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Luo GF, Chen CY, Wang J, Yue HY, Tian Y, Yang P, Li YK, Li Y. FOXD3 may be a new cellular target biomarker as a hypermethylation gene in human ovarian cancer. Cancer Cell Int 2019; 19:44. [PMID: 30858761 PMCID: PMC6394078 DOI: 10.1186/s12935-019-0755-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/12/2019] [Indexed: 02/08/2023] Open
Abstract
Background FOXD3 is aberrantly regulated in several tumors, but its underlying mechanisms in ovarian cancer (OC) remains largely unknown. The present study aimed to explore the role and associated mechanisms of FOXD3 in OC. Methods Microarray data from GEO was used to analyze differential CpG sites and differentially methylated regions (DMR) in tumor tissues and Illumina 450 genome-wide methylation data was employed. The FOXD3 expression level was determined through qRT-PCR and western blot analysis. Wound healing test, colony formation and flow cytometry assay were utilized to analyze cell migration, proliferation abilities, cell cycle and cell apoptosis, respectively. Finally, the effect of FOXD3 on tumor growth was investigated through in vivo xenograft experiments. Results GEO data analysis showed that FOXD3 was hypermethylated in OC tissues. Also, qRT-PCR revealed that FOXD3 was low expressed and methylation-specific PCR (MSP) confirmed that the methylation level of FOXD3 was hypermethylated. Combined treatment of 5-aza-2′-deoxycytidine (5-Aza-dC) could synergistically restored FOXD3 expression. Finally, in vitro and in vivo experiments showed that demethylated FOXD3 decreased cell proliferation and migration abilities, and increased the cell apoptosis. In vivo experiment detected that demethylated FOXD3 restrained tumor growth. Conclusions FOXD3 could act as a tumor suppressor to inhibit cell proliferation, migration and promote cell apoptosis in OC cells. Electronic supplementary material The online version of this article (10.1186/s12935-019-0755-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gui-Fang Luo
- 1Department of Gynecology, The First Affiliated Hospital of University of South China, Hengyang, 421001 People's Republic of China
| | - Chang-Ye Chen
- 1Department of Gynecology, The First Affiliated Hospital of University of South China, Hengyang, 421001 People's Republic of China
| | - Juan Wang
- 2Clinical Anatomy & Reproductive Medicine Application Institute, Department of Histology and Embryology, University of South China, Hengyang, 421001 Hunan People's Republic of China
| | - Hai-Yan Yue
- 3Key Laboratory of Tumor Cellular and Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China, No. 28 West Changsheng Road, Hengyang, 421001 Hunan People's Republic of China
| | - Yong Tian
- 4Department of Obstetrics and Gynecology, Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi Clinical College of Wuhan University, Enshi, 445000 Hubei People's Republic of China
| | - Ping Yang
- 3Key Laboratory of Tumor Cellular and Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China, No. 28 West Changsheng Road, Hengyang, 421001 Hunan People's Republic of China
| | - Yu-Kun Li
- 3Key Laboratory of Tumor Cellular and Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China, No. 28 West Changsheng Road, Hengyang, 421001 Hunan People's Republic of China
| | - Yan Li
- 5Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, No. 932 South Lushan Road, Yuelu District, Changsha, 410013 Hunan People's Republic of China.,6Reproductive and Genetic Hospital of Citic-Xiangya, No. 84 Xiangya Road, Changsha, 410078 Hunan People's Republic of China
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Lee G, Bang L, Kim SY, Kim D, Sohn KA. Identifying subtype-specific associations between gene expression and DNA methylation profiles in breast cancer. BMC Med Genomics 2017; 10:28. [PMID: 28589855 PMCID: PMC5461552 DOI: 10.1186/s12920-017-0268-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Breast cancer is a complex disease in which different genomic patterns exists depending on different subtypes. Recent researches present that multiple subtypes of breast cancer occur at different rates, and play a crucial role in planning treatment. To better understand underlying biological mechanisms on breast cancer subtypes, investigating the specific gene regulatory system via different subtypes is desirable. METHODS Gene expression, as an intermediate phenotype, is estimated based on methylation profiles to identify the impact of epigenomic features on transcriptomic changes in breast cancer. We propose a kernel weighted l1-regularized regression model to incorporate tumor subtype information and further reveal gene regulations affected by different breast cancer subtypes. For the proper control of subtype-specific estimation, samples from different breast cancer subtype are learned at different rate based on target estimates. Kolmogorov Smirnov test is conducted to determine learning rate of each sample from different subtype. RESULTS It is observed that genes that might be sensitive to breast cancer subtype show prediction improvement when estimated using our proposed method. Comparing to a standard method, overall performance is also enhanced by incorporating tumor subtypes. In addition, we identified subtype-specific network structures based on the associations between gene expression and DNA methylation. CONCLUSIONS In this study, kernel weighted lasso model is proposed for identifying subtype-specific associations between gene expressions and DNA methylation profiles. Identification of subtype-specific gene expression associated with epigenomic changes might be helpful for better planning treatment and developing new therapies.
