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Gadwal A, Purohit P, Khokhar M, Vishnoi JR, Pareek P, Choudhary R, Elhence P, Banerjee M, Sharma P. In silico analysis of differentially expressed-aberrantly methylated genes in breast cancer for prognostic and therapeutic targets. Clin Exp Med 2023; 23:3847-3866. [PMID: 37029310 DOI: 10.1007/s10238-023-01060-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/28/2023] [Indexed: 04/09/2023]
Abstract
Breast cancer (BC) is the leading cause of death among women across the globe. Abnormal gene expression plays a crucial role in tumour progression, carcinogenesis and metastasis of BC. The alteration of gene expression may be through aberrant gene methylation. In the present study, differentially expressed genes which may be regulated by DNA methylation and their pathways associated with BC have been identified. Expression microarray datasets GSE10780, GSE10797, GSE21422, GSE42568, GSE61304, GSE61724 and one DNA methylation profile dataset GSE20713 were downloaded from Gene Expression Omnibus database (GEO). Differentially expressed-aberrantly methylated genes were identified using online Venn diagram tool. Based on fold change expression of differentially expressed-aberrantly methylated genes were chosen through heat map. Protein-protein interaction (PPI) network of the hub genes was constructed by Search Tool for the Retrieval of Interacting Genes (STRING). Gene expression and DNA methylation level of the hub genes were validated through UALCAN. Overall survival analysis of the hub genes was analysed through Kaplan-Meier plotter database for BC. A total of 72 upregulated-hypomethylated genes and 92 downregulated-hypermethylated genes were obtained from GSE10780, GSE10797, GSE21422, GSE42568, GSE61304, GSE61724, and GSE20713 datasets by GEO2R and Venn diagram tool. PPI network of the upregulated-hypomethylated hub genes (MRGBP, MANF, ARF3, HIST1H3D, GSK3B, HJURP, GPSM2, MATN3, KDELR2, CEP55, GSPT1, COL11A1, and COL1A1) and downregulated-hypermethylated hub genes were constructed (APOD, DMD, RBPMS, NR3C2, HOXA9, AMKY2, KCTD9, and EDN1). All the differentially expressed hub genes expression was validated in UALCAN database. 4 in 13 upregulated-hypomethylated and 5 in 8 downregulated-hypermethylated hub genes to be significantly hypomethylated or hypermethylated in BC were confirmed using UALCAN database (p < 0.05). MANF, HIST1H3D, HJURP, GSK3B, GPSM2, MATN3, KDELR2, CEP55, COL1A1, APOD, RBPMS, NR3C2, HOXA9, ANKMY2, and EDN1 were significantly (p < 0.05) associated with poor overall survival (OS). The identified aberrantly methylated-differentially expressed genes and their related pathways and function in BC can serve as novel diagnostic and prognostic biomarkers and therapeutic targets.Please confirm if the author names are presented accurately and in the correct sequence (given name, middle name/initial, family name). Author 4 Given name: [Jeewan Ram] Last name [Vishnoi]. Also, kindly confirm the details in the metadata are correct.It is correct.
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Affiliation(s)
- Ashita Gadwal
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India
| | - Purvi Purohit
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India.
| | - Manoj Khokhar
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India
| | - Jeewan Ram Vishnoi
- Department of Oncosurgery, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India
| | - Puneet Pareek
- Department of Radiation Oncology, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India
| | - Ramkaran Choudhary
- Department of General Surgery, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India
| | - Poonam Elhence
- Department of Pathology, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India
| | - Mithu Banerjee
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India
| | - Praveen Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Basni Industrial Area, MIA 2nd Phase, Basni, Jodhpur, Rajasthan, 342005, India
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Current Update on Nanotechnology-Based Approaches in Ovarian Cancer Therapy. Reprod Sci 2023; 30:335-349. [PMID: 35585292 DOI: 10.1007/s43032-022-00968-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/06/2022] [Indexed: 10/18/2022]
Abstract
Ovarian cancer is one of the leading causes of cancer-related deaths among women. The drawbacks of conventional therapeutic strategies encourage researchers to look for alternative strategies, including nanotechnology. Nanotechnology is one of the upcoming domains of science that is rechanneled towards targeted cancer therapy and diagnosis. Nanocarriers such as dendrimers, liposomes, polymer micelles, and polymer nanoparticles present distinct surface characteristics in morphology, surface chemistry, and mode of action that help differentiate normal and malignant cells, which paves the way for target-specific drug delivery. Similarly, nanoparticles have been strategically utilized as efficacious vehicles to deliver drugs that alter the epigenetic modifications in epigenetic therapy. Some studies suggest that the use of specialized target-modified nanoparticles in siRNA-based nanotherapy prevents internalization and improves the antitumor activity of siRNA by ensuring unrestrained entry of siRNA into the tumor vasculature and efficient intracellular delivery of siRNA. Moreover, research findings highlight the significance of utilizing nanoparticles as depots for photosensitive drugs in photodynamic therapy. The applicability of nanoparticles is further extended to medical imaging. They serve as contrast agents in combination with conventional imaging modalities such as MRI, CT, and fluorescence-based imaging to produce vivid and enhanced images of tumors. Therefore, this review aims to explore and delve deeper into the advent of various nanotechnology-based therapeutic and imaging techniques that provide non-invasive and effective means to tackle ovarian cancers.
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Tune BXJ, Sim MS, Poh CL, Guad RM, Woon CK, Hazarika I, Das A, Gopinath SCB, Rajan M, Sekar M, Subramaniyan V, Fuloria NK, Fuloria S, Batumalaie K, Wu YS. Matrix Metalloproteinases in Chemoresistance: Regulatory Roles, Molecular Interactions, and Potential Inhibitors. JOURNAL OF ONCOLOGY 2022; 2022:3249766. [PMID: 35586209 PMCID: PMC9110224 DOI: 10.1155/2022/3249766] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 02/08/2023]
Abstract
Cancer is one of the major causes of death worldwide. Its treatments usually fail when the tumor has become malignant and metastasized. Metastasis is a key source of cancer recurrence, which often leads to resistance towards chemotherapeutic agents. Hence, most cancer-related deaths are linked to the occurrence of chemoresistance. Although chemoresistance can emerge through a multitude of mechanisms, chemoresistance and metastasis share a similar pathway, which is an epithelial-to-mesenchymal transition (EMT). Matrix metalloproteinases (MMPs), a class of zinc and calcium-chelated enzymes, are found to be key players in driving cancer migration and metastasis through EMT induction. The aim of this review is to discuss the regulatory roles and associated molecular mechanisms of specific MMPs in regulating chemoresistance, particularly EMT initiation and resistance to apoptosis. A brief presentation on their potential diagnostic and prognostic values was also deciphered. It also aimed to describe existing MMP inhibitors and the potential of utilizing other strategies to inhibit MMPs to reduce chemoresistance, such as upstream inhibition of MMP expressions and MMP-responsive nanomaterials to deliver drugs as well as epigenetic regulations. Hence, manipulation of MMP expression can be a powerful tool to aid in treating patients with chemo-resistant cancers. However, much still needs to be done to bring the solution from bench to bedside.
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Affiliation(s)
- Bernadette Xin Jie Tune
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Maw Shin Sim
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Selangor 47500, Malaysia
| | - Rhanye Mac Guad
- Department of Biomedical Science and Therapeutics, Faculty of Medicine and Health Science, Universiti Malaysia Sabah, Kota Kinabalu, 88400 Sabah, Malaysia
| | - Choy Ker Woon
- Department of Anatomy, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh, 47000 Selangor, Malaysia
| | - Iswar Hazarika
- Department of Pharmacology, Girijananda Chowdhury Institute of Pharmaceutical Science, Guwahati 781017, India
| | - Anju Das
- Department of Pharmacology, Royal School of Pharmacy, Royal Global University, Guwahati 781035, India
| | - Subash C. B. Gopinath
- Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UniMAP), Arau, 02600 Perlis, Malaysia
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, Kangar, 01000 Perlis, Malaysia
| | - Mariappan Rajan
- Department of Natural Products Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai 625021, India
| | - Mahendran Sekar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Health Sciences, Royal College of Medicine Perak, Universiti Kuala Lumpur, Ipoh 30450, Perak, Malaysia
| | - Vetriselvan Subramaniyan
- Department of Pharmacology, School of Medicine, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Selangor 42610, Malaysia
| | | | - Shivkanya Fuloria
- Faculty of Pharmacy, AIMST University, Semeling, Bedong, Kedah 08100, Malaysia
| | - Kalaivani Batumalaie
- Department of Biomedical Sciences, Faculty of Health Sciences, Asia Metropolitan University, 81750 Johor Bahru, Malaysia
| | - Yuan Seng Wu
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Selangor 47500, Malaysia
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Selangor 47500, Malaysia
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Karimzadeh MR, Pourdavoud P, Ehtesham N, Qadbeigi M, Asl MM, Alani B, Mosallaei M, Pakzad B. Regulation of DNA methylation machinery by epi-miRNAs in human cancer: emerging new targets in cancer therapy. Cancer Gene Ther 2020; 28:157-174. [PMID: 32773776 DOI: 10.1038/s41417-020-00210-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/24/2020] [Accepted: 07/29/2020] [Indexed: 12/13/2022]
Abstract
Disruption in DNA methylation processes can lead to alteration in gene expression and function that would ultimately result in malignant transformation. In this way, studies have shown that, in cancers, methylation-associated silencing inactivates tumor suppressor genes, as effectively as mutations. DNA methylation machinery is composed of several genes, including those with DNA methyltransferases activity, proteins that bind to methylated cytosine in the promoter region, and enzymes with demethylase activity. Based on a prominent body of evidence, DNA methylation machinery could be regulated by microRNAs (miRNAs) called epi-miRNAs. Numerous studies demonstrated that dysregulation in DNA methylation regulators like upstream epi-miRNAs is indispensable for carcinogenesis; consequently, the malignant capacity of these cells could be reversed by restoring of this regulatory system in cancer. Conceivably, recognition of these epi-miRNAs in cancer cells could not only reveal novel molecular entities in carcinogenesis, but also render promising targets for cancer therapy. In this review, at first, we have an overview of the methylation alteration in cancers, and the effect of this phenomenon in miRNAs expression and after that, we conduct an in-depth discussion about the regulation of DNA methylation regulators by epi-miRNAs in cancer cells.
