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Zhang Y, Wang Q, Xue H, Guo Y, Wei S, Li F, Gong L, Pan W, Jiang P. Epigenetic Regulation of Autophagy in Bone Metabolism. FUNCTION 2024; 5:zqae004. [PMID: 38486976 PMCID: PMC10935486 DOI: 10.1093/function/zqae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 03/17/2024] Open
Abstract
The skeletal system is crucial for supporting bodily functions, protecting vital organs, facilitating hematopoiesis, and storing essential minerals. Skeletal homeostasis, which includes aspects such as bone density, structural integrity, and regenerative processes, is essential for normal skeletal function. Autophagy, an intricate intracellular mechanism for degrading and recycling cellular components, plays a multifaceted role in bone metabolism. It involves sequestering cellular waste, damaged proteins, and organelles within autophagosomes, which are then degraded and recycled. Autophagy's impact on bone health varies depending on factors such as regulation, cell type, environmental cues, and physiological context. Despite being traditionally considered a cytoplasmic process, autophagy is subject to transcriptional and epigenetic regulation within the nucleus. However, the precise influence of epigenetic regulation, including DNA methylation, histone modifications, and non-coding RNA expression, on cellular fate remains incompletely understood. The interplay between autophagy and epigenetic modifications adds complexity to bone cell regulation. This article provides an in-depth exploration of the intricate interplay between these two regulatory paradigms, with a focus on the epigenetic control of autophagy in bone metabolism. Such an understanding enhances our knowledge of bone metabolism-related disorders and offers insights for the development of targeted therapeutic strategies.
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Affiliation(s)
- Yazhou Zhang
- Department of Foot and Ankle Surgery, Tengzhou Central People’s Hospital, Tengzhou 277500, China
| | - Qianqian Wang
- Department of Pediatric Intensive Care Unit, Tengzhou Central People’s Hospital, Tengzhou 277500, China
| | - Hongjia Xue
- Department of Computer Science, University College London, London, WC1E 6BT, UK
| | - Yujin Guo
- Institute of Clinical Pharmacy & Pharmacology, Jining First People’s Hospital, Jining 272000, China
| | - Shanshan Wei
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, China
- Department of Graduate, Shandong Academy of Medical Sciences, Shandong First Medical University, Jinan 250000, China
| | - Fengfeng Li
- Department of Neurosurgery, Tengzhou Central People’s Hospital, Tengzhou 277500, China
| | - Linqiang Gong
- Department of Gastroenterology, Tengzhou Central People's Hospital, Tengzhou 277500, China
| | - Weiliang Pan
- Department of Foot and Ankle Surgery, Tengzhou Central People’s Hospital, Tengzhou 277500, China
| | - Pei Jiang
- Translational Pharmaceutical Laboratory, Jining First People’s Hospital, Shandong First Medical University, Jining 272000, China
- Institute of Translational Pharmacy, Jining Medical Research Academy, Jining 272000, China
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2
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Hawkins-Hooker A, Visonà G, Narendra T, Rojas-Carulla M, Schölkopf B, Schweikert G. Getting personal with epigenetics: towards individual-specific epigenomic imputation with machine learning. Nat Commun 2023; 14:4750. [PMID: 37550323 PMCID: PMC10406842 DOI: 10.1038/s41467-023-40211-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/18/2023] [Indexed: 08/09/2023] Open
Abstract
Epigenetic modifications are dynamic mechanisms involved in the regulation of gene expression. Unlike the DNA sequence, epigenetic patterns vary not only between individuals, but also between different cell types within an individual. Environmental factors, somatic mutations and ageing contribute to epigenetic changes that may constitute early hallmarks or causal factors of disease. Epigenetic modifications are reversible and thus promising therapeutic targets for precision medicine. However, mapping efforts to determine an individual's cell-type-specific epigenome are constrained by experimental costs and tissue accessibility. To address these challenges, we developed eDICE, an attention-based deep learning model that is trained to impute missing epigenomic tracks by conditioning on observed tracks. Using a recently published set of epigenomes from four individual donors, we show that transfer learning across individuals allows eDICE to successfully predict individual-specific epigenetic variation even in tissues that are unmapped in a given donor. These results highlight the potential of machine learning-based imputation methods to advance personalized epigenomics.
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Affiliation(s)
- Alex Hawkins-Hooker
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
- Empirical Inference Department, Max-Planck Institute for Intelligent Systems, Max-Planck-Ring 4, Tübingen, 72076, Germany.