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Affiliation(s)
- Garam Lee
- Department of Software and Computer Engineering, Ajou University, Suwon, 16499, South Korea
| | - Lisa Bang
- Biomedical & Translational Informatics Institute, Geisinger Health System, Danville, PA, USA
| | - So Yeon Kim
- Department of Software and Computer Engineering, Ajou University, Suwon, 16499, South Korea
| | - Dokyoon Kim
- Biomedical & Translational Informatics Institute, Geisinger Health System, Danville, PA, USA. .,The Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
| | - Kyung-Ah Sohn
- Department of Software and Computer Engineering, Ajou University, Suwon, 16499, South Korea.
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Identifying epigenetically dysregulated pathways from pathway-pathway interaction networks. Comput Biol Med 2016; 76:160-7. [PMID: 27454244 DOI: 10.1016/j.compbiomed.2016.06.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND Identification of pathways that show significant difference in activity between disease and control samples have been an interesting topic of research for over a decade. Pathways so identified serve as potential indicators of aberrations in phenotype or a disease condition. Recently, epigenetic mechanisms such as DNA methylation are known to play an important role in altering the regulatory mechanism of biological pathways. It is reasonable to think that a set of genes that show significant difference in expression and methylation interact together to form a network of pathways. Existing pathway identification methods fail to capture the complex interplay between interacting pathways. RESULTS This paper proposes a novel framework to identify biological pathways that are dysregulated by epigenetic mechanisms. Experiments on four benchmark cancer datasets and comparison with state-of-the-art pathway identification methods reveal the effectiveness of the proposed approach. CONCLUSION The proposed framework incorporates both topology and biological relationships of pathways. Comparison with state-of-the-art techniques reveals promising results. Epigenetic signatures identified from pathway interaction networks can help to advance Molecular Pathological Epidemiology (MPE) research efforts by predicting tumor molecular changes.
