65211
| | - Fang Jia
- Dept of Veterinary Medicine and Surgery, University of Missouri-Columbia, Columbia, MO 65211
- Research Service, Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65211
| | - Ethan R. Balkin
- Area of Pathobiology, University of Missouri-Columbia, Columbia MO 65211
| | - Michael R. Lewis
- Dept of Veterinary Medicine and Surgery, University of Missouri-Columbia, Columbia, MO 65211
- Research Service, Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65211
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23
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Sheng W, Qian Y, Wang H, Ma X, Zhang P, Diao L, An Q, Chen L, Ma D, Huang G. DNA methylation status of NKX2-5, GATA4 and HAND1 in patients with tetralogy of fallot. BMC Med Genomics 2013; 6:46. [PMID: 24182332 PMCID: PMC3819647 DOI: 10.1186/1755-8794-6-46] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/29/2013] [Indexed: 12/21/2022] Open
Abstract
Background NKX2-5, GATA4 and HAND1 are essential for heart development, however, little is known regarding their epigenetic regulation in the pathogenesis of tetralogy of fallot (TOF). Methods Methylation levels were measured in three regions of NKX2-5 (M1: -1596 bp ~ -1374 bp, M2: -159 bp ~ 217 bp and M3: 1058 bp ~ 1524 bp), one region of GATA4 (M: -392 bp ~ 107 bp) and three regions of HAND1 (M1: -887 bp ~ -414 bp, M2: -436 bp ~ 2 bp and M3: 37 bp ~ 398 bp) using the Sequenom MassARRAY platform. QRT-PCR was used to analyze NKX2-5 and HAND1 mRNA levels in the right ventricular myocardium of TOF patients. Results TOF patients had a significantly higher NKX2-5_M3 median methylation level than controls (41.65% vs. 22.18%; p = 0.0074; interquartile range [IQR]: 30.46%–53.35%, N = 30 and 20.07%–24.31%, N = 5; respectively). The HAND1_M1 median methylation level was also significantly higher in TOF patients than controls (30.05% vs. 17.54%; p = 0.0054; IQR: 20.77%–40.89%, N = 30 and IQR: 14.69%–20.64%; N = 6; respectively). The methylation statuses of NKX2-5_M1, NKX2-5_M2, GATA4_M, HAND1_M2 or HAND1_M3 were not significantly different in TOF patients compared to controls. The methylation values for NKX2-5_M3 were negatively correlated with mRNA levels (r = - 0.463, p = 0.010, N = 30) and there was a significant association between HAND1_M1 methylation status and mRNA levels (r = - 0.524, p = 0.003, N = 30) in TOF patients. Conclusions Aberrant methylation statuses of the NKX2-5 gene body and HAND1 promoter regions are associated with the regulation of gene transcription in TOF patients and may play an important role in the pathogenesis of TOF.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Duan Ma
- Children Hospital of Fudan University, Shanghai 201102, China.
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24
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Enjuanes A, Albero R, Clot G, Navarro A, Beà S, Pinyol M, Martín-Subero JI, Klapper W, Staudt LM, Jaffe ES, Rimsza L, Braziel RM, Delabie J, Cook JR, Tubbs RR, Gascoyne R, Connors JM, Weisenburger DD, Greiner TC, Chan WC, López-Guillermo A, Rosenwald A, Ott G, Campo E, Jares P. Genome-wide methylation analyses identify a subset of mantle cell lymphoma with a high number of methylated CpGs and aggressive clinicopathological features. Int J Cancer 2013; 133:2852-63. [PMID: 23754783 DOI: 10.1002/ijc.28321] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 04/23/2013] [Indexed: 01/02/2023]
Abstract
Mantle cell lymphoma (MCL) is a B-cell neoplasm with an aggressive clinical behavior characterized by the t(11;14)(q13;q32) and cyclin D1 overexpression. To clarify the potential contribution of altered DNA methylation in the development and/or progression of MCL, we performed genome-wide methylation profiling of a large cohort of primary MCL tumors (n = 132), MCL cell lines (n = 6) and normal lymphoid tissue samples (n = 31), using the Infinium HumanMethylation27 BeadChip. DNA methylation was compared to gene expression, chromosomal alterations and clinicopathological parameters. Primary MCL displayed a heterogeneous methylation pattern dominated by DNA hypomethylation when compared to normal lymphoid samples. A total of 454 hypermethylated and 875 hypomethylated genes were identified as differentially methylated in at least 10% of primary MCL. Annotation analysis of hypermethylated genes recognized WNT pathway inhibitors and several tumor suppressor genes as frequently methylated, and a substantial fraction of these genes (22%) showed a significant downregulation of their transcriptional levels. Furthermore, we identified a subset of tumors with extensive CpG methylation that had an increased proliferation signature, higher number of chromosomal alterations and poor prognosis. Our results suggest that a subset of MCL displays a dysregulation of DNA methylation characterized by the accumulation of CpG hypermethylation highly associated with increased proliferation that may influence the clinical behavior of the tumors.
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Affiliation(s)
- Anna Enjuanes
- Genomics Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
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25
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Taylor KH, Briley A, Wang Z, Cheng J, Shi H, Caldwell CW. Aberrant Epigenetic Gene Regulation in Lymphoid Malignancies. Semin Hematol 2013; 50:38-47. [DOI: 10.1053/j.seminhematol.2013.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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26
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Mahapatra S, Klee EW, Young CYF, Sun Z, Jimenez RE, Klee GG, Tindall DJ, Donkena KV. Global methylation profiling for risk prediction of prostate cancer. Clin Cancer Res 2012; 18:2882-95. [PMID: 22589488 DOI: 10.1158/1078-0432.ccr-11-2090] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The aim of this study was to investigate the promoter hypermethylation as diagnostic markers to detect malignant prostate cells and as prognostic markers to predict the clinical recurrence of prostate cancer. EXPERIMENTAL DESIGN DNA was isolated from prostate cancer and normal adjacent tissues. After bisulfite conversion, methylation of 14,495 genes was evaluated using the Methylation27 microarrays in 238 prostate tissues. We analyzed methylation profiles in four different groups: (i) tumor (n = 198) versus matched normal tissues (n = 40), (ii) recurrence (n = 123) versus nonrecurrence (n = 75), (iii) clinical recurrence (n = 80) versus biochemical recurrence (n = 43), and (iv) systemic recurrence (n = 36) versus local recurrence (n = 44). Group 1, 2, 3, and 4 genes signifying biomarkers for diagnosis, prediction of recurrence, clinical recurrence, and systemic progression were determined. Univariate and multivariate analyses were conducted to predict risk of recurrence. We validated the methylation of genes in 20 independent tissues representing each group by pyrosequencing. RESULTS Microarray analysis revealed significant methylation of genes in four different groups of prostate cancer tissues. The sensitivity and specificity of methylation for 25 genes from 1, 2, and 4 groups and 7 from group 3 were shown. Validation of genes by pyrosequencing from group 1 (GSTP1, HIF3A, HAAO, and RARβ), group 2 (CRIP1, FLNC, RASGRF2, RUNX3, and HS3ST2), group 3 (PHLDA3, RASGRF2, and TNFRSF10D), and group 4 (BCL11B, POU3F3, and RASGRF2) confirmed the microarray results. CONCLUSIONS Our study provides a global assessment of DNA methylation in prostate cancer and identifies the significance of genes as diagnostic and progression biomarkers of prostate cancer.