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Affiliation(s)
- Mohammad Reza Karimzadeh
- Department of medical Genetics, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | | | - Naeim Ehtesham
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Masood Movahedi Asl
- Non-Communicable Diseases Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrang Alani
- Department of Applied Cell Sciences, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Meysam Mosallaei
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bahram Pakzad
- Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran.
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Adeodato CSR, Alves GG, Botelho AMN, Caldas IP, Gonçalves FP, Pinto LFR, Lima SCS, Fagundes MCN, Masterson D, Scelza P, Scelza MFZ. Association of DNA sequence-independent genetic regulatory mechanisms with apical periodontitis: A scoping review. Arch Oral Biol 2020; 115:104737. [PMID: 32387743 DOI: 10.1016/j.archoralbio.2020.104737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Different studies in the last decade have proposed that gene expression alterations that are independent of the DNA sequence may also play an important role in periapical disease. The present study aimed to assess the available evidence supporting a relationship between these alterations and apical periodontitis through a scoping review. DESIGN Specific strategies were developed for different databases (MEDLINE via PubMed, Cochrane Library, Scopus, Web of Science, and Virtual Health Library) and a search performed by March 1st, 2019. The evidence sources were selected according to the eligibility criteria and underwent a critical appraisal of methodological quality. RESULTS The initial search retrieved 212 references, with eight eligible articles after the removal of replicates and application of exclusion criteria. Five studies identified altered DNA methylation on inflammatory response genes (FOXP3, CXCL3, FADD, MMP2, MMP9, IFNG, IL4, IL12) on AP patients. Three others identified the alterations on the expression of several microRNAs (miR-29b, 106b, 125b, 143, 146a, 155, 198) during AP. No evidence was identified regarding mechanisms of histone methylation, or of epigenetic heritability or stability. CONCLUSIONS There is available evidence for the involvement of different genetic regulatory mechanisms independent of changes in DNA sequence in the development or severity of apical periodontitis. However, due to methodological limitations, further research must be performed before novel therapies and diagnostic tools for AP may arise from these data.
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Affiliation(s)
- Caroline Sousa Ribeiro Adeodato
- Post-graduation Program in Dentistry of Fluminense Federal University (UFF), Mario Santos Braga Street, no 28, 24020-140, Niteroi, RJ, Brazil
| | - Gutemberg Gomes Alves
- Clinical Research Unit of the Antonio Pedro Hospital, Fluminense Federal University, Niteroi, RJ, Brazil
| | - Ana Maria Nunes Botelho
- Laboratory of Experimental Culture Cell (LECCel), Faculty of Dentistry, Fluminense Federal University (UFF) Mario Santos Braga Street, no 28, 24020-140, Niteroi, RJ, Brazil
| | - Isleine Portal Caldas
- Post-graduation Program in Dentistry of Fluminense Federal University (UFF), Mario Santos Braga Street, no 28, 24020-140, Niteroi, RJ, Brazil
| | - Fabiano Palmeira Gonçalves
- Post-graduation Program in Dentistry of Fluminense Federal University (UFF), Mario Santos Braga Street, no 28, 24020-140, Niteroi, RJ, Brazil
| | - Luis Felipe Ribeiro Pinto
- Molecular Carcinogenesis Program of National Cancer Institute (INCA), Andre Cavalcanti Street, no 37, 20231-050, Rio de Janeiro, Brazil
| | - Sheila Coelho Soares Lima
- Molecular Carcinogenesis Program of National Cancer Institute (INCA), Andre Cavalcanti Street, no 37, 20231-050, Rio de Janeiro, Brazil
| | - Marina Chianello Nicolau Fagundes
- Molecular Carcinogenesis Program of National Cancer Institute (INCA), Andre Cavalcanti Street, no 37, 20231-050, Rio de Janeiro, Brazil
| | - Daniele Masterson
- Central Library of the Health Science Center University Federal of Rio de Janeiro (UFRJ), Carlos Chagas Filho Avenue, no 373, 21940-902, Rio de Janeiro, Brazil
| | - Pantaleo Scelza
- Geriatric Dentistry Department, Faculty of Dentistry of Fluminense Federal University (UFF), Mario Santos Braga Street, no 28, 24020-140, Niteroi, RJ, Brazil
| | - Miriam Fátima Zaccaro Scelza
- Laboratory of Experimental Culture Cell (LECCel), Faculty of Dentistry, Fluminense Federal University (UFF) Mario Santos Braga Street, no 28, 24020-140, Niteroi, RJ, Brazil; Geriatric Dentistry Department, Faculty of Dentistry of Fluminense Federal University (UFF), Mario Santos Braga Street, no 28, 24020-140, Niteroi, RJ, Brazil; Endodontics Department, Faculty of Dentistry, Fluminense Federal University (UFF) Mario Santos Braga Street, no 28, 24020-140, Niteroi, RJ, Brazil.
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Wang C, Feng Y, Zhang C, Cheng D, Wu R, Yang Y, Sargsyan D, Kumar D, Kong AN. PTEN deletion drives aberrations of DNA methylome and transcriptome in different stages of prostate cancer. FASEB J 2019; 34:1304-1318. [PMID: 31914691 DOI: 10.1096/fj.201901205rr] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 12/11/2022]
Abstract
Phosphatase and tensin homolog located on chromosome 10 (PTEN) is a tumor suppressor gene and one of the most frequently mutated/deleted genes in human prostate cancer (PCa). However, how PTEN deletion would impact the epigenome and transcriptome alterations remain unknown. This hypothesis was tested in a prostate-specific PTEN-/- (KO) mouse prostatic adenocarcinoma model through DNA methyl-Seq and RNA-Seq analyses. Examination of cancer genomic datasets revealed that PTEN is expressed at lower levels in PTEN-deleted tumor samples than in normal solid tissue samples. Methylome and transcriptome profiling identified several inflammatory responses and immune response signaling pathways, including NF-kB signaling, IL-6 signaling, LPS/IL-1-mediated inhibition of RXR Function, PI3K in B lymphocytes, iCOS-iCOSL in T helper cells, and the role of NFAT in regulating the immune response, were affected by PTEN deletion. Importantly, a small subset of genes that showed DNA hypermethylation or hypomethylation was correlated with decreased or increased gene expression including CXCL1. quantitative polymerase chain reaction analyses of representative genes validated the RNA-Seq results. Histopathological examinations showed that the severity of prostatic intraepithelial neoplasia and inflammation development gradually increased as PTEN null mice aged. Collectively, these findings suggest that loss of PTEN drives global changes in DNA CpG methylation and transcriptomic gene expression and highly associated with several inflammatory and immune molecular pathways during PCa development. These biomarkers could be valuable molecular targets for cancer drug discovery and development against PCa.
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Affiliation(s)
- Chao Wang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Yaping Feng
- Genomics Core Facility, Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Chengyue Zhang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - David Cheng
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Graduate Program of Pharmaceutical Sciences, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Renyi Wu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Yuqing Yang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Davit Sargsyan
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Graduate Program of Pharmaceutical Sciences, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Dibyendu Kumar
- Genomics Core Facility, Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Ah-Ng Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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Non-coding RNAs: Regulators of glioma cell epithelial-mesenchymal transformation. Pathol Res Pract 2019; 215:152539. [DOI: 10.1016/j.prp.2019.152539] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/29/2019] [Accepted: 07/12/2019] [Indexed: 12/14/2022]
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Gonzalez-Molina J, Gramolelli S, Liao Z, Carlson JW, Ojala PM, Lehti K. MMP14 in Sarcoma: A Regulator of Tumor Microenvironment Communication in Connective Tissues. Cells 2019; 8:cells8090991. [PMID: 31466240 PMCID: PMC6770050 DOI: 10.3390/cells8090991] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/24/2019] [Accepted: 08/27/2019] [Indexed: 12/12/2022] Open
Abstract
Sarcomas are deadly malignant tumors of mesenchymal origin occurring at all ages. The expression and function of the membrane-type matrix metalloproteinase MMP14 is closely related to the mesenchymal cell phenotype, and it is highly expressed in most sarcomas. MMP14 regulates the activity of multiple extracellular and plasma membrane proteins, influencing cell–cell and cell–extracellular matrix (ECM) communication. This regulation mediates processes such as ECM degradation and remodeling, cell invasion, and cancer metastasis. Thus, a comprehensive understanding of the biology of MMP14 in sarcomas will shed light on the mechanisms controlling the key processes in these diseases. Here, we provide an overview of the function and regulation of MMP14 and we discuss their relationship with clinical and pre-clinical MMP14 data in both adult and childhood sarcomas.
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Affiliation(s)
- Jordi Gonzalez-Molina
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 17177 Stockholm, Sweden.
- Department of Oncology-Pathology, Karolinska Institutet, 17176 Stockholm, Sweden.
| | - Silvia Gramolelli
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Zehuan Liao
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 17177 Stockholm, Sweden
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Joseph W Carlson
- Department of Oncology-Pathology, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Päivi M Ojala
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
- Section of Virology, Division of Infectious Diseases, Department of Medicine, Imperial College London, London W2 1NY, UK
| | - Kaisa Lehti
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 17177 Stockholm, Sweden.
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland.
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Yang SD, Ahn SH, Kim JI. 3-Oxoacid CoA transferase 1 as a therapeutic target gene for cisplatin-resistant ovarian cancer. Oncol Lett 2017; 15:2611-2618. [PMID: 29434981 DOI: 10.3892/ol.2017.7560] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/03/2017] [Indexed: 01/28/2023] Open
Abstract
Ovarian cancer (OC) is the second leading cause of mortality from gynecological malignancies and has the highest mortality rate worldwide. As it is commonly asymptomatic during the early stages of the disease, >70% of patients with OC are diagnosed at advanced stages with metastasis. Despite treatment methods, including optimal debulking surgery and chemotherapy with the platinum-based drug cisplatin, OC recurrence is often inevitable, with an overall 5-year survival rate of 45%, mostly due to the steady development of cisplatin resistance. To identify genes involved in cisplatin resistance, the present study determined the half-maximal inhibitory concentrations of eight different OC cell lines and classified them into two groups (sensitive and resistant). mRNA expression was analyzed with GeneChip Human Gene 1.0 ST Arrays, and DNA methylation profiles were evaluated with the HumanMethylation450 BeadChip. Using an integrated approach of analyzing gene expression levels and DNA methylation profiles simultaneously, 26 genes were selected that were differentially expressed and methylated between the resistant and sensitive groups. Among these 26 genes, 3-oxoacid CoA transferase 1 (OXCT1), which was demonstrated to be downregulated and hypermethylated at promoter CpGs in the cisplatin-resistant group compared with the cisplatin-sensitive group, was selected for further investigation. Treatment with a DNA methyltransferase inhibitor restored hypermethylation-mediated gene silencing of OXCT1 in the cisplatin-resistant group, but not in the cisplatin-sensitive group. Furthermore, overexpression of OXCT1 conferred sensitivity to cisplatin in OC cells. The results of the present study suggest that OXCT1 serves an important role in conferring cisplatin sensitivity, and may provide a potential therapeutic target for cisplatin chemotherapy in patients with recurrent OC.