- Centre for Artificial Intelligence, University College London, London, UK.
| | - Giovanni Visonà
- Empirical Inference Department, Max-Planck Institute for Intelligent Systems, Max-Planck-Ring 4, Tübingen, 72076, Germany
| | - Tanmayee Narendra
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
- Interfaculty Institute for Biomedical Informatics, University of Tübingen, Sand 13, Tübingen, 72076, Germany
| | - Mateo Rojas-Carulla
- Empirical Inference Department, Max-Planck Institute for Intelligent Systems, Max-Planck-Ring 4, Tübingen, 72076, Germany
| | - Bernhard Schölkopf
- Empirical Inference Department, Max-Planck Institute for Intelligent Systems, Max-Planck-Ring 4, Tübingen, 72076, Germany
| | - Gabriele Schweikert
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
- Interfaculty Institute for Biomedical Informatics, University of Tübingen, Sand 13, Tübingen, 72076, Germany.
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3
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Liu R, Ding Y, Li W, Li S, Li X, Zhao D, Zhang Y, Wei G, Zhang X. Protective role of curcumin on broiler liver by modulating aflatoxin B1-induced DNA methylation and CYPs expression. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 260:115086. [PMID: 37269612 DOI: 10.1016/j.ecoenv.2023.115086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/05/2023]
Abstract
The purpose of this study was to investigate the role of epigenetic DNA methylation and CYPs expression in AFB1-exposed broiler liver and the protective effect of curcumin. Sixty-four one-day-old AA broilers were randomly divided into four groups, including control group, AFB1 group (1 mg/kg AFB1), curcumin + AFB1 group (1 mg/kg curcumin) and curcumin group (300 mg/kg curcumin). Histological observation, CYP450 enzyme activities, the expression levels of DNA methyltransferases and CYP450 enzymes, and the overall DNA methylation level in broiler liver were investigated. Dietary AFB1 was found to induce severe liver injury in broilers, upregulate the mRNA and protein expression of CYP450 enzymes (CYP1A1, CYP1A2 and CYP3A4) and the enzyme activities of CYP1A2 and CYP3A4. According to HPLC, qPCR and western blot analyses, the overall DNA methylation level and the mRNA and protein expression of DNA methyltransferases (DNMT1, DNMT3a and DNMT3b) in the liver were significantly increased after AFB1 exposure. Importantly, the Pearson test and correlation analysis data revealed that the overall DNA methylation level of broiler liver was positively correlated with DNMTs, while CYP1A1, CYP1A2 and CYP3A4 were negatively correlated. Surprisingly, curcumin supplementation strongly ameliorated AFB1-induced hepatotoxicity by restoring the histological changes, decreasing the expression and enzymatic activity of liver CYP450 enzymes (CYP1A1, CYP1A2, and CYP3A4), and increasing the overall DNA methylation level and the expression of DNMTs. Taken together, we concluded that curcumin could protect against AFB1-induced liver injury by mediating the effects of DNA methylation and CYPs expression.
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Affiliation(s)
- Ruimeng Liu
- Key Laboratory of Animal Disease Control, College of Basic Veterinary Medicine, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, Heilongjiang, China
| | - Yixin Ding
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Weina Li
- Key Laboratory of Animal Disease Control, College of Basic Veterinary Medicine, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, Heilongjiang, China
| | - Sihong Li
- Animal Genome Engineering Research Team, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiaoting Li
- School of Agricultural Science and Engineering, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Dongmei Zhao
- Key Laboratory of Animal Disease Control, College of Basic Veterinary Medicine, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, Heilongjiang, China
| | - Yixin Zhang
- Key Laboratory of Animal Disease Control, College of Basic Veterinary Medicine, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, Heilongjiang, China
| | - Gaoqiang Wei
- Key Laboratory of Animal Disease Control, College of Basic Veterinary Medicine, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, Heilongjiang, China
| | - Xiuying Zhang
- Key Laboratory of Animal Disease Control, College of Basic Veterinary Medicine, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, Heilongjiang, China.
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LRF/ZBTB7A conservation accentuates its potential as a therapeutic target for the hematopoietic disorders. Gene 2020; 760:145020. [PMID: 32755656 DOI: 10.1016/j.gene.2020.145020] [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: 04/16/2020] [Revised: 06/02/2020] [Accepted: 07/30/2020] [Indexed: 11/22/2022]
Abstract
Conserved sequences across species have always provided valuable insights to improve our understanding on the human genome's entity and the interplay among different loci. Lymphoma/leukemia related factor (LRF) is encoded by ZBTB7A gene and belongs to an evolutionarily conserved family of transcription factors, implicated in vital cellular functions. The present data, demonstrating the wide-spread and the high overlap of the LRF/ZBTB7A recognition sites with genomic segments identified as CpG islands in the human genome, suggest that its binding capacity strongly depends on a specific sequence-encoded feature within CpGs. We have previously shown that de-methylation of the CpG island 326 lying in the ZBTB7A gene promoter is associated with impaired pharmacological induction of fetal hemoglobin in β-type hemoglobinopathies patients. Within this context we aimed to investigate the extent of the LRF/ZBTB7A conservation among primates and mouse genome, focusing our interest also on the CpG island flanking the gene's promoter region, in an effort to further establish its epigenetic regulatory role in human hematopoiesis and pharmacological involvement in hematopoietic disorders. Comparative analysis of the human ZBTB7A nucleotide and amino acid sequences and orthologous sequences among non-human primates and mouse, exhibited high conservation scores. Pathway analysis, clearly indicated that LRF/ZBTB7A influences conserved cellular processes. These data in conjunction with the high levels of expression foremost in hematopoietic tissues, highlighted LRF/ZBTB7A as an essential factor operating indisputably during hematopoiesis.