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Affiliation(s)
- Saswati Mahapatra
- Department of Urology and Laboratory Medicine and Pathology, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota 55905, USA
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27
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Rahmatpanah FB, Carstens S, Hooshmand SI, Welsh EC, Sjahputera O, Taylor KH, Bennett LB, Shi H, Davis JW, Arthur GL, Shanafelt TD, Kay NE, Wooldridge JE, Caldwell CW. Large-scale analysis of DNA methylation in chronic lymphocytic leukemia. Epigenomics 2012; 1:39-61. [PMID: 20495622 DOI: 10.2217/epi.09.10] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
AIMS B-cell chronic lymphocytic leukemia (CLL) is a heterogeneous malignancy that clinically ranges from indolent to rapidly progressive. CLL, like other cancers, can be affected by epigenetic alterations. MATERIALS & METHODS A microarray discovery-based study was initiated to determine DNA methylation in CLL cases with a range of CD38 expression (1–92%). RESULTS Many loci were either methylated or unmethylated across all CD38 levels, but differential methylation was also observed for some genes. Genomic sequencing of DLEU7 confirmed extensive cytosine methylation preferentially in patient samples with low CD38 expression, whereas NRP2, SFRP2 and ADAM12 were more commonly methylated in those with high CD38 expression. CONCLUSION This study demonstrates that CLL is affected by CpG island methylation in some genes that segregate with CD38 expression levels, while most others show similar methylation patterns across all levels. The CpG island methylation in certain functional gene groups and pathway-associated genes that are known to be deregulated in CLL provides additional insights into the CLL methylome and epigenetic contribution to cellular dysfunction. It will now be useful to investigate the effectiveness of epigenetic therapeutic reversal of these alterations to develop effective treatments for the disease.
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Affiliation(s)
- Farahnaz B Rahmatpanah
- Department of Pathology and Anatomical Sciences, Ellis Fischel Cancer Center, University of Missouri School of Medicine, Columbia, Missouri 65212, USA
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28
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Halldórsdóttir AM, Kanduri M, Marincevic M, Mansouri L, Isaksson A, Göransson H, Axelsson T, Agarwal P, Jernberg-Wiklund H, Stamatopoulos K, Sander B, Ehrencrona H, Rosenquist R. Mantle cell lymphoma displays a homogenous methylation profile: a comparative analysis with chronic lymphocytic leukemia. Am J Hematol 2012; 87:361-7. [PMID: 22374828 DOI: 10.1002/ajh.23115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 01/03/2012] [Indexed: 01/25/2023]
Abstract
Mantle cell lymphoma (MCL) and chronic lymphocytic leukemia (CLL) are mature CD5(+) B-cell malignancies with different biological/clinical characteristics. We recently reported an association between different prognostic subgroups of CLL (i.e., IGHV mutated and unmutated) and genomic methylation pattern. However, the relationship between DNA methylation and prognostic markers, such as the proliferation gene expression signature, has not been investigated in MCL. We applied high-resolution methylation microarrays (27,578 CpG sites) to assess the global DNA methylation profiles in 20 MCL (10 each with high/low proliferation signature) and 30 CLL (15 poor-prognostic IGHV unmutated subset #1 and 15 good-prognostic IGHV mutated subset #4) samples. Notably, MCL and each CLL subset displayed distinct genomic methylation profiles. After unsupervised hierarchical clustering, 17/20 MCL cases formed a cluster separate from CLL, while CLL subsets #1 and #4 formed subclusters. Surprisingly, few differentially methylated genes (n = 6) were identified between high vs. low proliferation MCL. In contrast, distinct methylation profiles were demonstrated for MCL and CLL. Importantly, certain functional classes of genes were preferentially methylated in either disease. For instance, developmental genes, in particular homeobox transcription factor genes (e.g., HLXB9, HOXA13), were more highly methylated in MCL, whereas apoptosis-related genes were enriched among targets methylated in CLL (e.g., CYFIP2, NR4A1). Results were validated using pyrosequencing, RQ-PCR and reexpression of specific genes. In summary, the methylation profile of MCL was homogeneous and no correlation with the proliferation signature was observed. Compared to CLL, however, marked differences were discovered such as the preferential methylation of homeobox genes in MCL.
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MESH Headings
- Apoptosis Regulatory Proteins/genetics
- Azacitidine/analogs & derivatives
- Azacitidine/pharmacology
- Cell Division
- Cell Line, Tumor/drug effects
- Cell Line, Tumor/metabolism
- CpG Islands/drug effects
- DNA (Cytosine-5-)-Methyltransferase 1
- DNA (Cytosine-5-)-Methyltransferases/antagonists & inhibitors
- DNA Methylation/drug effects
- DNA, Neoplasm/chemistry
- DNA, Neoplasm/genetics
- Decitabine
- Female
- Gene Expression Regulation, Leukemic
- Gene Expression Regulation, Neoplastic/drug effects
- Genes, Homeobox
- Genes, Immunoglobulin
- Histone Deacetylase Inhibitors/pharmacology
- Humans
- Hydroxamic Acids/pharmacology
- Immunoglobulin Heavy Chains/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Lymphoma, Mantle-Cell/genetics
- Lymphoma, Mantle-Cell/metabolism
- Male
- Neoplasm Proteins/genetics
- Sequence Analysis, DNA
- Transcription Factors/genetics
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Lv J, Liu H, Su J, Wu X, Liu H, Li B, Xiao X, Wang F, Wu Q, Zhang Y. DiseaseMeth: a human disease methylation database. Nucleic Acids Res 2011; 40:D1030-5. [PMID: 22135302 PMCID: PMC3245164 DOI: 10.1093/nar/gkr1169] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is an important epigenetic modification for genomic regulation in higher organisms that plays a crucial role in the initiation and progression of diseases. The integration and mining of DNA methylation data by methylation-specific PCR and genome-wide profiling technology could greatly assist the discovery of novel candidate disease biomarkers. However, this is difficult without a comprehensive DNA methylation repository of human diseases. Therefore, we have developed DiseaseMeth, a human disease methylation database (http://bioinfo.hrbmu.edu.cn/diseasemeth). Its focus is the efficient storage and statistical analysis of DNA methylation data sets from various diseases. Experimental information from over 14 000 entries and 175 high-throughput data sets from a wide number of sources have been collected and incorporated into DiseaseMeth. The latest release incorporates the gene-centric methylation data of 72 human diseases from a variety of technologies and platforms. To facilitate data extraction, DiseaseMeth supports multiple search options such as gene ID and disease name. DiseaseMeth provides integrated gene methylation data based on cross-data set analysis for disease and normal samples. These can be used for in-depth identification of differentially methylated genes and the investigation of gene–disease relationship.