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Affiliation(s)
- San-Duk Yang
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 110-799, Republic of Korea
| | - So Hee Ahn
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, Republic of Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 110-799, Republic of Korea.,Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, Republic of Korea
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Sonnenburg D, Spinella MJ, Albany C. Epigenetic Targeting of Platinum Resistant Testicular Cancer. Curr Cancer Drug Targets 2017; 16:789-795. [PMID: 26694252 DOI: 10.2174/1568009616666151222150359] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/11/2015] [Accepted: 12/18/2015] [Indexed: 02/08/2023]
Abstract
The involvement of epigenetic aberrations in the development and progression of tumors is now well established. However, little is known of the epigenetic alterations in testicular cancer and particularly in platinum refractory germ cell tumors. Germ cell derived testicular cancers, as compared to somatic tumors, appear to have a unique epigenetic profile that features more extensive DNA hypomethylation. Emerging data from clinical specimens suggest that epigenetic aberrations, especially DNA hypermethylation, can contribute to chemotherapy resistance and poor clinical outcomes in testicular germ cell tumors. Recent data indicate that testicular cancer cells, even those resistant to platinum, are highly sensitive to low doses of demethylating agents. Based on these promising preclinical studies, we suggest that DNA methylation inhibitors in combination with chemotherapeutic agents may offer a path to overcome acquired drug resistance in testicular cancer, laying the foundation and rationale for testing this class of epigenetic drugs in the clinical setting. In this mini-review we provide a brief overview of the promise of DNA methylation therapy to treat patients with refractory cancer of the testes.
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Affiliation(s)
| | | | - Costantine Albany
- Department of Medicine, Indiana University Melvin and Bren Simon Cancer Center, 535 Barnhull Drive RT-473, Indianapolis, IN 46202, USA.
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Lee MH, Cho ER, Lim JE, Jee SH. Association between serum persistent organic pollutants and DNA methylation in Korean adults. ENVIRONMENTAL RESEARCH 2017; 158:333-341. [PMID: 28672131 DOI: 10.1016/j.envres.2017.06.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/17/2017] [Accepted: 06/19/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Exposure to persistent organic pollutants (POPs) has been associated with epigenetic changes such as DNA methylation, which can influence human health. However, the association between POPs and DNA methylation by sex was not shown in previous studies. OBJECTIVES We investigated the association between POPs and DNA methylation in men and women using a larger population. METHODS A cross-sectional study was conducted using the data of 444 Koreans (253 men and 191 women). Measurements for sixteen different POPs, including six organochlorine pesticides (OCPs) and ten polychlorinated biphenyls (PCBs) were taken in serum. DNA methylation via Alu and LINE-1 in peripheral leukocytes was measured by pyrosequencing. To evaluate the association between POPs and DNA methylation, the Pearson's correlation and multiple linear regression analyses were performed. RESULTS Except for PCB52 and PCB101, we found significant inverse associations between p,p'-DDE, cis-Heptachlor epoxide, and PCBs and Alu assay in men after adjusting for age, BMI, smoking status, and alcohol consumption (β = -0.67 for p,p'-DDE; -0.28 for cis-Heptachlor epoxide; in the range from -0.43 to -1.60 for PCBs). In women, PCB153 and PCB180 showed statistically significant inverse association with Alu assay (β = -0.22 for PCB153; -0.22 for PCB180). Except for PCB101, p,p'-DDE and PCBs were positively associated with LINE-1 assay in women (β = 0.48 for p,p'-DDE; in the range from 0.40-0.89 for PCBs) while p,p'-DDE, PCB153, and PCB180 showed positive associations with LINE-1 assay in men (β = 0.55 for p,p'-DDE; 0.65 for PCB153; 1.02 for PCB180). CONCLUSIONS We found that several POPs were associated with global DNA hypomethylation in the Alu assay for men and global DNA hypermethylation in the LINE-1 assay for women.
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Affiliation(s)
- Mi Hwa Lee
- Institute for Health and Society, Hanyang University, Seoul, Republic of Korea
| | - Eo Rin Cho
- Institute for Health Promotion & Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea
| | - Jung-Eun Lim
- Institute for Health Promotion & Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea; College of Pharmacy, Ewha Womans University, Seoul, Republic of Korea
| | - Sun Ha Jee
- Institute for Health Promotion & Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea.
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13
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DNA methylation-regulated microRNA pathways in ovarian serous cystadenocarcinoma: A meta-analysis. Comput Biol Chem 2016; 65:154-164. [DOI: 10.1016/j.compbiolchem.2016.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/07/2016] [Indexed: 12/31/2022]
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14
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Prestegui-Martel B, Bermúdez-Lugo JA, Chávez-Blanco A, Dueñas-González A, García-Sánchez JR, Pérez-González OA, Padilla-Martínez II, Fragoso-Vázquez MJ, Mendieta-Wejebe JE, Correa-Basurto AM, Méndez-Luna D, Trujillo-Ferrara J, Correa-Basurto J. N-(2-hydroxyphenyl)-2-propylpentanamide, a valproic acid aryl derivative designed in silico with improved anti-proliferative activity in HeLa, rhabdomyosarcoma and breast cancer cells. J Enzyme Inhib Med Chem 2016; 31:140-149. [PMID: 27483122 DOI: 10.1080/14756366.2016.1210138] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Epigenetic alterations are associated with cancer and their targeting is a promising approach for treatment of this disease. Among current epigenetic drugs, histone deacetylase (HDAC) inhibitors induce changes in gene expression that can lead to cell death in tumors. Valproic acid (VPA) is a HDAC inhibitor that has antitumor activity at mM range. However, it is known that VPA is a hepatotoxic drug. Therefore, the aim of this study was to design a set of VPA derivatives adding the arylamine core of the suberoylanilide hydroxamic acid (SAHA) with different substituents at its carboxyl group. These derivatives were submitted to docking simulations to select the most promising compound. The compound 2 (N-(2-hydroxyphenyl)-2-propylpentanamide) was the best candidate to be synthesized and evaluated in vitro as an anti-cancer agent against HeLa, rhabdomyosarcoma and breast cancer cell lines. Compound 2 showed a better IC50 (μM range) than VPA (mM range) on these cancer cells. And also, 2 was particularly effective on triple negative breast cancer cells. In conclusion, 2 is an example of drugs designed in silico that show biological properties against human cancer difficult to treat as triple negative breast cancer.
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Affiliation(s)
- Berenice Prestegui-Martel
- a Laboratorio de Modelado Molecular y Bioinformática , Laboratorio de Bioquímica, Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional , Plan de San Luis y Díaz Mirón, Ciudad de México , México
| | - Jorge Antonio Bermúdez-Lugo
- a Laboratorio de Modelado Molecular y Bioinformática , Laboratorio de Bioquímica, Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional , Plan de San Luis y Díaz Mirón, Ciudad de México , México
| | - Alma Chávez-Blanco
- b División de Investigación Básica, Instituto Nacional de Cancerología , Tlalpan, Sección XVI, Ciudad de México , México
| | - Alfonso Dueñas-González
- c Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México/Instituto Nacional de Cancerología , Ciudad de México , México
| | - José Rubén García-Sánchez
- d Laboratorio de Oncología Molecular y Estrés Oxidativo , Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional , Plan de San Luis y Díaz Mirón, Ciudad de México , México
| | - Oscar Alberto Pérez-González
- e Laboratorio de Oncología Experimental , Instituto Nacional de Pediatría , Coyoacán, Insurgentes Cuicuilco, Ciudad de México , México , and
| | - Itzia Irene Padilla-Martínez
- f Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional , Barrio La Laguna Ticomán, Ciudad de México , México
| | - Manuel Jonathan Fragoso-Vázquez
- a Laboratorio de Modelado Molecular y Bioinformática , Laboratorio de Bioquímica, Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional , Plan de San Luis y Díaz Mirón, Ciudad de México , México
| | - Jessica Elena Mendieta-Wejebe
- a Laboratorio de Modelado Molecular y Bioinformática , Laboratorio de Bioquímica, Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional , Plan de San Luis y Díaz Mirón, Ciudad de México , México
| | - Ana María Correa-Basurto
- a Laboratorio de Modelado Molecular y Bioinformática , Laboratorio de Bioquímica, Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional , Plan de San Luis y Díaz Mirón, Ciudad de México , México
| | - David Méndez-Luna
- a Laboratorio de Modelado Molecular y Bioinformática , Laboratorio de Bioquímica, Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional , Plan de San Luis y Díaz Mirón, Ciudad de México , México
| | - José Trujillo-Ferrara
- a Laboratorio de Modelado Molecular y Bioinformática , Laboratorio de Bioquímica, Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional , Plan de San Luis y Díaz Mirón, Ciudad de México , México
| | - José Correa-Basurto
- a Laboratorio de Modelado Molecular y Bioinformática , Laboratorio de Bioquímica, Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional , Plan de San Luis y Díaz Mirón, Ciudad de México , México
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15
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KOUKOURA OURANIA, SIFAKIS STAVROS, SPANDIDOS DEMETRIOSA. DNA methylation in endometriosis (Review). Mol Med Rep 2016; 13:2939-48. [PMID: 26934855 PMCID: PMC4805102 DOI: 10.3892/mmr.2016.4925] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/22/2016] [Indexed: 12/01/2022] Open
Abstract
Endometriosis is defined by the presence and growth of functional endometrial tissue, outside the uterine cavity, primarily in the ovaries, pelvic peritoneum and rectovaginal septum. Although it is a benign disease, it presents with malignant characteristics, such as invasion to surrounding tissues, metastasis to distant locations and recurrence following treatment. Accumulating evidence suggests that various epigenetic aberrations may play an essential role in the pathogenesis of endometriosis. Aberrant DNA methylation represents a possible mechanism repsonsible for this disease, linking gene expression alterations observed in endometriosis with hormonal and environmental factors. Several lines of evidence indicate that endometriosis may partially be due to selective epigenetic deregulations influenced by extrinsic factors. Previous studies have shed light into the epigenetic component of endometriosis, reporting variations in the epigenetic patterns of genes known to be involved in the aberrant hormonal, immunologic and inflammatory status of endometriosis. Although recent studies, utilizing advanced molecular techniques, have allowed us to further elucidate the possible association of DNA methylation with altered gene expression, whether these molecular changes represent the cause or merely the consequence of the disease is a question which remains to be answered. This review provides an overview of the current literature on the role of DNA methylation in the pathophysiology and malignant evolution of endometriosis. We also provide insight into the mechanisms through which DNA methylation-modifying agents may be the next step in the research of the pharmaceutical treatment of endometriosis.
