1
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Cao P, Li H, Wang P, Zhang X, Guo Y, Zhao K, Guo J, Li X, Nashun B. DNA Hypomethylation-Mediated Transcription Dysregulation Participates in Pathogenesis of Polycystic Ovary Syndrome. THE AMERICAN JOURNAL OF PATHOLOGY 2024:S0002-9440(24)00072-5. [PMID: 38403164 DOI: 10.1016/j.ajpath.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/31/2024] [Accepted: 02/09/2024] [Indexed: 02/27/2024]
Abstract
Polycystic ovary syndrome (PCOS) is a highly heterogeneous and genetically complex endocrine disorder. Although the etiology remains mostly elusive, growing evidence suggested abnormal changes of DNA methylation correlate well with systemic and tissue-specific dysfunctions in PCOS. A dehydroepiandrosterone-induced PCOS-like mouse model was generated, which has a similar metabolic and reproductive phenotype as human patients with PCOS, and was used to experimentally validate the potential role of aberrant DNA methylation in PCOS in this study. Integrated DNA methylation and transcriptome analysis revealed the potential role of genomic DNA hypomethylation in transcription regulation of PCOS and identified several key candidate genes, including BMP4, Adcy7, Tnfaip3, and Fas, which were regulated by aberrant DNA hypomethylation. Moreover, i.p. injection of S-adenosylmethionine increased the overall DNA methylation level of PCOS-like mice and restored expression of the candidate genes to similar levels as the control, alleviating reproductive and metabolic abnormalities in PCOS-like mice. These findings provided direct evidence showing the importance of normal DNA methylation in epigenetic regulation of PCOS and potential targets for diagnosis and treatment of the disease.
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Affiliation(s)
- Pengbo Cao
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China; Inner Mongolia Qilu Pharmaceutical Company, Hohhot, China
| | - Haoran Li
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Peijun Wang
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Xinna Zhang
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yuxuan Guo
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Keyu Zhao
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Jiaojiao Guo
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Xihe Li
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China; Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animals, Hohhot, China
| | - Buhe Nashun
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China.
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2
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Zamora-Fuentes JM, Hernández-Lemus E, Espinal-Enríquez J. Methylation-related genes involved in renal carcinoma progression. Front Genet 2023; 14:1225158. [PMID: 37693315 PMCID: PMC10486271 DOI: 10.3389/fgene.2023.1225158] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/25/2023] [Indexed: 09/12/2023] Open
Abstract
Renal carcinomas are a group of malignant tumors often originating in the cells lining the small tubes in the kidney responsible for filtering waste from the blood and urine production. Kidney tumors arise from the uncontrolled growth of cells in the kidneys and are responsible for a large share of global cancer-related morbidity and mortality. Understanding the molecular mechanisms driving renal carcinoma progression results crucial for the development of targeted therapies leading to an improvement of patient outcomes. Epigenetic mechanisms such as DNA methylation are known factors underlying the development of several cancer types. There is solid experimental evidence of relevant biological functions modulated by methylation-related genes, associated with the progression of different carcinomas. Those mechanisms can often be associated to different epigenetic marks, such as DNA methylation sites or chromatin conformation patterns. Currently, there is no definitive method to establish clear relations between genetic and epigenetic factors that influence the progression of cancer. Here, we developed a data-driven method to find methylation-related genes, so we could find relevant bonds between gene co-expression and methylation-wide-genome regulation patterns able to drive biological processes during the progression of clear cell renal carcinoma (ccRC). With this approach, we found out genes such as ITK oncogene that appear hypomethylated during all four stages of ccRC progression and are strongly involved in immune response functions. Also, we found out relevant tumor suppressor genes such as RAB25 hypermethylated, thus potentially avoiding repressed functions in the AKT signaling pathway during the evolution of ccRC. Our results have relevant implications to further understand some epigenetic-genetic-affected roles underlying the progression of renal cancer.