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Affiliation(s)
- Jie Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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30
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Abstract
NK-like (NKL) homeobox genes code for transcription factors, which can act as key regulators in fundamental cellular processes. NKL genes have been implicated in divergent types of cancer. In this review, we summarize the involvement of NKL genes in cancer and leukemia in particular. NKL genes can act as tumor-suppressor genes and as oncogenes, depending on tissue type. Aberrant expression of NKL genes is especially common in T-cell acute lymphoblastic leukemia (T-ALL). In T-ALL, 8 NKL genes have been reported to be highly expressed in specific T-ALL subgroups, and in ~30% of cases, high expression is caused by chromosomal rearrangement of 1 of 5 NKL genes. Most of these NKL genes are normally not expressed in T-cell development. We hypothesize that the NKL genes might share a similar downstream effect that promotes leukemogenesis, possibly due to mimicking a NKL gene that has a physiological role in early hematopoietic development, such as HHEX. All eight NKL genes posses a conserved Eh1 repressor motif, which has an important role in regulating downstream targets in hematopoiesis and possibly in leukemogenesis as well. Identification of a potential common leukemogenic NKL downstream pathway will provide a promising subject for future studies.
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31
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Lee AP, Brenner S, Venkatesh B. Mouse transgenesis identifies conserved functional enhancers and cis-regulatory motif in the vertebrate LIM homeobox gene Lhx2 locus. PLoS One 2011; 6:e20088. [PMID: 21629789 PMCID: PMC3100342 DOI: 10.1371/journal.pone.0020088] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 04/17/2011] [Indexed: 12/03/2022] Open
Abstract
The vertebrate Lhx2 is a member of the LIM homeobox family of transcription factors. It is essential for the normal development of the forebrain, eye, olfactory system and liver as well for the differentiation of lymphoid cells. However, despite the highly restricted spatio-temporal expression pattern of Lhx2, nothing is known about its transcriptional regulation. In mammals and chicken, Crb2, Dennd1a and Lhx2 constitute a conserved linkage block, while the intervening Dennd1a is lost in the fugu Lhx2 locus. To identify functional enhancers of Lhx2, we predicted conserved noncoding elements (CNEs) in the human, mouse and fugu Crb2-Lhx2 loci and assayed their function in transgenic mouse at E11.5. Four of the eight CNE constructs tested functioned as tissue-specific enhancers in specific regions of the central nervous system and the dorsal root ganglia (DRG), recapitulating partial and overlapping expression patterns of Lhx2 and Crb2 genes. There was considerable overlap in the expression domains of the CNEs, which suggests that the CNEs are either redundant enhancers or regulating different genes in the locus. Using a large set of CNEs (810 CNEs) associated with transcription factor-encoding genes that express predominantly in the central nervous system, we predicted four over-represented 8-mer motifs that are likely to be associated with expression in the central nervous system. Mutation of one of them in a CNE that drove reporter expression in the neural tube and DRG abolished expression in both domains indicating that this motif is essential for expression in these domains. The failure of the four functional enhancers to recapitulate the complete expression pattern of Lhx2 at E11.5 indicates that there must be other Lhx2 enhancers that are either located outside the region investigated or divergent in mammals and fishes. Other approaches such as sequence comparison between multiple mammals are required to identify and characterize such enhancers.
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Affiliation(s)
- Alison P. Lee
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology,
A*STAR (Agency for Science, Technology and Research), Singapore,
Singapore
| | - Sydney Brenner
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology,
A*STAR (Agency for Science, Technology and Research), Singapore,
Singapore
| | - Byrappa Venkatesh
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology,
A*STAR (Agency for Science, Technology and Research), Singapore,
Singapore
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Enjuanes A, Fernàndez V, Hernández L, Navarro A, Beà S, Pinyol M, López-Guillermo A, Rosenwald A, Ott G, Campo E, Jares P. Identification of methylated genes associated with aggressive clinicopathological features in mantle cell lymphoma. PLoS One 2011; 6:e19736. [PMID: 21603610 PMCID: PMC3095614 DOI: 10.1371/journal.pone.0019736] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 04/05/2011] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Mantle cell lymphoma (MCL) is genetically characterized by the t(11;14)(q13;q32) translocation and a high number of secondary chromosomal alterations. The contribution of DNA methylation to MCL lymphomagenesis is not well known. We sought to identify epigenetically silenced genes in these tumours that might have clinical relevance. METHODOLOGY/PRINCIPAL FINDINGS To identify potential methylated genes in MCL we initially investigated seven MCL cell lines treated with epigenetic drugs and gene expression microarray profiling. The methylation status of selected candidate genes was validated by a quantitative assay and subsequently analyzed in a series of primary MCL (n = 38). After pharmacological reversion we identified 252 potentially methylated genes. The methylation analysis of a subset of these genes (n = 25) in the MCL cell lines and normal B lymphocytes confirmed that 80% of them were methylated in the cell lines but not in normal lymphocytes. The subsequent analysis in primary MCL identified five genes (SOX9, HOXA9, AHR, NR2F2, and ROBO1) frequently methylated in these tumours. The gene methylation events tended to occur in the same primary neoplasms and correlated with higher proliferation, increased number of chromosomal abnormalities, and shorter survival of the patients. CONCLUSIONS We have identified a set of genes whose methylation degree and gene expression levels correlate with aggressive clinicopathological features of MCL. Our findings also suggest that a subset of MCL might show a CpG island methylator phenotype (CIMP) that may influence the behaviour of the tumours.
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Affiliation(s)
- Anna Enjuanes
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Verònica Fernàndez
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Luis Hernández
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Alba Navarro
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Sílvia Beà
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Magda Pinyol
- Genomics Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | | | | | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Elías Campo
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Pedro Jares
- Hematopathology Section, Department of Anatomic Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
- Genomics Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
- * E-mail:
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Bibikova M, Fan JB. Genome-wide DNA methylation profiling. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 2:210-223. [PMID: 20836023 DOI: 10.1002/wsbm.35] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNA methylation plays a critical role in the regulation of gene expression. The ability to access the methylation status for a large number of genes or the entire genome should greatly facilitate the understanding of the nature of gene regulation in cells, and epigenetic mechanism of interactions between cells and environment. Microarray and sequencing-based DNA methylation profiling technologies have been developed to meet this goal. These methods can be categorized into three main classes based on how the methylation status is interrogated: discrimination of bisulfite induced C to T transition; cleavage of genomic DNA by methylation-sensitive restriction enzymes; and immunoprecipitation with methyl-binding protein or antibodies against methylated cytosines. With the development of next-generation sequencing technologies, genome-wide bisulfite sequencing has become a reality. Either whole- or reduced-genome approaches have been used to get the most comprehensive DNA methylation profiles in organisms of various genome sizes.