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Affiliation(s)
- OURANIA KOUKOURA
- Department of Obstetrics and Gynecology, University Hospital of Larissa, Larissa 41500, Greece
| | - STAVROS SIFAKIS
- Department of Obstetrics and Gynecology, University Hospital of Heraklion, Heraklion 71003, Greece
| | - DEMETRIOS A. SPANDIDOS
- Laboratory of Clinical Virology, University of Crete Medical School, Heraklion 71409, Greece
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16
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Chu MM, Fishman D. Risk assessment for epithelial ovarian cancer: proposing a new approach to a deadly problem. Scand J Clin Lab Invest Suppl 2015; 244:63-7; discussion 66-7. [PMID: 25083896 DOI: 10.3109/00365513.2014.936688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Presently the majority of women diagnosed with epithelial ovarian cancer (EOC) have advanced stage disease (III-IV) with a poor 5-year survival rate (12-30 %). This significantly contrasts when early stage disease is detected, which has a 5-year survival rate approximating 90 %. Therefore, detection of early stage disease is critical to making an impact on outcome. By using genetic algorithms, modifications of transvaginal ultrasonography and use of novel biomarkers, we propose a risk assessment profile to identify at-risk women and enable ovarian cancer screening to become a reality. Such a novel algorithm starts by applying classic genetic pedigree assessment and uses a panel of multiple biomarkers that identify both phenotypic and genotypic expression of high-risk markers followed with conventional ultrasound and advanced ultrasound techniques such as microvascular contrast-enhancement as a secondary test. We presently employ a multidisciplinary program incorporating genetics, molecular biology, tumor immunology, gynecologic oncology and diagnostic imaging to identify asymptomatic high risk women.
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Affiliation(s)
- Mary M Chu
- Mount Sinai Medical Center, Department of Obstetrics, Gynecology and Reproductive Science , New York , USA
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17
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Basse C, Arock M. The increasing roles of epigenetics in breast cancer: Implications for pathogenicity, biomarkers, prevention and treatment. Int J Cancer 2014; 137:2785-94. [PMID: 25410431 DOI: 10.1002/ijc.29347] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/14/2014] [Indexed: 12/14/2022]
Abstract
Nowadays, the mechanisms governing the occurrence of cancer are thought to be the consequence not only of genetic defects but also of epigenetic modifications. Therefore, epigenetic has become a very attractive and increasingly investigated field of research in order to find new ways of prevention and treatment of neoplasia, and this is particularly the case for breast cancer (BC). Thus, this review will first develop the main known epigenetic modifications that can occur in cancer and then expose the future role that control of epigenetic modifications might play in prevention, prognostication, follow-up and treatment of BC. Indeed, epigenetic biomarkers found in peripheral blood might become new tools to detect BC, to define its prognostic and to predict its outcome, whereas epi-drugs might have an increasing potential of development in the next future. However, if DNA methyltransferase inhibitors and histone desacetylase inhibitors have shown encouraging results in BC, their action remains nonspecific. Thus, additional clinical studies are needed to evaluate more precisely the effects of these molecules, even if they have provided encouraging results in cotreatment and combined therapies. This review will also deal with the potential of RNA interference (RNAi) as epi-drugs. Finally, we will focus on the potential prevention of BC through epigenetic based on diet and we will particularly develop the possible place of isothiocyanates from cruciferous vegetables or of Genistein from soybean in a dietary program that might potentially reduce the risk of BC in large populations.
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Affiliation(s)
- Clémence Basse
- Medical Oncology Unit, Anticancer Center Henri Becquerel, Rouen, France
| | - Michel Arock
- Molecular Oncology and Pharmacology, LBPA CNRS UMR8113, Ecole Normale Supérieure de Cachan, Cachan, France
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18
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Mehedintu C, Plotogea MN, Ionescu S, Antonovici M. Endometriosis still a challenge. J Med Life 2014; 7:349-57. [PMID: 25408753 PMCID: PMC4233437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 06/25/2014] [Indexed: 12/01/2022] Open
Abstract
Endometriosis is a debilitating disease with features of chronic inflammation. Endometriosis appears to be one of the most common benign gynecological proliferations in premenopausal women since it is estimated that 10-15% of reproductive aged women suffer from pelvic endometriosis. The biology of endometriosis is unclear. Despite its prevalence, this disease remains poorly understood and current studies prove that there is no relationship between the extent of the disease and its symptomatology. There is no blood test available for the diagnosis of endometriosis. Up to this point, there is no single very successful option for the treatment of endometriosis. Due to the relatively poor efficacy of hormonal therapy for endometriosis, several other experimental therapies are currently undergoing clinical trial.
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19
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Anestopoulos I, Voulgaridou GP, Georgakilas AG, Franco R, Pappa A, Panayiotidis MI. Epigenetic therapy as a novel approach in hepatocellular carcinoma. Pharmacol Ther 2014; 145:103-19. [PMID: 25205159 DOI: 10.1016/j.pharmthera.2014.09.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/02/2014] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common type of liver malignancy and one with high fatality. Its 5-year survival rate remains low and thus, there is a need for improvement of current treatment strategies as well as development of novel targeted methodologies in order to optimize existing therapeutic protocols. To this end, only recently, it was discovered that its pathophysiology also involves epigenetic alterations in DNA methylation, histone modifications and/or non-coding microRNA patterns. Unlike genetic events, epigenetic alterations are reversible and thus potentially considered to be an alternative option in cancer treatment protocols. In this review, we describe the general characteristics and resulted major alterations of the epigenetic machinery as well as current state of progress of epigenetic therapy (via different single or combinatorial experimental approaches) in HCC.
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Affiliation(s)
- Ioannis Anestopoulos
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Alexandros G Georgakilas
- School of Applied Mathematical & Physical Sciences, National Technical University of Athens, Athens, Greece
| | - Rodrigo Franco
- Redox Biology Center, School of Veterinary Medicine & Biomedical Sciences, Redox Biology Center, University of Nebraska-Lincoln, USA
| | - Aglaia Pappa
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece
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20
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Hatzimichael E, Lagos K, Sim VR, Briasoulis E, Crook T. Epigenetics in diagnosis, prognostic assessment and treatment of cancer: an update. EXCLI JOURNAL 2014; 13:954-76. [PMID: 26417314 PMCID: PMC4464089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 07/29/2014] [Indexed: 11/06/2022]
Abstract
Cancer cells contain multiple genetic and epigenetic changes. The relative specificity of many epigenetic changes for neoplastic cells has allowed the identification of diagnostic, prognostic and predictive biomarkers for a number of solid tumors and hematological malignancies. Moreover, epigenetically-acting drugs are already in routine use for cancer and numerous additional agents are in clinical trials. Here, we review recent progress in the development and application of epigenetic strategies for the diagnosis, risk stratification and treatment of cancer.
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Affiliation(s)
| | - Konstantinos Lagos
- Department of Haematology, University Hospital of Ioannina, Ioannina, Greece
| | - Van Ren Sim
- Dundee Cancer Center, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | | | - Tim Crook
- Dundee Cancer Center, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
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21
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Pucci M, Rapino C, Di Francesco A, Dainese E, D'Addario C, Maccarrone M. Epigenetic control of skin differentiation genes by phytocannabinoids. Br J Pharmacol 2014; 170:581-91. [PMID: 23869687 DOI: 10.1111/bph.12309] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 06/28/2013] [Accepted: 07/03/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND AND PURPOSE Endocannabinoid signalling has been shown to have a role in the control of epidermal physiology, whereby anandamide is able to regulate the expression of skin differentiation genes through DNA methylation. Here, we investigated the possible epigenetic regulation of these genes by several phytocannabinoids, plant-derived cannabinoids that have the potential to be novel therapeutics for various human diseases. EXPERIMENTAL APPROACH The effects of cannabidiol, cannabigerol and cannabidivarin on the expression of skin differentiation genes keratins 1 and 10, involucrin and transglutaminase 5, as well as on DNA methylation of keratin 10 gene, were investigated in human keratinocytes (HaCaT cells). The effects of these phytocannabinoids on global DNA methylation and the activity and expression of four major DNA methyltransferases (DNMT1, 3a, 3b and 3L) were also examined. KEY RESULTS Cannabidiol and cannabigerol significantly reduced the expression of all the genes tested in differentiated HaCaT cells, by increasing DNA methylation of keratin 10 gene, but cannabidivarin was ineffective. Remarkably, cannabidiol reduced keratin 10 mRNA through a type-1 cannabinoid (CB1 ) receptor-dependent mechanism, whereas cannabigerol did not affect either CB1 or CB2 receptors of HaCaT cells. In addition, cannabidiol, but not cannabigerol, increased global DNA methylation levels by selectively enhancing DNMT1 expression, without affecting DNMT 3a, 3b or 3L. CONCLUSIONS AND IMPLICATIONS These findings show that the phytocannabinoids cannabidiol and cannabigerol are transcriptional repressors that can control cell proliferation and differentiation. This indicates that they (especially cannabidiol) have the potential to be lead compounds for the development of novel therapeutics for skin diseases.