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Wang Z, Curry E, Montana G. Network-guided regression for detecting associations between DNA methylation and gene expression. ACTA ACUST UNITED AC 2014; 30:2693-701. [PMID: 24919878 DOI: 10.1093/bioinformatics/btu361] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION High-throughput profiling in biological research has resulted in the availability of a wealth of data cataloguing the genetic, epigenetic and transcriptional states of cells. These data could yield discoveries that may lead to breakthroughs in the diagnosis and treatment of human disease, but require statistical methods designed to find the most relevant patterns from millions of potential interactions. Aberrant DNA methylation is often a feature of cancer, and has been proposed as a therapeutic target. However, the relationship between DNA methylation and gene expression remains poorly understood. RESULTS We propose Network-sparse Reduced-Rank Regression (NsRRR), a multivariate regression framework capable of using prior biological knowledge expressed as gene interaction networks to guide the search for associations between gene expression and DNA methylation signatures. We use simulations to show the advantage of our proposed model in terms of variable selection accuracy over alternative models that do not use prior network information. We discuss an application of NsRRR to The Cancer Genome Atlas datasets on primary ovarian tumours. AVAILABILITY AND IMPLEMENTATION R code implementing the NsRRR model is available at http://www2.imperial.ac.uk/∼gmontana CONTACT giovanni.montana@kcl.ac.uk SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zi Wang
- Department of Mathematics, Imperial College London, London SW7 2AZ, Division of Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN and Department of Biomedical Engineering, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Edward Curry
- Department of Mathematics, Imperial College London, London SW7 2AZ, Division of Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN and Department of Biomedical Engineering, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Giovanni Montana
- Department of Mathematics, Imperial College London, London SW7 2AZ, Division of Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN and Department of Biomedical Engineering, King's College London, St Thomas' Hospital, London SE1 7EH, UK Department of Mathematics, Imperial College London, London SW7 2AZ, Division of Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN and Department of Biomedical Engineering, King's College London, St Thomas' Hospital, London SE1 7EH, UK
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Thériault BL, Basavarajappa HD, Lim H, Pajovic S, Gallie BL, Corson TW. Transcriptional and epigenetic regulation of KIF14 overexpression in ovarian cancer. PLoS One 2014; 9:e91540. [PMID: 24626475 PMCID: PMC3953446 DOI: 10.1371/journal.pone.0091540] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 02/13/2014] [Indexed: 02/06/2023] Open
Abstract
KIF14 (kinesin family member 14) is a mitotic kinesin and an important oncogene in several cancers. Tumor KIF14 expression levels are independently predictive of poor outcome, and in cancer cells KIF14 can modulate metastatic behavior by maintaining appropriate levels of cell adhesion and migration proteins at the cell membrane. Thus KIF14 is an exciting potential therapeutic target. Understanding KIF14's regulation in cancer cells is crucial to the development of effective and selective therapies to block its tumorigenic function(s). We previously determined that close to 30% of serous ovarian cancers (OvCa tumors) exhibit low-level genomic gain, indicating one mechanism of KIF14 overexpression in tumors. We now report on transcriptional and epigenetic regulation of KIF14. Through promoter deletion analyses, we identified one cis-regulatory region containing binding sites for Sp1, HSF1 and YY1. siRNA-mediated knockdown of these transcription factors demonstrated endogenous regulation of KIF14 overexpression by Sp1 and YY1, but not HSF1. ChIP experiments confirmed an enrichment of both Sp1 and YY1 binding to the endogenous KIF14 promoter in OvCa cell lines with high KIF14 expression. A strong correlation was seen in primary serous OvCa tumors between Sp1, YY1 and KIF14 expression, further evidence that these transcription factors are important players in KIF14 overexpression. Hypomethylation patterns were observed in primary serous OvCa tumors, suggesting a minor role for promoter methylation in the control of KIF14 gene expression. miRNA expression analysis determined that miR-93, miR-144 and miR-382 had significantly lower levels of expression in primary serous OvCa tumors than normal tissues; treatment of an OvCa cell line with miRNA mimics and inhibitors specifically modulated KIF14 mRNA levels, pointing to potential novel mechanisms of KIF14 overexpression in primary tumors. Our findings reveal multiple mechanisms of KIF14 upregulation in cancer cells, offering new targets for therapeutic interventions to reduce KIF14 in tumors, aiming at improved prognosis.
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Affiliation(s)
- Brigitte L. Thériault
- Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Halesha D. Basavarajappa
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, and Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Harvey Lim
- Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Sanja Pajovic
- Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Brenda L. Gallie
- Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Division of Visual Science, Toronto Western Hospital Research Institute, Toronto, Ontario, Canada
- Departments of Molecular Genetics and Ophthalmology, University of Toronto, Toronto, Ontario, Canada
| | - Timothy W. Corson
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, and Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
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