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Affiliation(s)
- Marina Bibikova
- Illumina, Inc., 9885 Towne Centre Drive, San Diego, CA 92121, USA
| | - Jian-Bing Fan
- Illumina, Inc., 9885 Towne Centre Drive, San Diego, CA 92121, USA
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Dieckmann M, Dietrich MF, Herz J. Lipoprotein receptors--an evolutionarily ancient multifunctional receptor family. Biol Chem 2011; 391:1341-63. [PMID: 20868222 DOI: 10.1515/bc.2010.129] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The evolutionarily ancient low-density lipoprotein (LDL) receptor gene family represents a class of widely expressed cell surface receptors. Since the dawn of the first primitive multicellular organisms, several structurally and functionally distinct families of lipoprotein receptors have evolved. In accordance with the now obsolete 'one-gene-one-function' hypothesis, these cell surface receptors were originally perceived as mere transporters of lipoproteins, lipids, and nutrients or as scavenger receptors, which remove other kinds of macromolecules, such as proteases and protease inhibitors from the extracellular environment and the cell surface. This picture has since undergone a fundamental change. Experimental evidence has replaced the perception that these receptors serve merely as cargo transporters. Instead it is now clear that the transport of macromolecules is inseparably intertwined with the molecular machinery by which cells communicate with each other. Lipoprotein receptors are essentially sensors of the extracellular environment that participate in a wide range of physiological processes by physically interacting and coevolving with primary signal transducers as co-regulators. Furthermore, lipoprotein receptors modulate cellular trafficking and localization of the amyloid precursor protein (APP) and the β-amyloid peptide (Aβ), suggesting a role in the pathogenesis of Alzheimer's disease. Moreover, compelling evidence shows that LDL receptor family members are involved in tumor development and progression.
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Affiliation(s)
- Marco Dieckmann
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9046, USA
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Lai HC, Lin YW, Huang RL, Chung MT, Wang HC, Liao YP, Su PH, Liu YL, Yu MH. Quantitative DNA methylation analysis detects cervical intraepithelial neoplasms type 3 and worse. Cancer 2010; 116:4266-74. [PMID: 20564139 DOI: 10.1002/cncr.25252] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND DNA methylation may be used a potential biomarker for detecting cervical cancer. The authors of this report used quantitative methylation analysis of 4 genes in a full spectrum of cervical lesions to test its potential clinical application. METHODS This hospital-based, retrospective, case-control study was conducted in 185 patients and included patients who had a normal uterine cervix (n = 53), cervical intraepithelial neoplasm type 1 (CIN1) (n = 37), CIN2 (n = 22), CIN3 (n = 24), carcinoma in situ (CIS) (n = 22), squamous cell carcinoma (SCC, n = 20), and adenocarcinoma (AC) (n = 7). Methylation levels of the genes sex-determining region Y, box 1 (SOX1); paired box gene 1 (PAX1); LIM homeobox transcription factor 1α (LMX1A), and NK6 transcription factor-related locus 1 (NKX6-1) were determined by using real-time methylation-specific polymerase chain reaction (PCR) amplification. Cutoff values of the percentage of methylation reference (PMR) for different diagnoses were determined to test the sensitivity and specificity and to generate receiver operating characteristic (ROC) curves. Two-sided Mann-Whitney U tests were used to test differences in PMR between groups. RESULTS The PMRs of the 4 genes were significantly higher in CIN3 and worse (CIN3+) lesions than the PMRs in specimens of normal cervix and CIN1 or CIN2 (P < .001). ROC curve analysis demonstrated that the sensitivity, specificity, and accuracy for detecting CIN3+ lesions were 0.88, 0.82, and 0.95, respectively, for SOX1; 0.78, 0.91, and 0.89, respectively, for PAX1; 0.77, 0.88, and 0.90, respectively, for LMX1A; and 0.93, 0.97, and 0.97, respectively, for NKX6-1. CONCLUSIONS The current results indicated that quantitative PCR-based testing for DNA methylation of 4 genes holds great promise for cervical cancer screening and warrants further population-based studies using standardized DNA methylation testing.
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Affiliation(s)
- Hung-Cheng Lai
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan, Republic of China.
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Eberth S, Schneider B, Rosenwald A, Hartmann EM, Romani J, Zaborski M, Siebert R, Drexler HG, Quentmeier H. Epigenetic regulation of CD44 in Hodgkin and non-Hodgkin lymphoma. BMC Cancer 2010; 10:517. [PMID: 20920234 PMCID: PMC2955612 DOI: 10.1186/1471-2407-10-517] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 09/29/2010] [Indexed: 12/19/2022] Open
Abstract
Background Epigenetic inactivation of tumor suppressor genes (TSG) by promoter CpG island hypermethylation is a hallmark of cancer. To assay its extent in human lymphoma, methylation of 24 TSG was analyzed in lymphoma-derived cell lines as well as in patient samples. Methods We screened for TSG methylation using methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) in 40 lymphoma-derived cell lines representing anaplastic large cell lymphoma, Burkitt lymphoma (BL), diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), Hodgkin lymphoma and mantle cell lymphoma (MCL) as well as in 50 primary lymphoma samples. The methylation status of differentially methylated CD44 was verified by methylation-specific PCR and bisulfite sequencing. Gene expression of CD44 and its reactivation by DNA demethylation was determined by quantitative real-time PCR and on the protein level by flow cytometry. Induction of apoptosis by anti-CD44 antibody was analyzed by annexin-V/PI staining and flow cytometry. Results On average 8 ± 2.8 of 24 TSG were methylated per lymphoma cell line and 2.4 ± 2 of 24 TSG in primary lymphomas, whereas 0/24 TSG were methylated in tonsils and blood mononuclear cells from healthy donors. Notably, we identified that CD44 was hypermethylated and transcriptionally silenced in all BL and most FL and DLBCL cell lines, but was usually unmethylated and expressed in MCL cell lines. Concordant results were obtained from primary lymphoma material: CD44 was not methylated in MCL patients (0/11) whereas CD44 was frequently hypermethylated in BL patients (18/29). In cell lines with CD44 hypermethylation, expression was re-inducible at mRNA and protein levels by treatment with the DNA demethylating agent 5-Aza-2'-deoxycytidine, confirming epigenetic regulation of CD44. CD44 ligation assays with a monoclonal anti-CD44 antibody showed that CD44 can mediate apoptosis in CD44+ lymphoma cells. CD44 hypermethylated, CD44- lymphoma cell lines were consistently resistant towards anti-CD44 induced apoptosis. Conclusion Our data show that CD44 is epigenetically regulated in lymphoma and undergoes de novo methylation in distinct lymphoma subtypes like BL. Thus CD44 may be a promising new epigenetic marker for diagnosis and a potential therapeutic target for the treatment of specific lymphoma subtypes.