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Affiliation(s)
- Mariangela Pucci
- Department of Biomedical Sciences, University of Teramo, Teramo, Italy
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22
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Hatzimichael E, Syed N, Lo Nigro C, Crook T. A blood test to identify when melanoma metastasizes: a reality for melanoma management? Melanoma Manag 2014; 1:11-14. [DOI: 10.2217/mmt.14.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Eleftheria Hatzimichael
- Interscience Molecular Oncology Laboratory, University of Ioannina Cancer Biobank Center, Ioannina, Greece
| | - Nel Syed
- Division of Brain Sciences, Imperial College, London, UK
| | - Cristiana Lo Nigro
- Laboratory of Cancer Genetics & Translational Oncology, Oncology Department, S. Croce University Hospital, Cuneo, Italy
| | - Tim Crook
- Dundee Cancer Center, University of Dundee, Ninewells Hospital & Medical School, Dundee, DD1 9SY, UK
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23
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Hatzimichael E, Syed N, Lo Nigro C, Rao B, Crook T. How detection of epigenetic alterations of blood-borne DNA could improve melanoma diagnosis. Expert Rev Mol Diagn 2014; 14:639-42. [PMID: 24926921 DOI: 10.1586/14737159.2014.928204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Detection in blood of the genetic and epigenetic changes present in metastatic cancers is opening up new possibilities in molecular diagnostics. A number of methodological and clinical issues await resolution before serum epigenetic biomarkers can be considered a routine part of the management of melanoma patients following primary excision. However, there is every possibility that blood testing for the presence of methylated DNA will become an integral part of the clinical follow-up of such patients. The ability to identify patients with subclinical (asymptomatic) metastatic melanoma, combined with new, highly active targeted and immunomodulatory agents, may lead to further improvements in outcomes for this patient population.
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Affiliation(s)
- Eleftheria Hatzimichael
- Interscience Molecular Oncology Laboratory, University of Ioannina Cancer Biobank Center, Ioannina, Greece
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24
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Farmen E, Hultman MT, Anglès d'Auriac M, Tollefsen KE. Development of a screening system for the detection of chemically induced DNA methylation alterations in a zebrafish liver cell line. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2014; 77:587-599. [PMID: 24754394 DOI: 10.1080/15287394.2014.887423] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Early molecular events with correlation to disease, such as aberrant DNA methylation, emphasize the importance of DNA methylation as a potential environmental biomarker. Currently, little is known regarding how various environmental contaminants and mixtures alter DNA methylation in aquatic organisms, and testing is both time- and labor-consuming. Therefore, the potential of an in vitro screening method was evaluated by exposing zebrafish liver cells (ZF-L) for 96 h to the nonmutagenic model substance 5'-azacytidine (AZA), as well as a selection of environmental pollutants such as sodium arsenite (NAS), 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), 17α-ethinylestradiol (EE2), and diethylstilbestrol (DES). Six single genes with reported and anticipated importance in cancer were selected for analysis. Methylation of gene promoter areas was monitored by bisulfite conversion and high-resolution melt (HRM) analysis after exposure to sublethal concentrations of the test compounds. Subsequently, results were validated with direct bisulfite sequencing. Exposure of ZF-L cells to 0.5 μM AZA for 96 h led to hypomethylation of genes with both low and high basal methylation indicating similarity to mechanism of action in mammals. Further, NAS, EE2, and DES were shown to induce significant alterations in methylation, whereas TCDD did not. It was concluded that cell line exposure in combination with HRM may provide an initial contaminant screening assay by quantifying DNA methylation alterations with high throughput capacity. In addition, the rapid determination of effects following contaminant exposure with this in vitro system points to the possibility for new in vivo applications to be useful for environmental monitoring.
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Affiliation(s)
- Eivind Farmen
- a Norwegian Institute for Water Research , Oslo , Norway
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25
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Siufi Neto J, Kho RM, Siufi DFDS, Baracat EC, Anderson KS, Abrão MS. Cellular, histologic, and molecular changes associated with endometriosis and ovarian cancer. J Minim Invasive Gynecol 2013; 21:55-63. [PMID: 23962574 DOI: 10.1016/j.jmig.2013.07.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 07/28/2013] [Accepted: 07/30/2013] [Indexed: 02/06/2023]
Abstract
Our understanding of the pathogenesis of endometriosis is rapidly evolving as early molecular events are increasingly identified. Endometriosis is associated with increased risk of ovarian cancer and exhibits neoplastic phenotypes including invasion of stromal tissue and lymphatic spread to distant organs. This review of the literature establishes the clinical, epidemiologic, and pathologic correlation between endometriosis and low-grade ovarian cancer. Genetic studies have demonstrated that endometriotic lesions have mutations in genes directly related to neoplasms, in particular the p53, KRAS, PTEN, and ARID1A genes, which suggests a direct transition from a subset of endometriotic lesions to invasive carcinomas. The identification of both genetic and epigenetic biomarkers including microRNAs are essential for identifying patients at risk for the transition to neoplasia.
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Affiliation(s)
| | - Rosanne M Kho
- Department of Surgical Gynecology, Mayo Clinic Arizona, Phoenix
| | | | - Edmund Chada Baracat
- Department of Obstetrics and Gynecology, University of the State of São Paulo, São Paulo, Brazil
| | | | - Maurício Simões Abrão
- Department of Obstetrics and Gynecology, University of the State of São Paulo, São Paulo, Brazil
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26
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Epigenetic drug combination induces genome-wide demethylation and altered gene expression in neuro-ectodermal tumor-derived cell lines. Cell Oncol (Dordr) 2013; 36:351-62. [PMID: 23864224 DOI: 10.1007/s13402-013-0140-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2013] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Epigenetic alterations are inherent to cancer cells, and epigenetic drugs are currently primarily used to treat hematological malignancies. Pediatric neuro-ectodermal tumors originate from neural crest cells and also exhibit epigenetic alterations involving e.g. apoptotic pathways, which suggests that these tumors may also be sensitive to epigenetic drugs. This notion prompted us to assess molecular and functional effects of low dosage epigenetic drugs in neuro-ectodermal tumor-derived cell lines of pediatric origin. RESULTS In 17 neuroblastoma (NBL) and 5 peripheral primitive neuro-ectodermal tumor (PNET) cell lines a combination treatment of 5-aza-2'-deoxycytidine (DAC) and Trichostatin A (TSA) at nanomolar dosages was found to reduce proliferation and to induce wide-spread DNA demethylation, accompanied by major changes in gene expression profiles. Approximately half of the genes that were significantly up-regulated upon treatment exhibited a significant demethylation in their promoter regions. In the NBL cell lines, almost every cellular pathway (193/200) investigated showed expression alterations after treatment, especially a marked up-regulation of genes in the p53 pathway. The combination treatment also resulted in up-regulation of known epigenetically regulated genes such as X-chromosomal genes, tissue-specific genes and a limited number of imprinted genes, as well as known tumor suppressor genes and oncogenes. CONCLUSIONS Nanomolar dosages of epigenetic drugs have a dramatic impact on the genomes of neuro-ectodermal tumor-derived cell lines, including alterations in DNA methylation and concomitant alterations in gene expression.
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Nguyen L, Cardenas-Goicoechea SJ, Gordon P, Curtin C, Momeni M, Chuang L, Fishman D. Biomarkers for early detection of ovarian cancer. ACTA ACUST UNITED AC 2013; 9:171-85; quiz 186-7. [PMID: 23477323 DOI: 10.2217/whe.13.2] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ovarian cancer is the most lethal gynecological malignancy. However, effective screening strategies have not been established and continue to be elusive. A good screening test must adequately address validity, reliability, yield, cost, acceptance and follow-up services. An ideal screening test for ovarian cancer must have a high sensitivity in order to correctly diagnose all women with the disease and a high specificity to avoid false-positive results. The current screening modalities of bimanual examination, CA-125 and transvaginal ultrasonography together allow us to detect only 30-45% of women with early-stage disease. Recent developments in proteomic and genomic research have identified a number of potential biomarkers. Although panels of tumor markers and proteomic-based technologies may improve the positive predictive value, all markers require validation and interfacing with newly developed diagnostic imaging technologies. While a large amount of information on miRNAs has been promising, much remains to be elucidated. This review will examine the current status of biomarkers and technologies of interest in the effort of early detection of ovarian cancer.
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Affiliation(s)
- Long Nguyen
- Mount Sinai Medical Center, New York, NY 10029, USA.
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Nigro CL, Wang H, McHugh A, Lattanzio L, Matin R, Harwood C, Syed N, Hatzimichael E, Briasoulis E, Merlano M, Evans A, Thompson A, Leigh I, Fleming C, Inman GJ, Proby C, Crook T. Methylated Tissue Factor Pathway Inhibitor 2 (TFPI2) DNA in Serum Is a Biomarker of Metastatic Melanoma. J Invest Dermatol 2013; 133:1278-85. [DOI: 10.1038/jid.2012.493] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Zhang C, Su ZY, Khor TO, Shu L, Kong ANT. Sulforaphane enhances Nrf2 expression in prostate cancer TRAMP C1 cells through epigenetic regulation. Biochem Pharmacol 2013; 85:1398-404. [PMID: 23416117 DOI: 10.1016/j.bcp.2013.02.010] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 02/06/2013] [Accepted: 02/07/2013] [Indexed: 02/07/2023]
Abstract
Growing evidence suggests epigenetic alteration is involved during the development and progression of prostate cancer. Previously, we found Nrf2, a key regulator of cellular antioxidant defense systems, was silenced through epigenetic mechanism during tumorigenesis in vivo TRAMP mice and in vitro TRAMP C1 cells. Sulforaphane (SFN) in cruciferous vegetable has been demonstrated to be a potent cancer prevention agent for years. The aim of this study is to investigate the potential of SFN to restore Nrf2 expression in TRAMP C1 cells through epigenetic modifications. Bisulfite genomic sequencing results indicated that SFN treatment led to demethylation of the first 5 CpGs in the promoter region of the Nrf2 gene in TRAMP C1 cells. Using methylation DNA immunoprecipitation (MeDIP) assay, SFN significantly reduced the ratio of anti-mecyt antibody binding to the Nrf2 promoter containing the first 5 CpGs. SFN increased mRNA and protein expressions of Nrf2 and Nrf2 downstream target gene NQO-1. In addition, SFN decreased the protein levels of DNMT1 and DNMT3a. SFN treatment also attenuated the protein expression levels of HDACs 1, 4, 5, and 7 while increased the level of active chromatin marker acetyl-Histone 3 (Ac-H3). SFN treatments also increased chromatin-immunoprecipitated DNA of Nrf2 gene promoter using anti-Ac-H3 antibody. Taken together, our current study shows that SFN regulates Nrf2's CpGs demethylation and reactivation in TRAMP C1 cells, suggesting SFN may exert its chemopreventive effect in part via epigenetic modifications of Nrf2 gene with subsequent induction of its downstream anti-oxidative stress pathway.