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Affiliation(s)
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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3
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Giulietti M, Cecati M, Sabanovic B, Scirè A, Cimadamore A, Santoni M, Montironi R, Piva F. The Role of Artificial Intelligence in the Diagnosis and Prognosis of Renal Cell Tumors. Diagnostics (Basel) 2021; 11:206. [PMID: 33573278 PMCID: PMC7912267 DOI: 10.3390/diagnostics11020206] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 02/07/2023] Open
Abstract
The increasing availability of molecular data provided by next-generation sequencing (NGS) techniques is allowing improvement in the possibilities of diagnosis and prognosis in renal cancer. Reliable and accurate predictors based on selected gene panels are urgently needed for better stratification of renal cell carcinoma (RCC) patients in order to define a personalized treatment plan. Artificial intelligence (AI) algorithms are currently in development for this purpose. Here, we reviewed studies that developed predictors based on AI algorithms for diagnosis and prognosis in renal cancer and we compared them with non-AI-based predictors. Comparing study results, it emerges that the AI prediction performance is good and slightly better than non-AI-based ones. However, there have been only minor improvements in AI predictors in terms of accuracy and the area under the receiver operating curve (AUC) over the last decade and the number of genes used had little influence on these indices. Furthermore, we highlight that different studies having the same goal obtain similar performance despite the fact they use different discriminating genes. This is surprising because genes related to the diagnosis or prognosis are expected to be tumor-specific and independent of selection methods and algorithms. The performance of these predictors will be better with the improvement in the learning methods, as the number of cases increases and by using different types of input data (e.g., non-coding RNAs, proteomic and metabolic). This will allow for more precise identification, classification and staging of cancerous lesions which will be less affected by interpathologist variability.
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Affiliation(s)
- Matteo Giulietti
- Department of Specialistic Clinical & Odontostomatological Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (M.G.); (M.C.); (B.S.)
| | - Monia Cecati
- Department of Specialistic Clinical & Odontostomatological Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (M.G.); (M.C.); (B.S.)
| | - Berina Sabanovic
- Department of Specialistic Clinical & Odontostomatological Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (M.G.); (M.C.); (B.S.)
| | - Andrea Scirè
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60126 Ancona, Italy;
| | - Alessia Cimadamore
- Section of Pathological Anatomy, Polytechnic University of Marche, United Hospitals, 60126 Ancona, Italy; (A.C.); (R.M.)
| | - Matteo Santoni
- Oncology Unit, Macerata Hospital, 62012 Macerata, Italy;
| | - Rodolfo Montironi
- Section of Pathological Anatomy, Polytechnic University of Marche, United Hospitals, 60126 Ancona, Italy; (A.C.); (R.M.)
| | - Francesco Piva
- Department of Specialistic Clinical & Odontostomatological Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (M.G.); (M.C.); (B.S.)
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4
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Gu Y, Niu S, Wang Y, Duan L, Pan Y, Tong Z, Zhang X, Yang Z, Peng B, Wang X, Han X, Li Y, Cheng T, Liu Y, Shang L, Liu T, Yang X, Sun M, Jiang S, Zhang C, Zhang N, Ye Q, Gao S. DMDRMR-Mediated Regulation of m 6A-Modified CDK4 by m 6A Reader IGF2BP3 Drives ccRCC Progression. Cancer Res 2020; 81:923-934. [PMID: 33293428 DOI: 10.1158/0008-5472.can-20-1619] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/09/2020] [Accepted: 12/03/2020] [Indexed: 11/16/2022]
Abstract
Aberrant N 6-methyladenosine (m6A) modification has emerged as a driver of tumor initiation and progression, yet how long noncoding RNAs (lncRNA) are involved in the regulation of m6A remains unknown. Here we utilize data from 12 cancer types from The Cancer Genome Atlas to comprehensively map lncRNAs that are potentially deregulated by DNA methylation. A novel DNA methylation-deregulated and RNA m6A reader-cooperating lncRNA (DMDRMR) facilitated tumor growth and metastasis in clear cell renal cell carcinoma (ccRCC). Mechanistically, DMDRMR bound insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) to stabilize target genes, including the cell-cycle kinase CDK4 and three extracellular matrix components (COL6A1, LAMA5, and FN1), by specifically enhancing IGF2BP3 activity on them in an m6A-dependent manner. Consequently, DMDRMR and IGF2BP3 enhanced the G1-S transition, thus promoting cell proliferation in ccRCC. In patients with ccRCC, high coexpression of DMDRMR and IGF2BP3 was associated with poor outcomes. Our findings reveal that DMDRMR cooperates with IGF2BP3 to regulate target genes in an m6A-dependent manner and may represent a potential diagnostic, prognostic, and therapeutic target in ccRCC. SIGNIFICANCE: This study demonstrates that the lncRNA DMDRMR acts as a cofactor for IGF2BP3 to stabilize target genes in an m6A-dependent manner, thus exerting essential oncogenic roles in ccRCC.