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Affiliation(s)
- Sonja Eberth
- DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
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Choi JH, Li Y, Guo J, Pei L, Rauch TA, Kramer RS, Macmil SL, Wiley GB, Bennett LB, Schnabel JL, Taylor KH, Kim S, Xu D, Sreekumar A, Pfeifer GP, Roe BA, Caldwell CW, Bhalla KN, Shi H. Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing. PLoS One 2010; 5. [PMID: 20927367 PMCID: PMC2947499 DOI: 10.1371/journal.pone.0013020] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2010] [Accepted: 08/21/2010] [Indexed: 12/16/2022] Open
Abstract
Background Follicular lymphoma (FL) is a form of non-Hodgkin's lymphoma (NHL) that arises from germinal center (GC) B-cells. Despite the significant advances in immunotherapy, FL is still not curable. Beyond transcriptional profiling and genomics datasets, there currently is no epigenome-scale dataset or integrative biology approach that can adequately model this disease and therefore identify novel mechanisms and targets for successful prevention and treatment of FL. Methodology/Principal Findings We performed methylation-enriched genome-wide bisulfite sequencing of FL cells and normal CD19+ B-cells using 454 sequencing technology. The methylated DNA fragments were enriched with methyl-binding proteins, treated with bisulfite, and sequenced using the Roche-454 GS FLX sequencer. The total number of bases covered in the human genome was 18.2 and 49.3 million including 726,003 and 1.3 million CpGs in FL and CD19+ B-cells, respectively. 11,971 and 7,882 methylated regions of interest (MRIs) were identified respectively. The genome-wide distribution of these MRIs displayed significant differences between FL and normal B-cells. A reverse trend in the distribution of MRIs between the promoter and the gene body was observed in FL and CD19+ B-cells. The MRIs identified in FL cells also correlated well with transcriptomic data and ChIP-on-Chip analyses of genome-wide histone modifications such as tri-methyl-H3K27, and tri-methyl-H3K4, indicating a concerted epigenetic alteration in FL cells. Conclusions/Significance This study is the first to provide a large scale and comprehensive analysis of the DNA methylation sequence composition and distribution in the FL epigenome. These integrated approaches have led to the discovery of novel and frequent targets of aberrant epigenetic alterations. The genome-wide bisulfite sequencing approach developed here can be a useful tool for profiling DNA methylation in clinical samples.
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Affiliation(s)
- Jeong-Hyeon Choi
- Center of Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, United States of America
| | - Yajun Li
- Medical College of Georgia Cancer Center, Medical College of Georgia, Augusta, Georgia, United States of America
| | - Juyuan Guo
- Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Lirong Pei
- Medical College of Georgia Cancer Center, Medical College of Georgia, Augusta, Georgia, United States of America
| | - Tibor A. Rauch
- Division of Biology, City of Hope Beckman Research Institute, Duarte, California, United States of America
| | - Robin S. Kramer
- Department of Computer Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Simone L. Macmil
- Advanced Center for Genome Technology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Graham B. Wiley
- Advanced Center for Genome Technology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Lynda B. Bennett
- Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Jennifer L. Schnabel
- Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Kristen H. Taylor
- Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Sun Kim
- Center of Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, United States of America
| | - Dong Xu
- Division of Biology, City of Hope Beckman Research Institute, Duarte, California, United States of America
| | - Arun Sreekumar
- Medical College of Georgia Cancer Center, Medical College of Georgia, Augusta, Georgia, United States of America
| | - Gerd P. Pfeifer
- Department of Computer Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Bruce A. Roe
- Advanced Center for Genome Technology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Charles W. Caldwell
- Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Kapil N. Bhalla
- Medical College of Georgia Cancer Center, Medical College of Georgia, Augusta, Georgia, United States of America
| | - Huidong Shi
- Medical College of Georgia Cancer Center, Medical College of Georgia, Augusta, Georgia, United States of America
- * E-mail:
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Tong WG, Wierda WG, Lin E, Kuang SQ, Bekele BN, Estrov Z, Wei Y, Yang H, Keating MJ, Garcia-Manero G. Genome-wide DNA methylation profiling of chronic lymphocytic leukemia allows identification of epigenetically repressed molecular pathways with clinical impact. Epigenetics 2010; 5:499-508. [PMID: 20484983 PMCID: PMC3322493 DOI: 10.4161/epi.5.6.12179] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We performed a genome-wide analysis of aberrant DNA methylation in chronic lymphocytic leukemia (CLL) using methylated CpG island amplification (MCA) coupled with a promoter microarray. We identified 280 potential targets of aberrant DNA methylation in CLL. These genes were located more frequently in chromosomes 19 (16%, p=0.001), 16 (11%, p=0.001), 17 (10%, p=0.02) and 11 (9%, p=0.02) and could be grouped in several functional networks. Methylation status was confirmed for 22 of these genes (SOX11, DLX1, FAM62C, SOX14, RSPO1, ADCY5, HAND2,SPOCK, MLL, ING1, PRIMA1, BCL11B, LTBP2, BNC1, NR2F2, SALL1, GALGT2, LHX1, DLX4, KLK10, TFAP2 and APP) in 78 CLL patients by pyrosequencing. As a proof of principle, we analyzed the expression of 2 genes, PRIMA1 and APP, in primary cells and of GALGT2, TFAP2C and PRIMA1 in leukemia cells. There was an inverse association between methylation and gene expression. This could be reversed by treatment with 5-aza-2'-deoxycytidine in cell lines. Treatment in a clinical trial with 5-azacitidine resulted in decreased methylation of LINE, DLX4 and SALL1 in the peripheral blood B-cells of patients with CLL. IgVH mutational status or ZAP-70 expression were not associated with specific methylation profiles. By multivariate analysis, methylation of LINE and APP was associated with shorter overall survival (p = 0.045 and 0.0035, respectively). This study demonstrates that aberrant DNA methylation is common and has potential prognostic and therapeutic value in CLL.
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Affiliation(s)
- Wei-Gang Tong
- Department of Leukemia; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - William G. Wierda
- Department of Leukemia; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - E. Lin
- Department of Biostatistics; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - Shao-Qing Kuang
- Department of Leukemia; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - B. Nebiyou Bekele
- Department of Biostatistics; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - Zeev Estrov
- Department of Leukemia; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - Yue Wei
- Department of Leukemia; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - Hui Yang
- Department of Leukemia; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - Michael J Keating
- Department of Leukemia; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
| | - Guillermo Garcia-Manero
- Department of Leukemia; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA
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Abstract
Expression profiling has shown 2 main and clinically distinct subtypes of diffuse large B-cell lymphomas (DLBCLs): germinal-center B cell-like (GCB) and activated B cell-like (ABC) DLBCLs. Further work has shown that these subtypes are partially characterized by distinct genetic alterations and different survival. Here, we show with the use of an assay that measures DNA methylation levels of 50,000 CpG motifs distributed among more than 14,000 promoters that these 2 DLBCL subtypes are also characterized by distinct epigenetic profiles. DNA methylation and gene expression profiling were performed on a cohort of 69 patients with DLBCL. After assigning ABC or GCB labels with a Bayesian expression classifier trained on an independent dataset, a supervised analysis identified 311 differentially methylated probe sets (263 unique genes) between ABC and GCB DLBCLs. Integrated analysis of methylation and gene expression showed a core tumor necrosis factor-α signaling pathway as the principal differentially perturbed gene network. Sixteen genes overlapped between the core ABC/GCB methylation and expression signatures and encoded important proteins such as IKZF1. This reduced gene set was an accurate predictor of ABC and GCB subtypes. Collectively, the data suggest that epigenetic patterning contributes to the ABC and GCB DLBCL phenotypes and could serve as useful biomarker.