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Affiliation(s)
- Chengyue Zhang
- Center for Cancer Prevention Research, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, USA
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Chiou YS, Sang S, Cheng KH, Ho CT, Wang YJ, Pan MH. Peracetylated (−)-epigallocatechin-3-gallate (AcEGCG) potently prevents skin carcinogenesis by suppressing the PKD1-dependent signaling pathway in CD34 + skin stem cells and skin tumors. Carcinogenesis 2013; 34:1315-22. [DOI: 10.1093/carcin/bgt042] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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Kaplun L, Fridman AL, Chen W, Levin NK, Ahsan S, Petrucelli N, Barrick JL, Gold R, Land S, Simon MS, Morris RT, Munkarah AR, Tainsky MA. Variants in the Signaling Protein TSAd are Associated with Susceptibility to Ovarian Cancer in BRCA1/2 Negative High Risk Families. Biomark Insights 2012; 7:151-7. [PMID: 23300341 PMCID: PMC3528110 DOI: 10.4137/bmi.s10815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A substantial fraction of familial ovarian cancer cases cannot be attributed to specific genetic factors. The discovery of additional susceptibility genes will permit a more accurate assessment of hereditary cancer risk and allow for monitoring of predisposed women in order to intervene at the earliest possible stage. We focused on a population with elevated familial breast and ovarian cancer risk. In this study, we identified a SNP rs926103 whose minor allele is associated with predisposition to ovarian but not breast cancer in a Caucasian high-risk population without BRCA1/BRCA2 mutations. We have found that the allelic variation of rs926103, which alters amino acid 52 of the encoded protein SH2D2A/TSAd, results in differences in the activity of this protein involved in multiple signal transduction pathways, including regulation of immune response, tumor vascularization, cell growth, and differentiation. Our observation provides a novel candidate genetic biomarker of elevated ovarian cancer risk in members of high-risk families without BRCA1/2 mutations, as well as a potential therapeutic target, TSAd.
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Affiliation(s)
- Ludmila Kaplun
- Program in Molecular Imaging and Biomarkers, Wayne State University School of Medicine, Detroit MI. ; Department of Oncology, Wayne State University School of Medicine, Detroit MI
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Back SJ, Im M, Sohn KC, Choi DK, Shi G, Jeong NJ, Lee Y, Seo YJ, Kim CD, Lee JH. Epigenetic Modulation of Gene Expression during Keratinocyte Differentiation. Ann Dermatol 2012; 24:261-6. [PMID: 22879708 PMCID: PMC3412233 DOI: 10.5021/ad.2012.24.3.261] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 07/26/2011] [Accepted: 08/01/2011] [Indexed: 02/03/2023] Open
Abstract
Background Epigenetic modulation of gene expression occurs by various methods, including DNA methylation and histone modification. DNA methylation of specific genes may affect the chromatin structure, preventing access by the transcriptional machinery. Although gene expression is dramatically changed during keratinocyte differentiation, there is no evidence of epigenetic modulation during the process of epidermal stratification. Objective We investigated whether epigenetic modulation is involved in keratinocyte differentiation-specific gene regulation. Methods We used trypsin to produce epidermal fragmentation (named T1-T4) and performed a morphological analysis using hematoxylin-eosin stain and cytokeratin expression based on reverse transcription polymerase chain reaction. We then constructed a DNA methylation microarray. Results Each epidermal fragment showed morphological features of the epithelial layer. T1 represented the basal layer, T2 was the spinous layer, T3 was the granular layer, and T4 was the cornified layer. The level of the K14 proliferation marker was increased in the T1 fraction, and the level of K10 differentiation marker was increased in the T2-T4 fractions. Using a methylation microarray with the T1 and T4 fractions, we obtained many hypermethylated and hypomethylated genes from differentiated keratinocytes. Conclusion The importance of epigenetic modulation in target gene expression during keratinocyte differentiation is identified.
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Affiliation(s)
- Seung Ju Back
- Department of Dermatology, Chungnam National University School of Medicine, Daejeon, Korea
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Lo Nigro C, Monteverde M, Lee S, Lattanzio L, Vivenza D, Comino A, Syed N, McHugh A, Wang H, Proby C, Garrone O, Merlano M, Hatzimichael E, Briasoulis E, Gojis O, Palmieri C, Jordan L, Quinlan P, Thompson A, Crook T. NT5E CpG island methylation is a favourable breast cancer biomarker. Br J Cancer 2012; 107:75-83. [PMID: 22653144 PMCID: PMC3389412 DOI: 10.1038/bjc.2012.212] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Relapse risk assessment and individual treatment recommendations remain suboptimal for breast cancer patients. In the light of existing preclinical and clinical data, we studied NT5E (5'-nucleotidase, ecto) expression and NT5E CpG island methylation in breast cancer. METHODS We used RT-PCR, qPCR, methylation-specific PCR and pyrosequencing to analyse NT5E in breast carcinoma cell lines and primary and breast carcinomas. RESULTS NT5E CpG island methylation was inversely associated with NT5E expression in breast carcinoma cell lines. In clinical series, patients whose primary tumours had NT5E CpG island methylation were less likely to develop metastasis (P=0.003, OR=0.34, 95% CI: 0.17-0.69). In 3/4 paired samples, NT5E was methylated in primary tumours and demethylated in CNS metastases. Patients progressing to non-visceral as compared with visceral metastases were more likely to have NT5E CpG island methylation in primary tumours (P=0.01, OR=11.8). Patients with tumours lacking detectable methylation had shorter disease-free survival (DFS) (P=0.001, HR=2.7) and overall survival (OS) (P=0.001, HR=3). The favourable prognostic value of NT5E methylation was confirmed in oestrogen receptor negative (P=0.011, HR=3.27, 95% CI: 1.31-8.12) and in triple negative cases (P=0.004; HR=6.2, 95% CI: 1.9-20). Moreover, we observed a more favourable outcome to adjuvant chemotherapy in patients whose tumours were positive for NT5E CpG island methylation: DFS (P=0.0016, HR=5.1, 95% CI: 1.8-14.37) and OS (P=0.0005, HR=7.4, 95% CI: 2.416-23.08). CONCLUSION NT5E CpG island methylation is a promising breast cancer biomarker.
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Affiliation(s)
- C Lo Nigro
- Laboratory of Cancer Genetics and Translational Oncology, Oncology Department, S. Croce General Hospital, Cuneo, Italy
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NT5E (CD73) is epigenetically regulated in malignant melanoma and associated with metastatic site specificity. Br J Cancer 2012; 106:1446-52. [PMID: 22454080 PMCID: PMC3326678 DOI: 10.1038/bjc.2012.95] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Background: Novel prognostic biomarkers and therapeutic strategies are urgently required for malignant melanoma. Ecto-5-prime-nucleotidase (NT5E; CD73) overexpression has been reported in several human cancers. The mechanism(s) underlying deregulated expression and the clinical consequences of changes in expression are not known. Methods: We used RT–PCR, qPCR, methylation-specific PCR and pyrosequencing to analyse expression and regulation of NT5E in malignant melanoma cell lines and primary and metastatic melanomas. Results: NT5E is subject to epigenetic regulation in melanoma. NT5E mRNA is downregulated by methylation-dependent transcriptional silencing in the melanoma cell lines SKMel2, SKMel23, WM35, Mel501, Mel505 and C81–61 and expression is reactivated by azacytidine. In contrast, the CpG island is unmethylated and the gene expressed in cultured normal melanocytes. In clinical cases of melanoma, methylation in the NT5E CpG island occurs in both primary and metastatic melanomas and correlates with transcriptional downregulation of NT5E mRNA. Relapse with metastatic disease, particularly to the visceral sites and brain, is more common in primary melanomas lacking NT5E methylation. Primary melanomas with methylation in NT5E show limited metastatic potential or more commonly metastasise predominantly to nodal sites rather than viscera and brain (P=0.01). Conclusion: Deregulation of NT5E expression in melanoma occurs via epigenetic changes in the NT5E CpG island. Confirmation of our results in larger clinical series would support the candidacy of NT5E as a clinical biomarker in melanoma, which could be applied in both primary and relapsed disease. Inhibition of NT5E may have therapeutic potential in melanoma, particularly in patients with more aggressive disease metastatic to viscera or the brain.
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Fu Y, Nachtigal MW. Analysis of epigenetic alterations to proprotein convertase genes in disease. Methods Mol Biol 2012; 768:231-45. [PMID: 21805246 DOI: 10.1007/978-1-61779-204-5_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Epigenetic alterations produce heritable changes in phenotype or gene expression without changing DNA sequence. Modified levels of gene expression contribute to a variety of human diseases encompassing genetic disorders, pediatric syndromes, autoimmune disease, aging, and cancer. Alterations in proprotein convertase gene expression are associated with numerous disease states; however, the underlying mechanism for changes in PC gene expression remains understudied. Epigenetic changes in gene expression profiles can be accomplished through modification of chromatin, specifically via chemical modification of DNA bases (methylation of cytosine) or associated histone proteins (acetylation or methylation). In general, active chromatin is associated with low DNA methylation status and histone acetylation, whereas silenced gene are typically in inactive regions of chromatin exhibiting DNA hypermethylation and histone deacetylation. This chapter will provide in-depth protocols to analyze epigenetic alterations in proprotein convertase gene expression using the PCSK6 gene in the context of human ovarian cancer as a model system.
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Affiliation(s)
- YangXin Fu
- Department of Obstetrics and Gynecology, University of Alberta, Edmonton, AB, Canada.
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Ntziachristos P, Tsirigos A, Van Vlierberghe P, Nedjic J, Trimarchi T, Flaherty MS, Ferres-Marco D, da Ros V, Tang Z, Siegle J, Asp P, Hadler M, Rigo I, De Keersmaecker K, Patel J, Huynh T, Utro F, Poglio S, Samon JB, Paietta E, Racevskis J, Rowe JM, Rabadan R, Levine RL, Brown S, Pflumio F, Dominguez M, Ferrando A, Aifantis I. Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia. Nat Med 2012; 18:298-301. [PMID: 22237151 PMCID: PMC3274628 DOI: 10.1038/nm.2651] [Citation(s) in RCA: 402] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 12/21/2011] [Indexed: 12/13/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an immature hematopoietic malignancy driven mainly by oncogenic activation of NOTCH1 signaling1. In this study we report the presence of loss-of-function mutations and deletions of EZH2 and SUZ12 genes, encoding critical components of the Polycomb Repressive Complex 2 (PRC2) complex2,3, in 25% of T-ALLs. To further study the role of the PRC2 complex in T-ALL, we used NOTCH1-induced animal models of the disease, as well as human T-ALL samples, and combined locus-specific and global analysis of NOTCH1-driven epigenetic changes. These studies demonstrated that activation of NOTCH1 specifically induces loss of the repressive mark lysine-27 tri-methylation of histone 3 (H3K27me3)4 by antagonizing the activity of the Polycomb Repressive Complex 2 (PRC2) complex. These studies demonstrate a tumor suppressor role for the PRC2 complex in human leukemia and suggest a hitherto unrecognized dynamic interplay between oncogenic NOTCH1 and PRC2 function for the regulation of gene expression and cell transformation.