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Affiliation(s)
- Yinmin Gu
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Shaoxi Niu
- Department of Urology, The First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yang Wang
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Liqiang Duan
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Yongbo Pan
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Zhou Tong
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Xu Zhang
- Department of Urology, The First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zhenyu Yang
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Bo Peng
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiaodong Wang
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiaoqi Han
- Medical College, Guizhou University, Guiyang, China
| | - Yuxin Li
- Pharmaceutical Analysis, College of Pharmacy, Beihua University, Jilin, China
| | - Tianyou Cheng
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Yajuan Liu
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Lina Shang
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Tongfeng Liu
- Medical College, Guizhou University, Guiyang, China
| | - Xiwang Yang
- Medical College, Guizhou University, Guiyang, China
| | - Minxuan Sun
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Siyuan Jiang
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Chang Zhang
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Ning Zhang
- College of Life Science, Northwest A&F University, Yangling, China
| | - Qinong Ye
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Collaborative Innovation Center for Cancer Medicine, Beijing, China
| | - Shan Gao
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China. .,Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
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5
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Cancer-driving mutations and variants of components of the membrane trafficking core machinery. Life Sci 2020; 264:118662. [PMID: 33127517 DOI: 10.1016/j.lfs.2020.118662] [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: 09/22/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
The core machinery for vesicular membrane trafficking broadly comprises of coat proteins, RABs, tethering complexes and SNAREs. As cellular membrane traffic modulates key processes of mitogenic signaling, cell migration, cell death and autophagy, its dysregulation could potentially results in increased cell proliferation and survival, or enhanced migration and invasion. Changes in the levels of some components of the core machinery of vesicular membrane trafficking, likely due to gene amplifications and/or alterations in epigenetic factors (such as DNA methylation and micro RNA) have been extensively associated with human cancers. Here, we provide an overview of association of membrane trafficking with cancer, with a focus on mutations and variants of coat proteins, RABs, tethering complex components and SNAREs that have been uncovered in human cancer cells/tissues. The major cellular and molecular cancer-driving or suppression mechanisms associated with these components of the core membrane trafficking machinery shall be discussed.
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6
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O’Sullivan MJ, Lindsay AJ. The Endosomal Recycling Pathway-At the Crossroads of the Cell. Int J Mol Sci 2020; 21:ijms21176074. [PMID: 32842549 PMCID: PMC7503921 DOI: 10.3390/ijms21176074] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 08/17/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022] Open
Abstract
The endosomal recycling pathway lies at the heart of the membrane trafficking machinery in the cell. It plays a central role in determining the composition of the plasma membrane and is thus critical for normal cellular homeostasis. However, defective endosomal recycling has been linked to a wide range of diseases, including cancer and some of the most common neurological disorders. It is also frequently subverted by many diverse human pathogens in order to successfully infect cells. Despite its importance, endosomal recycling remains relatively understudied in comparison to the endocytic and secretory transport pathways. A greater understanding of the molecular mechanisms that support transport through the endosomal recycling pathway will provide deeper insights into the pathophysiology of disease and will likely identify new approaches for their detection and treatment. This review will provide an overview of the normal physiological role of the endosomal recycling pathway, describe the consequences when it malfunctions, and discuss potential strategies for modulating its activity.