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Taylor KH, Shi H, Caldwell CW. Next generation sequencing: advances in characterizing the methylome. Genes (Basel) 2010; 1. [PMID: 24710039 PMCID: PMC3954092 DOI: 10.3390/genes1010143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Epigenetic modifications play an important role in lymphoid malignancies. This has been evidenced by the large body of work published using microarray technologies to generate methylation profiles for numerous types and subtypes of lymphoma and leukemia. These studies have shown the importance of defining the epigenome so that we can better understand the biology of lymphoma. Recent advances in DNA sequencing technology have transformed the landscape of epigenomic analysis as we now have the ability to characterize the genome-wide distribution of chromatin modifications and DNA methylation using next-generation sequencing. To take full advantage of the throughput of next-generation sequencing, there are many methodologies that have been developed and many more that are currently being developed. Choosing the appropriate methodology is fundamental to the outcome of next-generation sequencing studies. In this review, published technologies and methodologies applicable to studying the methylome are presented. In addition, progress towards defining the methylome in lymphoma is discussed and prospective directions that have been made possible as a result of next-generation sequencing technology. Finally, methodologies are introduced that have not yet been published but that are being explored in the pursuit of defining the lymphoma methylome.
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Affiliation(s)
- Kristen H Taylor
- University of Missouri-Columbia School of Medicine, Ellis Fischel Cancer Center, Columbia, MO 65212, USA.
| | - Huidong Shi
- Medical College of Georgia, Augusta, GA 30912, USA.
| | - Charles W Caldwell
- University of Missouri-Columbia School of Medicine, Ellis Fischel Cancer Center, Columbia, MO 65212, USA.
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Next Generation Sequencing: Advances in Characterizing the Methylome. Genes (Basel) 2010; 1:143-65. [DOI: 10.3390/genes1020143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 06/22/2010] [Accepted: 06/28/2010] [Indexed: 12/17/2022] Open
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Lu YJ, Wu CS, Li HP, Liu HP, Lu CY, Leu YW, Wang CS, Chen LC, Lin KH, Chang YS. Aberrant methylation impairs low density lipoprotein receptor-related protein 1B tumor suppressor function in gastric cancer. Genes Chromosomes Cancer 2010; 49:412-24. [PMID: 20095042 DOI: 10.1002/gcc.20752] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DNA methylation plays a significant role in tumor progression. In this study, we used CpG microarray and differential methylation hybridization approaches to identify low density lipoprotein receptor-related protein 1B (LRP1B) as a novel epigenetic target in gastric cancer. LRP1B was hypermethylated in four gastric cancer cell lines, and low LRP1B mRNA expression was associated with high methylation levels in gastric cancer cell lines. Addition of a DNA methylation inhibitor (5-Aza-dC) restored the mRNA expression of LRP1B in these cell lines, indicating that DNA methylation is involved in regulating LRP1B expression. In 45 out of 74 (61%) clinical samples, LRP1B was highly methylated; LRP1B mRNA expression was significantly lower in 15 out of 19 (79%, P < 0.001) gastric tumor tissues than in corresponding adjacent normal tissues. In addition, ectopic expression of mLRP1B4 in gastric cancer cell lines suppressed cell growth, colony formation and tumor formation in nude mice. These results collectively indicate that LRP1B is a functional tumor suppressor gene in gastric cancer and that is regulated by DNA methylation.
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Affiliation(s)
- Yen-Jung Lu
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
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Ectodomains of the LDL receptor-related proteins LRP1b and LRP4 have anchorage independent functions in vivo. PLoS One 2010; 5:e9960. [PMID: 20383322 PMCID: PMC2850915 DOI: 10.1371/journal.pone.0009960] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Accepted: 03/02/2010] [Indexed: 01/20/2023] Open
Abstract
Background The low-density lipoprotein (LDL) receptor gene family is a highly conserved group of membrane receptors with diverse functions in developmental processes, lipoprotein trafficking, and cell signaling. The low-density lipoprotein (LDL) receptor-related protein 1b (LRP1B) was reported to be deleted in several types of human malignancies, including non-small cell lung cancer. Our group has previously reported that a distal extracellular truncation of murine Lrp1b that is predicted to secrete the entire intact extracellular domain (ECD) is fully viable with no apparent phenotype. Methods and Principal Findings Here, we have used a gene targeting approach to create two mouse lines carrying internally rearranged exons of Lrp1b that are predicted to truncate the protein closer to the N-terminus and to prevent normal trafficking through the secretary pathway. Both mutations result in early embryonic lethality, but, as expected from the restricted expression pattern of LRP1b in vivo, loss of Lrp1b does not cause cellular lethality as homozygous Lrp1b-deficient blastocysts can be propagated normally in culture. This is similar to findings for another LDL receptor family member, Lrp4. We provide in vitro evidence that Lrp4 undergoes regulated intramembraneous processing through metalloproteases and γ-secretase cleavage. We further demonstrate negative regulation of the Wnt signaling pathway by the soluble extracellular domain. Conclusions and Significance Our results underline a crucial role for Lrp1b in development. The expression in mice of truncated alleles of Lrp1b and Lrp4 with deletions of the transmembrane and intracellular domains leads to release of the extracellular domain into the extracellular space, which is sufficient to confer viability. In contrast, null mutations are embryonically (Lrp1b) or perinatally (Lrp4) lethal. These findings suggest that the extracellular domains of both proteins may function as a scavenger for signaling ligands or signal modulators in the extracellular space, thereby preserving signaling thresholds that are critical for embryonic development, as well as for the clear, but poorly understood role of LRP1b in cancer.
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Bennett LB, Taylor KH, Arthur GL, Rahmatpanah FB, Hooshmand SI, Caldwell CW. Epigenetic regulation of WNT signaling in chronic lymphocytic leukemia. Epigenomics 2010; 2:53-70. [PMID: 20473358 PMCID: PMC2869094 DOI: 10.2217/epi.09.43] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Certain WNT and WNT network target genes are expressed at higher or lower levels in chronic lymphocytic leukemia compared with normal B-cells. This includes upregulation of nuclear complex genes, as well as genes for cytoplasmic proteins and WNT ligands and their cognate receptors. In addition, epigenetic silencing of several negative regulators of the WNT pathway have been identified. The balance between epigenetic downregulation of negative effector genes and increased expression of positive effector genes demonstrate that the epigenetic downregulation of WNT antagonists is one mechanism, perhaps the main mechanism, that is permissive to active WNT signaling in chronic lymphocytic leukemia. Moreover, constitutive activation of the WNT network and target genes is likely to impact on additional interacting signaling pathways. Based on published studies, we propose a model of WNT signaling that involves mainly permissive expression, and sometimes overexpression, of positive effectors and downregulation of negative regulators in the network. In this model, DNA methylation, histone modifications and altered expression of microRNA molecules interact to allow continuous WNT signaling.