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Affiliation(s)
- Panagiotis Ntziachristos
- Howard Hughes Medical Institute and Department of Pathology, New York University School of Medicine, New York, New York, USA
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Abstract
Ovarian cancer is the most lethal gynecological cancer. Due to few early symptoms and a lack of early detection strategies, most patients are diagnosed with advanced-stage disease. Most of these patients, although initially responsive, eventually develop drug resistance. In this chapter, epigenetic changes in ovarian cancer are described. Various epigenetic changes including CpG island methylation and histone modification have been identified in ovarian cancer. These aberrations are associated with distinct disease subtypes and present in circulating serum of ovarian cancer patients. Several epigenetic changes have shown promise for their diagnostic, prognostic, and predictive capacity but still need further validation.In contrast to DNA mutations and deletions, epigenetic modifications are potentially reversible by epigenetic therapies. Promising preclinical studies show epigenetic drugs to enhance gene re-expression and drug sensitivity in ovarian cancer cell lines and animal models.
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Krutovskikh V, Partensky C. [New insights in oncology: epigenetics and cancer stem cells]. Cancer Radiother 2011; 15:716-22. [PMID: 22079560 DOI: 10.1016/j.canrad.2011.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 04/29/2011] [Accepted: 05/21/2011] [Indexed: 12/22/2022]
Abstract
Cancer is a multi-etiologic, multistage disease with a prevalent genetic component, which happens when a large number of genes, critical for cell growth, death, differentiation, migration, and metabolic plasticity are altered irreversibly, so as to either "gain" (oncogenes) or "lose" (tumour suppressors) their function. Recent discoveries have revealed the previously underestimated etiologic importance of multiple epigenetic, that is to say, reversible factors (histone modifications, DNA methylation, non-coding RNA) involved in the transcriptional and post-transcriptional regulation of proteins, indispensable for the control of cancerous phenotype. Stable alterations of epigenetic machinery ("epimutations") turn out to play a critical role at different steps of carcinogenesis. In addition, due to substantial recent progress in stem cell biology, the new concept of cancer stem cells has emerged. This, along with newly discovered epigenetic cancer mechanisms, gives rise to a hope to overcome radio- and chemo-resistance and to eradicate otherwise incurable neoplasms.
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Affiliation(s)
- V Krutovskikh
- Centre International de Recherche sur le Cancer, 150, cours Albert-Thomas, 69372 Lyon cedex 08, France
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Pharmacodynamics of curcumin as DNA hypomethylation agent in restoring the expression of Nrf2 via promoter CpGs demethylation. Biochem Pharmacol 2011; 82:1073-8. [DOI: 10.1016/j.bcp.2011.07.065] [Citation(s) in RCA: 182] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 07/01/2011] [Accepted: 07/06/2011] [Indexed: 12/15/2022]
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Epigenetic regulation of nuclear PI-PLCbeta1 signaling pathway in low-risk MDS patients during azacitidine treatment. Leukemia 2011; 26:943-50. [PMID: 22033492 DOI: 10.1038/leu.2011.300] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Phosphoinositide-phospholipase C (PI-PLC) beta1 can be considered a specific target for demethylating therapy in high-risk myelodysplastic syndrome (MDS) patients, as azacitidine treatment has been associated with a PI-PLCbeta1-specific promoter demethylation, and induction of PI-PLCbeta1 gene and protein expression. However, little is known about the molecular effect of azacitidine in low-risk MDS or the functional mechanisms linked with azacitidine effect on PI-PLCbeta1 promoter. In the present study, we further investigated the role of epigenetic regulation of PI-PLCbeta1, mainly focusing on the structure of the PI-PLCbeta1 promoter. We first examined the effect of azacitidine on PI-PLCbeta1 promoter methylation and gene expression in low-risk MDS. Moreover, we studied the expression of key molecules associated with the nuclear inositide signaling pathways, such as cyclin D3. By applying a chromatin immunoprecipitation method, we also studied the correlation between the demethylating effect of azacitidine and the degree of recruitment to PI-PLCbeta1 promoter of some transcription factors implicated in hematopoietic stem cell proliferation and differentiation, as well as of the methyl-CpG-binding domain proteins, which specifically interact with methylated DNA. Taken together, our results hint at a specific involvement of PI-PLCbeta1 in epigenetic mechanisms, and are particularly consistent with the hypothesis of a role for PI-PLCbeta1 in azacitidine-induced myeloid differentiation.
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Ari F, Napieralski R, Ulukaya E, Dere E, Colling C, Honert K, Krüger A, Kiechle M, Schmitt M. Modulation of protein expression levels and DNA methylation status of breast cancer metastasis genes by anthracycline-based chemotherapy and the demethylating agent decitabine. Cell Biochem Funct 2011; 29:651-9. [DOI: 10.1002/cbf.1801] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 06/07/2011] [Accepted: 08/01/2011] [Indexed: 01/13/2023]
Affiliation(s)
- Ferda Ari
- Department of Biology; Faculty of Science and Art; Uludag University; Bursa; Turkey
| | - Rudolf Napieralski
- Department of Obstetrics and Gynecology; Technische Universitaet Muenchen; Klinikum rechts der Isar; Munich; Germany
| | - Engin Ulukaya
- Department of Medical Biochemistry; Medical School of Uludag University; Bursa; Turkey
| | - Egemen Dere
- Department of Biology; Faculty of Science and Art; Uludag University; Bursa; Turkey
| | - Christoph Colling
- Department of Obstetrics and Gynecology; Technische Universitaet Muenchen; Klinikum rechts der Isar; Munich; Germany
| | - Katja Honert
- Institute for Experimental Oncology and Therapy Research; Technische Universitaet Muenchen; Klinikum rechts der Isar; Munich; Germany
| | - Achim Krüger
- Institute for Experimental Oncology and Therapy Research; Technische Universitaet Muenchen; Klinikum rechts der Isar; Munich; Germany
| | - Marion Kiechle
- Department of Obstetrics and Gynecology; Technische Universitaet Muenchen; Klinikum rechts der Isar; Munich; Germany
| | - Manfred Schmitt
- Department of Obstetrics and Gynecology; Technische Universitaet Muenchen; Klinikum rechts der Isar; Munich; Germany
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Wang Z, Yuan X, Jiao N, Zhu H, Zhang Y, Tong J. CDH13 and FLBN3 gene methylation are associated with poor prognosis in colorectal cancer. Pathol Oncol Res 2011; 18:263-70. [PMID: 21796503 DOI: 10.1007/s12253-011-9437-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 07/07/2011] [Indexed: 12/17/2022]
Abstract
The aim of this study was to identify potential epigenetic prognostic biomarkers for colorectal cancer (CRC) in the Chinese population. The methylation status of five tumor suppressor genes (CDH13, DLEC1, FBLN3, hMHL1 and RUNX3) was determined using manual microdissection followed by methylation-specific PCR in 85 paired CRC specimens and adjacent normal tissue. The results showed that methylation frequencies in cancerous tissues were 31.8% for CDH13, 37.6% for DLEC1, 38.8% for FBLN3, 22.4% for hMHL1 and 27.1% for RUNX3, all of which were significantly higher than in corresponding normal tissue. Furthermore, CDH13 methylation was associated with poor differentiation (P = 0.019) and tended to be predominant in advanced stages (P = 0.084); FBLN3 methylation was associated with advanced stages (P = 0.027) and lymph node metastasis (P = 0.029). Accordingly, the methylation status of CDH13 (P = 0.022), FBLN3 (P = 0.008), CDH13 and/or FBLN3 (P = 0.001) predicted adverse overall survival in CRC, while hMHL1 methylation showed a protective role in survival (P = 0.046). Cox proportional hazard models further indicated that CDH13 and/or FBLN3 methylation, but not that of hMHL1, was an independent prognostic factor for CRC. In conclusion, we found CDH13 and FBLN3 gene methylation are potential biomarkers for poor prognosis in CRC.
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Affiliation(s)
- Zhu Wang
- Department of Oncology, Yangzhou No.1 People's Hospital, The second Clinical School of Yangzhou University, Number 368, Mid Hanjiang Road, Yangzhou, 225009, China.
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Chernov AV, Strongin AY. Epigenetic regulation of matrix metalloproteinases and their collagen substrates in cancer. Biomol Concepts 2011; 2:135-147. [PMID: 21779312 DOI: 10.1515/bmc.2011.017] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Our review covers the recent epigenetic data that are focused on matrix metalloproteinases (MMPs), their inhibitors (tissue inhibitors of MMPs; TIMPs) and collagen substrates. Twenty-four MMPs, four TIMPs and at least 28 collagen types are known in humans. The MMP activity regulates the functionality of multiple extracellular matrix proteins, cytokines, growth factors and cell signaling and adhesion receptors. Aberrantly enhanced MMP proteolysis affects multiple cell functions, including proliferation, migration and invasion. This aberrant MMP proteolysis is frequently recorded in cancer. Recent evidence, however, indicates that several MMPs function as tumor suppressors in cancer. Their inhibition could have pro-tumorigenic effects (making them anti-targets), counterbalancing the benefits of target inhibition and leading to adverse effects in cancer patients. The current epigenetic data suggest that there are distinct multi-layered epigenetic mechanisms that regulate MMPs, TIMPs and collagens. We show that in certain cancer types, epigenetic signatures of selected MMPs exhibit stem cell-like characteristics. Epigenetic mechanisms appear to play an especially important role in glioblastoma multiforme. Glioblastomas/gliomas synthesize de novo and then deposit collagens into the brain parenchyma. The collagen deposition, combined with an enhanced MMP activity in glioblastomas/gliomas, facilitates rapid invasion of tumor cells through the brain. It is tempting to hypothesize that the epigenetic mechanisms which control MMPs, TIMPs and collagens and, consequently, tumor cell invasion, represent promising drug targets and that in the near future these targets will be challenged pharmacologically.