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7
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Mahmood N, Arakelian A, Cheishvili D, Szyf M, Rabbani SA. S-adenosylmethionine in combination with decitabine shows enhanced anti-cancer effects in repressing breast cancer growth and metastasis. J Cell Mol Med 2020; 24:10322-10337. [PMID: 32720467 PMCID: PMC7521255 DOI: 10.1111/jcmm.15642] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/22/2020] [Accepted: 06/26/2020] [Indexed: 12/11/2022] Open
Abstract
Abnormal DNA methylation orchestrates many of the cancer‐related gene expression irregularities such as the inactivation of tumour suppressor genes through hypermethylation as well as activation of prometastatic genes through hypomethylation. The fact that DNA methylation abnormalities can be chemically reversed positions the DNA methylation machinery as an attractive target for anti‐cancer drug development. However, although in vitro studies suggested that targeting concordantly hypo‐ and hypermethylation is of benefit in suppressing both oncogenic and prometastatic functions of breast cancer cells, this has never been tested in a therapeutic setting in vivo. In this context, we investigated the combined therapeutic effects of an approved nutraceutical agent S‐adenosylmethionine (SAM) and FDA‐approved hypomethylating agent decitabine using the MDA‐MB‐231 xenograft model of breast cancer and found a pronounced reduction in mammary tumour volume and lung metastasis compared to the animals in the control and monotherapy treatment arms. Immunohistochemical assessment of the primary breast tumours showed a significantly reduced expression of proliferation (Ki‐67) and angiogenesis (CD31) markers following combination therapy as compared to the control group. Global transcriptome and methylome analyses have revealed that the combination therapy regulates genes from several key cancer‐related pathways that are abnormally expressed in breast tumours. To our knowledge, this is the first preclinical study demonstrating the anti‐cancer therapeutic potential of using a combination of methylating (SAM) and demethylating agent (decitabine) in vivo. Results from this study provide a molecularly founded rationale for clinically testing a combination of agents targeting the epigenome to reduce the morbidity and mortality from breast cancer.
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Affiliation(s)
- Niaz Mahmood
- Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
| | - Ani Arakelian
- Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
| | - David Cheishvili
- Department of Molecular Biology, Ariel University, Ariel, Israel.,Gerald Bronfman Department of Oncology, McGill University, Montréal, QC, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montréal, QC, Canada.,HKG Epitherapeutics, Hong Kong, China
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC, Canada
| | - Shafaat A Rabbani
- Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
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8
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Peters I, Merseburger AS, Tezval H, Lafos M, Tabrizi PF, Mazdak M, Wolters M, Kuczyk MA, Serth J, von Klot CA. The Prognostic Value of DNA Methylation Markers in Renal Cell Cancer: A Systematic Review. KIDNEY CANCER 2020. [DOI: 10.3233/kca-190069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Inga Peters
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | | | - Hossein Tezval
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Marcel Lafos
- Department of Pathology, Hannover Medical School, Hannover, Germany
| | - Pouriya Faraj Tabrizi
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Mehrdad Mazdak
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Mathias Wolters
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Markus A. Kuczyk
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Jürgen Serth
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
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9
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Xu L, He J, Cai Q, Li M, Pu X, Guo Y. An effective seven-CpG-based signature to predict survival in renal clear cell carcinoma by integrating DNA methylation and gene expression. Life Sci 2020; 243:117289. [PMID: 31926254 DOI: 10.1016/j.lfs.2020.117289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/29/2019] [Accepted: 01/07/2020] [Indexed: 12/16/2022]
Abstract
AIMS Currently, using clinicopathological risk factors only is not far from effective to evaluate the risk of disease progression in renal clear cell carcinoma (KIRC) patients. Molecular biomarkers might improve risk stratification of KIRC. DNA methylation occurs the whole process of tumor development and transcriptional disorders are also one of the important characteristics of tumor. Hence, this study aims to develop an effective and independent prognostic signature for KIRC patients by Integrating DNA methylation and gene expression. MAIN METHODS Difference analysis was conducted on DNA methylation sites and gene expression data. The Spearman's rank correlation and univariate Cox regression analysis were used to screen out the CpG sites that related with RNAs' expression and KIRC patients' overall survival. Then, a five-CpG-based prognostic classifier was established using LASSO Cox regression method. KEY FINDINGS The seven-CpG-based classifier can successfully divide KIRC patients into high-risk from low-risk groups, even after adjustment for standard clinical prognostic factors, such as age, stage, gender and grade. Moreover, the seven-CpG-based signature was more effective as independent prognostic factors than the combined model of these clinical factors. Six differential mRNA genes corresponding to the seven CpG sites are all related to human cancers by functional exploration. The gene functional and pathway enrichment analysis found that genes in immune-related pathways were remarkably different in high and low-risk groups. SIGNIFICANCE The new seven-CpG-based signature could helpfully provide insights into the underlying mechanism of KIRC and may be a powerful independent biomarker for predicting of the survival of KIRC patients.