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Affiliation(s)
| | | | | | | | | | - Charles W Caldwell
- Author for correspondence: Department of Pathology & Anatomical Sciences, Ellis Fischel Cancer Center, University of Missouri, 115 Business Loop I-70 West, Columbia, MO 65203, USA, Tel.: +1 573 882 1234, Fax: +1 573 884 5206,
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Mutai H, Nagashima R, Sugitani Y, Noda T, Fujii M, Matsunaga T. Expression of Pou3f3/Brn-1 and its genomic methylation in developing auditory epithelium. Dev Neurobiol 2010; 69:913-30. [PMID: 19743445 DOI: 10.1002/dneu.20746] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the mammalian cochlea, both the sensory cells-called hair cells (HCs)-and nonsensory cells such as supporting cells (SCs) and mesenchymal cells participate in proper auditory function through the expression of various functional molecules. During development, expression of certain genes is repressed through genomic methylation, one of the major epigenetic regulatory mechanisms. We explored the genomic regions that were differentially methylated in rat auditory epithelium at postnatal day 1 (P1) and P14 using amplification of intermethylated sites (AIMS). An AIMS fragment was mapped to the 3'-flanking region of Pou3f3/Brn-1. Bisulfite-converted PCR and quantitative methylation-specific PCR showed that the methylation frequency of the AIMS region and the adjacent CpG island was increased at P14, when the expression of Pou3f3 and the noncoding RNAs nearby decreased. Expression of de novo DNA methyltransferases 3a and 3b also suggests a role of epigenetic regulation during postnatal inner ear development. Immunohistochemical analysis showed that Pou3f3 was expressed specifically in the SCs and mesenchymal cells in the cochlea and established that Pou3f3 is a new cell-type marker for studying inner ear development. Mice deficient in Pou3f3 or Pou3f2 plus Pou3f3 did not exhibit any abnormality in the embryonic cochlea. Absence of Pou3f3 affected neither the proliferation nor the differentiation activities of HC progenitor cells. Pou3f3 may, however, be important for the maintenance or functional development of the postnatal cochlea. This is the first report to study involvement of an epigenetic regulatory mechanism in the developing mammalian auditory epithelium.
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Affiliation(s)
- Hideki Mutai
- Laboratory of Auditory Disorders, National Institute of Sensory Organs, National Tokyo Medical Center, Tokyo, Japan
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Bryan JN, Jabbes M, Berent LM, Arthur GL, Taylor KH, Rissetto KC, Henry CJ, Rahmatpanah F, Rankin WV, Villamil JA, Lewis MR, Caldwell CW. Hypermethylation of the DLC1 CpG island does not alter gene expression in canine lymphoma. BMC Genet 2009; 10:73. [PMID: 19912643 PMCID: PMC2784477 DOI: 10.1186/1471-2156-10-73] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 11/13/2009] [Indexed: 12/12/2022] Open
Abstract
Background This study is a comparative epigenetic evaluation of the methylation status of the DLC1 tumor suppressor gene in naturally-occurring canine lymphoma. Canine non-Hodgkin's lymphoma (NHL) has been proposed to be a relevant preclinical model that occurs spontaneously and may share causative factors with human NHL due to a shared home environment. The canine DLC1 mRNA sequence was derived from normal tissue. Using lymphoid samples from 21 dogs with NHL and 7 normal dogs, the methylation status of the promoter CpG island of the gene was defined for each sample using combined bisulfite restriction analysis (COBRA), methylation-specific PCR (MSP), and bisulfite sequencing methods. Relative gene expression was determined using real-time PCR. Results The mRNA sequence of canine DLC1 is highly similar to the human orthologue and contains all protein functional groups, with 97% or greater similarity in functional regions. Hypermethylation of the 5' and 3' flanking regions of the promoter was statistically significantly associated with the NHL phenotype, but was not associated with silencing of expression or differences in survival. Conclusion The canine DLC1 is constructed highly similarly to the human gene, which has been shown to be an important tumor suppressor in many forms of cancer. As in human NHL, the promoter CpG island of DLC1 in canine NHL samples is abnormally hypermethylated, relative to normal lymphoid tissue. This study confirms that hypermethylation occurs in canine cancers, further supporting the use of companion dogs as comparative models of disease for evaluation of carcinogenesis, biomarker diagnosis, and therapy.
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Affiliation(s)
- Jeffrey N Bryan
- Dept of Veterinary Medicine and Surgery, University of Missouri-Columbia, 65211, USA.
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Hypomethylation and expression of BEX2, IGSF4 and TIMP3 indicative of MLL translocations in acute myeloid leukemia. Mol Cancer 2009; 8:86. [PMID: 19835597 PMCID: PMC2770485 DOI: 10.1186/1476-4598-8-86] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 10/16/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Translocations of the Mixed Lineage Leukemia (MLL) gene occur in a subset (5%) of acute myeloid leukemias (AML), and in mixed phenotype acute leukemias in infancy - a disease with extremely poor prognosis. Animal model systems show that MLL gain of function mutations may contribute to leukemogenesis. Wild-type (wt) MLL possesses histone methyltransferase activity and functions at the level of chromatin organization by affecting the expression of specific target genes. While numerous MLL fusion proteins exert a diverse array of functions, they ultimately serve to induce transcription of specific genes. Hence, acute lymphoblastic leukemias (ALL) with MLL mutations (MLLmu) exhibit characteristic gene expression profiles including high-level expression of HOXA cluster genes. Here, we aimed to relate MLL mutational status and tumor suppressor gene (TSG) methylation/expression in acute leukemia cell lines. RESULTS Using MS-MLPA (methylation-specific multiplex ligation-dependent probe amplification assay), methylation of 24 different TSG was analyzed in 28 MLLmu and MLLwt acute leukemia cell lines. On average, 1.8/24 TSG were methylated in MLLmu AML cells, while 6.2/24 TSG were methylated in MLLwt AML cells. Hypomethylation and expression of the TSG BEX2, IGSF4 and TIMP3 turned out to be characteristic of MLLmu AML cell lines. MLLwt AML cell lines displayed hypermethylated TSG promoters resulting in transcriptional silencing. Demethylating agents and inhibitors of histone deacetylases restored expression of BEX2, IGSF4 and TIMP3, confirming epigenetic silencing of these genes in MLLwt cells. The positive correlation between MLL translocation, TSG hypomethylation and expression suggested that MLL fusion proteins were responsible for dysregulation of TSG expression in MLLmu cells. This concept was supported by our observation that Bex2 mRNA levels in MLL-ENL transgenic mouse cell lines required expression of the MLL fusion gene. CONCLUSION These results suggest that the conspicuous expression of the TSG BEX2, IGSF4 and TIMP3 in MLLmu AML cell lines is the consequence of altered epigenetic properties of MLL fusion proteins.