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Affiliation(s)
- Andrei V Chernov
- Cancer Research Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
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Felter SP, Conolly RB, Bercu JP, Bolger PM, Boobis AR, Bos PMJ, Carthew P, Doerrer NG, Goodman JI, Harrouk WA, Kirkland DJ, Lau SS, Llewellyn GC, Preston RJ, Schoeny R, Schnatter AR, Tritscher A, van Velsen F, Williams GM. A proposed framework for assessing risk from less-than-lifetime exposures to carcinogens. Crit Rev Toxicol 2011; 41:507-44. [DOI: 10.3109/10408444.2011.552063] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Pedersen KS, Bamlet WR, Oberg AL, de Andrade M, Matsumoto ME, Tang H, Thibodeau SN, Petersen GM, Wang L. Leukocyte DNA methylation signature differentiates pancreatic cancer patients from healthy controls. PLoS One 2011; 6:e18223. [PMID: 21455317 PMCID: PMC3063802 DOI: 10.1371/journal.pone.0018223] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Accepted: 02/24/2011] [Indexed: 02/04/2023] Open
Abstract
Pancreatic adenocarcinoma (PaC) is one of most difficult tumors to treat. Much of this is attributed to the late diagnosis. To identify biomarkers for early detection, we examined DNA methylation differences in leukocyte DNA between PaC cases and controls in a two-phase study. In phase I, we measured methylation levels at 1,505 CpG sites in treatment-naïve leukocyte DNA from 132 never-smoker PaC patients and 60 never-smoker healthy controls. We found significant differences in 110 CpG sites (false discovery rate <0.05). In phase II, we tested and validated 88 of 96 phase I selected CpG sites in 240 PaC cases and 240 matched controls (p≤0.05). Using penalized logistic regression, we built a prediction model consisting of five CpG sites (IL10_P348, LCN2_P86, ZAP70_P220, AIM2_P624, TAL1_P817) that discriminated PaC patients from controls (C-statistic = 0.85 in phase I; 0.76 in phase II). Interestingly, one CpG site (LCN2_P86) alone could discriminate resectable patients from controls (C-statistic = 0.78 in phase I; 0.74 in phase II). We also performed methylation quantitative trait loci (methQTL) analysis and identified three CpG sites (AGXT_P180_F, ALOX12_E85_R, JAK3_P1075_R) where the methylation levels were significantly associated with single nucleotide polymorphisms (SNPs) (false discovery rate <0.05). Our results demonstrate that epigenetic variation in easily obtainable leukocyte DNA, manifested by reproducible methylation differences, may be used to detect PaC patients. The methylation differences at certain CpG sites are partially attributable to genetic variation. This study strongly supports future epigenome-wide association study using leukocyte DNA for biomarker discovery in human diseases.
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Affiliation(s)
- Katrina S. Pedersen
- Department of Internal Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - William R. Bamlet
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Ann L. Oberg
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Martha E. Matsumoto
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Hui Tang
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Stephen N. Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Gloria M. Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Liang Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
- * E-mail:
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Kim YH, Lee HC, Kim SY, Yeom YI, Ryu KJ, Min BH, Kim DH, Son HJ, Rhee PL, Kim JJ, Rhee JC, Kim HC, Chun HK, Grady WM, Kim YS. Epigenomic analysis of aberrantly methylated genes in colorectal cancer identifies genes commonly affected by epigenetic alterations. Ann Surg Oncol 2011; 18:2338-47. [PMID: 21298349 DOI: 10.1245/s10434-011-1573-y] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2010] [Indexed: 02/06/2023]
Abstract
BACKGROUND Determination of the profile of genes that are commonly methylated aberrantly in colorectal cancer (CRC) will have substantial value for diagnostic and therapeutic applications. However, there is limited knowledge of the DNA methylation pattern in CRC. MATERIALS AND METHODS We analyzed the methylation profile of 27,578 CpG sites spanning more than 14,000 genes in CRC and in the adjacent normal mucosa with bead-chip array-based technology. RESULTS We identified 621 CpG sites located in promoter regions and CpG islands that were greatly hypermethylated in CRC compared to normal mucosa. The genes on chromosome 18 showed promoter hypermethylation most frequently. According to gene ontology analysis, the most common biologically relevant class of genes affected by methylation was the class associated with the cadherin signaling pathway. Compared to the genome-wide expression array, mRNA expression was more likely to be downregulated in the genes demonstrating promoter hypermethylation, even though this was not statistically significant. We validated ten CpG sites that were hypermethylated (ADHFE1, BOLL, SLC6A15, ADAMTS5, TFPI2, EYA4, NPY, TWIST1, LAMA1, GAS7) and 2 CpG sites showing hypomethylation (MAEL, SFT2D3) in CRC compared to the normal mucosa in the array studies using pyrosequencing. The methylation status measured by pyrosequencing was consistent with the methylation array data. CONCLUSIONS Methylation profiling based on bead-chip arrays is an effective method for screening aberrantly methylated genes in CRC. In addition, we identified novel methylated genes that are candidate diagnostic or prognostic markers for CRC.
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Affiliation(s)
- Young-Ho Kim
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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Mirbahai L, Williams TD, Zhan H, Gong Z, Chipman JK. Comprehensive profiling of zebrafish hepatic proximal promoter CpG island methylation and its modification during chemical carcinogenesis. BMC Genomics 2011; 12:3. [PMID: 21205313 PMCID: PMC3027158 DOI: 10.1186/1471-2164-12-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 01/04/2011] [Indexed: 01/07/2023] Open
Abstract
Background DNA methylation is an epigenetic mechanism associated with regulation of gene expression and it is modulated during chemical carcinogenesis. The zebrafish is increasingly employed as a human disease model; however there is a lack of information on DNA methylation in zebrafish and during fish tumorigenesis. Results A novel CpG island tiling array containing 44,000 probes, in combination with immunoprecipitation of methylated DNA, was used to achieve the first comprehensive methylation profiling of normal adult zebrafish liver. DNA methylation alterations were detected in zebrafish liver tumors induced by the environmental carcinogen 7, 12-dimethylbenz(a)anthracene. Genes significantly hypomethylated in tumors were associated particularly with proliferation, glycolysis, transcription, cell cycle, apoptosis, growth and metastasis. Hypermethylated genes included those associated with anti-angiogenesis and cellular adhesion. Of 49 genes that were altered in expression within tumors, and which also had appropriate CpG islands and were co-represented on the tiling array, approximately 45% showed significant changes in both gene expression and methylation. Conclusion The functional pathways containing differentially methylated genes in zebrafish hepatocellular carcinoma have also been reported to be aberrantly methylated during tumorigenesis in humans. These findings increase the confidence in the use of zebrafish as a model for human cancer in addition to providing the first comprehensive mapping of DNA methylation in the normal adult zebrafish liver.
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Affiliation(s)
- Leda Mirbahai
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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Lema C, Cunningham MJ. MicroRNAs and their implications in toxicological research. Toxicol Lett 2010; 198:100-5. [DOI: 10.1016/j.toxlet.2010.06.019] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 06/24/2010] [Accepted: 06/25/2010] [Indexed: 01/01/2023]
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High-throughput method for analyzing methylation of CpGs in targeted genomic regions. Proc Natl Acad Sci U S A 2010; 107:12587-92. [PMID: 20616066 DOI: 10.1073/pnas.1005173107] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A unique microarray-based method for determining the extent of DNA methylation has been developed. It relies on a selective enrichment of the regions to be assayed by target amplification by capture and ligation (mTACL). The assay is quantitatively accurate, relatively precise, and lends itself to high-throughput determination using nanogram amounts of DNA. The measurements using mTACLs are highly reproducible and in excellent agreement with those obtained by sequencing (r = 0.94). In the present work, the methylation status of >145,000 CpGs from 5,472 promoters in 221 samples was measured. The methylation levels of nearby CpGs are correlated, but the correlation falls off dramatically over several hundred base pairs. In some instances, nearby CpGs have very different levels of methylation. Comparison of normal and tumor samples indicates that in tumors, the promoter regions of genes involved in differentiation and signaling are preferentially hypermethylated, whereas those of housekeeping genes remain hypomethylated. mTACL is a platform for profiling the state of methylation of a large number of CpG in many samples in a cost-effective fashion, and is capable of scaling to much larger numbers of CpGs than those collected here.
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Zerilli F, Bonanno C, Shehi E, Amicarelli G, Adlerstein D, Makrigiorgos GM. Methylation-specific loop-mediated isothermal amplification for detecting hypermethylated DNA in simplex and multiplex formats. Clin Chem 2010; 56:1287-96. [PMID: 20551384 DOI: 10.1373/clinchem.2010.143545] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Aberrant DNA methylation of gene promoters and the associated silencing of tumor suppressor genes are recognized as mechanisms contributing to tumor development. Therefore, detection of promoter hypermethylation is becoming important for diagnosis, prognosis, and aiding the design of cancer therapies. We describe a novel isothermal method for the detection of DNA hypermethylation. METHODS Methylation-specific loop-mediated isothermal amplification (MS-LAMP) is a novel adaptation of LAMP. MS-LAMP was used for the highly specific detection of hypermethylated CpGs in the promoters of the CDKN2A [cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)], GATA5 (GATA binding protein 5), and DAPK1 (death-associated protein kinase 1) genes. The reactions occurred under isothermal conditions with 3 primer sets specific for methylated promoters. Both turbidimetry and fluorescence were used for detection. The MS-LAMP assay was validated with bisulfite-treated plasmid and genomic DNA controls of known methylation status and was applied to detect hypermethylation in 18 clinical tumor samples. A multiplex MS-LAMP for CDKN2A, GATA5, and DAPK1 was also validated with the aid of synthetic positive and negative controls. RESULTS The MS-LAMP assay showed high specificity with plasmid and genomic DNA targets in reactions carried out in <1 h. The assay had a detection limit of approximately 30 copies of methylated target sequence and a selectivity of 0.5% methylated DNA in a mixture with unmethylated DNA. Compared with methylation-specific PCR, the MS-LAMP assay detected lower rates of methylation in lung adenocarcinoma samples. Simultaneous multiplex detection of hypermethylation in the 3 targets (CDKN2A, GATA5, and DAPK1) was readily achieved with the MS-LAMP assay in both the turbidimetric and fluorescence detection formats. CONCLUSIONS MS-LAMP provides a highly specific isothermal method for methylation detection and is well suited for multiplex approaches.
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Affiliation(s)
- Francesco Zerilli
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
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