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Affiliation(s)
- Lei Xu
- College of Chemistry, Sichuan University, Chengdu, Sichuan, China
| | - Jian He
- College of Chemistry, Sichuan University, Chengdu, Sichuan, China
| | - Qihang Cai
- College of Chemistry, Sichuan University, Chengdu, Sichuan, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, Sichuan, China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu, Sichuan, China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu, Sichuan, China.
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10
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Rab25 and RCP in cancer progression. Arch Pharm Res 2019; 42:101-112. [DOI: 10.1007/s12272-019-01129-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/29/2019] [Indexed: 01/10/2023]
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11
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Skrypek N, Bruneel K, Vandewalle C, De Smedt E, Soen B, Loret N, Taminau J, Goossens S, Vandamme N, Berx G. ZEB2 stably represses RAB25 expression through epigenetic regulation by SIRT1 and DNMTs during epithelial-to-mesenchymal transition. Epigenetics Chromatin 2018; 11:70. [PMID: 30445998 PMCID: PMC6240308 DOI: 10.1186/s13072-018-0239-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/09/2018] [Indexed: 12/29/2022] Open
Abstract
Background Epithelial mesenchymal transition (EMT) is tightly regulated by a network of transcription factors (EMT-TFs). Among them is the nuclear factor ZEB2, a member of the zinc-finger E-box binding homeobox family. ZEB2 nuclear localization has been identified in several cancer types, and its overexpression is correlated with the malignant progression. ZEB2 transcriptionally represses epithelial genes, such as E-cadherin (CDH1), by directly binding to the promoter of the genes it regulates and activating mesenchymal genes by a mechanism in which there is no full agreement. Recent studies showed that EMT-TFs interact with epigenetic regulatory enzymes that alter the epigenome, thereby providing another level of control. The role of epigenetic regulation on ZEB2 function is not well understood. In this study, we aimed to characterize the epigenetic effect of ZEB2 repressive function on the regulation of a small Rab GTPase RAB25. Results Using cellular models with conditional ZEB2 expression, we show a clear transcriptional repression of RAB25 and CDH1. RAB25 contributes to the partial suppression of ZEB2-mediated cell migration. Furthermore, a highly significant reverse correlation between RAB25 and ZEB2 expression in several human cancer types could be identified. Mechanistically, ZEB2 binds specifically to E-box sequences on the RAB25 promoter. ZEB2 binding is associated with the local increase in DNA methylation requiring DNA methyltransferases as well as histone deacetylation (H3K9Ac) depending on the activity of SIRT1. Surprisingly, SIRT1 and DNMTs did not interact directly with ZEB2, and while SIRT1 inhibition decreased the stability of long-term repression, it did not prevent down-regulation of RAB25 and CDH1 by ZEB2. Conclusions ZEB2 expression is resulting in drastic changes at the chromatin level with both clear DNA hypermethylation and histone modifications. Here, we revealed that SIRT1-mediated H3K9 deacetylation helps to maintain gene repression but is not required for the direct ZEB2 repressive function. Targeting epigenetic enzymes to prevent EMT is an appealing approach to limit cancer dissemination, but inhibiting SIRT1 activity alone might have limited effect and will require drug combination to efficiently prevent EMT. Electronic supplementary material The online version of this article (10.1186/s13072-018-0239-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolas Skrypek
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kenneth Bruneel
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Cindy Vandewalle
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Eva De Smedt
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Bieke Soen
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Nele Loret
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Joachim Taminau
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Steven Goossens
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Centre for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
| | - Niels Vandamme
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Data Mining and Modeling for Biomedicine, VIB Inflammation Research Center, Ghent, Belgium.,VIB-UGent Center for Inflammation Research, Technologiepark 927, 9052, Ghent, Belgium
| | - Geert Berx
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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12
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Ren Y, Feng X, Xia X, Zhang Y, Zhang W, Su J, Wang Z, Xu Y, Zhou F. Gender specificity improves the early-stage detection of clear cell renal cell carcinoma based on methylomic biomarkers. Biomark Med 2018; 12:607-618. [PMID: 29707986 DOI: 10.2217/bmm-2018-0084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AIM The two genders are different ranging from the molecular to the phenotypic levels. But most studies did not use this important information. We hypothesize that the integration of gender information may improve the overall prediction accuracy. MATERIALS & METHODS A comprehensive comparative study was carried out to test the hypothesis. The classification of the stages I + II versus III + IV of the clear cell renal cell carcinoma samples was formulated as an example. RESULTS & CONCLUSION In most cases, female-specific model significantly outperformed both-gender model, as similarly for the male-specific model. Our data suggested that gender information is essential for building biomedical classification models and even a simple strategy of building two gender-specific models may outperform the gender-mixed model.