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Martin-Subero JI, Ammerpohl O, Bibikova M, Wickham-Garcia E, Agirre X, Alvarez S, Brüggemann M, Bug S, Calasanz MJ, Deckert M, Dreyling M, Du MQ, Dürig J, Dyer MJS, Fan JB, Gesk S, Hansmann ML, Harder L, Hartmann S, Klapper W, Küppers R, Montesinos-Rongen M, Nagel I, Pott C, Richter J, Román-Gómez J, Seifert M, Stein H, Suela J, Trümper L, Vater I, Prosper F, Haferlach C, Cigudosa JC, Siebert R. A comprehensive microarray-based DNA methylation study of 367 hematological neoplasms. PLoS One 2009; 4:e6986. [PMID: 19750229 PMCID: PMC2737286 DOI: 10.1371/journal.pone.0006986] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Accepted: 08/12/2009] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Alterations in the DNA methylation pattern are a hallmark of leukemias and lymphomas. However, most epigenetic studies in hematologic neoplasms (HNs) have focused either on the analysis of few candidate genes or many genes and few HN entities, and comprehensive studies are required. METHODOLOGY/PRINCIPAL FINDINGS Here, we report for the first time a microarray-based DNA methylation study of 767 genes in 367 HNs diagnosed with 16 of the most representative B-cell (n = 203), T-cell (n = 30), and myeloid (n = 134) neoplasias, as well as 37 samples from different cell types of the hematopoietic system. Using appropriate controls of B-, T-, or myeloid cellular origin, we identified a total of 220 genes hypermethylated in at least one HN entity. In general, promoter hypermethylation was more frequent in lymphoid malignancies than in myeloid malignancies, being germinal center mature B-cell lymphomas as well as B and T precursor lymphoid neoplasias those entities with highest frequency of gene-associated DNA hypermethylation. We also observed a significant correlation between the number of hypermethylated and hypomethylated genes in several mature B-cell neoplasias, but not in precursor B- and T-cell leukemias. Most of the genes becoming hypermethylated contained promoters with high CpG content, and a significant fraction of them are targets of the polycomb repressor complex. Interestingly, T-cell prolymphocytic leukemias show low levels of DNA hypermethylation and a comparatively large number of hypomethylated genes, many of them showing an increased gene expression. CONCLUSIONS/SIGNIFICANCE We have characterized the DNA methylation profile of a wide range of different HNs entities. As well as identifying genes showing aberrant DNA methylation in certain HN subtypes, we also detected six genes--DBC1, DIO3, FZD9, HS3ST2, MOS, and MYOD1--that were significantly hypermethylated in B-cell, T-cell, and myeloid malignancies. These might therefore play an important role in the development of different HNs.
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Affiliation(s)
- Jose I. Martin-Subero
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
- Cancer Epigenetics and Biology Program, Bellvitge Institute for Biomedical Research-Catalan Institute of Oncology, Barcelona, Spain
| | - Ole Ammerpohl
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | - Marina Bibikova
- Illumina, Inc., San Diego, California, United States of America
| | | | - Xabier Agirre
- Division of Cancer and Area of Cell Therapy and Hematology Service, Universidad de Navarra, Pamplona, Spain
| | - Sara Alvarez
- Molecular Cytogenetics Group, Centro Nacional Investigaciones Oncologicas, Madrid, Spain
| | - Monika Brüggemann
- Second Medical Department, Christian-Albrechts University, Kiel, Germany
| | - Stefanie Bug
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | | | - Martina Deckert
- Department of Neuropathology, University Hospital of Cologne, Cologne, Germany
| | - Martin Dreyling
- Department of Medicine III, University Hospital Grosshadern, Munich, Germany
| | - Ming Q. Du
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Jan Dürig
- Department of Hematology, University of Duisburg-Essen, Essen, Germany
| | | | - Jian-Bing Fan
- Illumina, Inc., San Diego, California, United States of America
| | - Stefan Gesk
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | - Martin-Leo Hansmann
- Institute of Pathology, University Hospital of Frankfurt, Frankfurt, Germany
| | - Lana Harder
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | - Sylvia Hartmann
- Institute of Pathology, University Hospital of Frankfurt, Frankfurt, Germany
| | - Wolfram Klapper
- Institute of Pathology, Christian-Albrechts University, Kiel, Germany
| | - Ralf Küppers
- Institute of Cell Biology, University of Duisburg-Essen, Essen, Germany
| | | | - Inga Nagel
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | - Christiane Pott
- Second Medical Department, Christian-Albrechts University, Kiel, Germany
| | - Julia Richter
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | - José Román-Gómez
- Reina Sofia Hospital, Instituto Maimonides de Investigación Biomédica de Córdoba, Cordoba, Spain
| | - Marc Seifert
- Institute of Cell Biology, University of Duisburg-Essen, Essen, Germany
| | - Harald Stein
- Institute of Pathology, Campus Benjamin Franklin, Berlin, Germany
| | - Javier Suela
- Molecular Cytogenetics Group, Centro Nacional Investigaciones Oncologicas, Madrid, Spain
| | - Lorenz Trümper
- Department of Hematology and Oncology, Georg-August University of Göttingen, Göttingen, Germany
| | - Inga Vater
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | - Felipe Prosper
- Division of Cancer and Area of Cell Therapy and Hematology Service, Universidad de Navarra, Pamplona, Spain
| | | | - Juan Cruz Cigudosa
- Molecular Cytogenetics Group, Centro Nacional Investigaciones Oncologicas, Madrid, Spain
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
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Abstract
Quantitative methylation profiling was performed using the Illumina GoldenGate Assay in untreated Follicular Lymphoma (FL) (164), paired pre- and post-transformation FL (20), benign haematopoietic (24) samples and purified B & T cells from two FL cases. Methylation values allowed separation of untreated FL samples from controls with one exception based primarily on tumour-specific gains of methylation typically occurring within CpG islands. Genes which are targets for epigenetic repression in stem cells by Polycomb Repressor Complex 2 were significantly overrepresented among hypermethylated genes. Methylation profiles were conserved in sequential FL and t-FL biopsies suggesting that widespread methylation represents an early event in lymphomagenesis and may not contribute substantially to transformation. Significant (p<0.05) correlation between FL methylation values and reduced gene expression was demonstrated for up to 28% of loci. Methylation changes occurred predominantly in B cells with variability in the amount of non-malignant tissue between samples preventing conclusive correlation with survival. This represents an important caveat in attributing prognostic relevance to methylation and future studies in cancer will optimally require purified tumour populations to address the impact of methylation on clinical outcome.
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Röhrs S, Romani J, Zaborski M, Drexler HG, Quentmeier H. Hypermethylation of Death-Associated Protein Kinase 1 differentiates natural killer cell lines from cell lines derived from T-acute lymphoblastic leukemia. Leukemia 2009; 23:1174-6. [PMID: 19212339 DOI: 10.1038/leu.2009.5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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