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Affiliation(s)
- Yanjiao Ren
- College of Computer Science & Technology, Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China.,College of Information Technology, Jilin Agricultural University, Changchun, Jilin 130118, China
| | - Xin Feng
- College of Computer Science & Technology, Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Xin Xia
- College of Software, Jilin University, Changchun, Jilin 130012, China
| | - Yexian Zhang
- College of Computer Science & Technology, Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Wenniu Zhang
- College of Computer Science & Technology, Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Jing Su
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
| | - Zhongyu Wang
- College of Computer Science & Technology, Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
| | - Ying Xu
- College of Computer Science & Technology, Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China.,Computational Systems Biology Lab, Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA.,College of Public Health, Jilin University, Changchun, Jilin 130012, China
| | - Fengfeng Zhou
- College of Computer Science & Technology, Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
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13
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Liu P, Zhou TF, Qiu BA, Yang YX, Zhu YJ, An Y, Zhao WC, Wu YT, Ma PF, Li JB, Xia NX. Methylation-Mediated Silencing of GATA5 Gene Suppresses Cholangiocarcinoma Cell Proliferation and Metastasis. Transl Oncol 2018; 11:585-592. [PMID: 29547757 PMCID: PMC5854920 DOI: 10.1016/j.tranon.2018.01.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/27/2018] [Accepted: 01/29/2018] [Indexed: 12/13/2022] Open
Abstract
Cholangiocarcinoma (CCA) is one of the most common hepatic and biliary malignancies, accounting for about 3% of all gastrointestinal tumors. GATA5 is a transcription factor capable of suppressing the development of various human cancer types. Transcriptional inactivation and CpG island (CGI) methylation of GATA3 and GATA5, two members of the GATA family of transcription factors, have been observed in some human cancers. But whether high-density CGI methylation of GATA5 is associated with the clinical course of CCA patients has not been clarified. Herein, we observed reduced expression of GATA5 in CCA tissues compared with noncancerous tissues. Treatment with the demethylating agent 5-aza-2'-deoxycytidine restored GATA5 expression in CCA cell lines. Furthermore, GATA5 expression was downregulated after treatment with IL-6 in human intrahepatic biliary epithelial cells. Upregulated GATA5 inhibited CCA cell growth and metastasis. Mechanistically, GATA5 suppressed CCA cell growth and metastasis via Wnt/β-catenin pathway. Specific β-catenin inhibitor or siRNA abolished the discrepancy of the proliferation and metastasis capacity between GATA5-overexpression CCA cells and their control cells, which further confirmed that Wnt/β-catenin was required in GATA5-inhibited CCA cell growth and metastasis.
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Affiliation(s)
- Peng Liu
- Department of Hepatobiliary surgery, Navy General Hospital, Beijing 100048, China
| | - Teng-Fei Zhou
- Department of Internal Medicine, the No. 313 Hospital of PLA, Huludao 125000, China
| | - Bao-An Qiu
- Department of Hepatobiliary surgery, Navy General Hospital, Beijing 100048, China
| | - Ying-Xiang Yang
- Department of Hepatobiliary surgery, Navy General Hospital, Beijing 100048, China
| | - Yong-Jian Zhu
- Department of Hepatobiliary surgery, Navy General Hospital, Beijing 100048, China
| | - Yang An
- Department of Hepatobiliary surgery, Navy General Hospital, Beijing 100048, China
| | - Wen-Chao Zhao
- Department of Hepatobiliary surgery, Navy General Hospital, Beijing 100048, China
| | - Yin-Tao Wu
- Department of Hepatobiliary surgery, Navy General Hospital, Beijing 100048, China
| | - Peng-Fei Ma
- Department of Hepatobiliary surgery, Navy General Hospital, Beijing 100048, China
| | - Jing-Bo Li
- Department of Hepatobiliary surgery, Navy General Hospital, Beijing 100048, China
| | - Nian-Xin Xia
- Department of Hepatobiliary surgery, Navy General Hospital, Beijing 100048, China.
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