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Dong Q, Li F, Xu Y, Xiao J, Xu Y, Shang D, Zhang C, Yang H, Tian Z, Mi K, Li X, Zhang Y. RNAactDrug: a comprehensive database of RNAs associated with drug sensitivity from multi-omics data. Brief Bioinform 2019; 21:2167-2174. [PMID: 31799597 DOI: 10.1093/bib/bbz142] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/30/2019] [Accepted: 10/17/2019] [Indexed: 12/16/2022] Open
Abstract
Drug sensitivity has always been at the core of individualized cancer chemotherapy. However, we have been overwhelmed by large-scale pharmacogenomic data in the era of next-generation sequencing technology, which makes it increasingly challenging for researchers, especially those without bioinformatic experience, to perform data integration, exploration and analysis. To bridge this gap, we developed RNAactDrug, a comprehensive database of RNAs associated with drug sensitivity from multi-omics data, which allows users to explore drug sensitivity and RNA molecule associations directly. It provides association data between drug sensitivity and RNA molecules including mRNAs, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) at four molecular levels (expression, copy number variation, mutation and methylation) from integrated analysis of three large-scale pharmacogenomic databases (GDSC, CellMiner and CCLE). RNAactDrug currently stores more than 4 924 200 associations of RNA molecules and drug sensitivity at four molecular levels covering more than 19 770 mRNAs, 11 119 lncRNAs, 438 miRNAs and 4155 drugs. A user-friendly interface enriched with various browsing sections augmented with advance search facility for querying the database is offered for users retrieving. RNAactDrug provides a comprehensive resource for RNA molecules acting in drug sensitivity, and it could be used to prioritize drug sensitivity-related RNA molecules, further promoting the identification of clinically actionable biomarkers in drug sensitivity and drug development more cost-efficiently by making this knowledge accessible to both basic researchers and clinical practitioners. Database URL: http://bio-bigdata.hrbmu.edu.cn/RNAactDrug.
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Affiliation(s)
- Qun Dong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Feng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yanjun Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yingqi Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Desi Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haixiu Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zihan Tian
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kai Mi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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6
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Zhao QQ, Jiang C, Gao Q, Zhang YY, Wang G, Chen XP, Wu SB, Tang J. Gene expression and methylation profiles identified CXCL3 and CXCL8 as key genes for diagnosis and prognosis of colon adenocarcinoma. J Cell Physiol 2019; 235:4902-4912. [PMID: 31709538 DOI: 10.1002/jcp.29368] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/30/2019] [Indexed: 01/03/2023]
Abstract
Colon adenocarcinoma (COAD) is one of the most common malignant tumors with high morbidity and mortality rates worldwide. Due to the poor clinical outcomes, it is indispensable to investigate novel biomarkers for the diagnosis and prognosis of COAD. The aim of this study is to explore key genes as potential biomarkers for the diagnosis and prognosis of COAD for clinical utility. Gene expression profiles (GSE44076 and GSE44861) and gene methylation profile (GSE29490) were analyzed to identify the aberrantly methylated-differentially expressed genes by R language and Perl software. Function enrichments were performed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Moreover, hub genes were identified through protein-protein interaction (PPI) network. Besides, key genes were found by the module analysis and The Cancer Genome Atlas (TCGA) survival analysis. Finally, TCGA data and quantitative real-time polymerase chain reaction (RT-qPCR) was used to validate the key genes involved in COAD. Our study found two hypomethylation-high-expression genes (CXCL3 and CXCL8) in COAD tissues compared with the adjacent normal tissues. These results were also confirmed by RT-qPCR with 25 pairs of COAD and adjacent normal tissues. Meanwhile, low expression of the two genes was associated with poor survival in patients with COAD. CXCL3 and CXCL8 may serve as key genes in the diagnosis and prognosis for COAD.
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Affiliation(s)
- Qing-Qing Zhao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chun Jiang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qian Gao
- Department of Clinical Laboratory Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Ying-Ying Zhang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guo Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiao-Ping Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shao-Bin Wu
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Jie Tang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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7
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Sanchez R, Yang X, Maher T, Mackenzie SA. Discrimination of DNA Methylation Signal from Background Variation for Clinical Diagnostics. Int J Mol Sci 2019; 20:E5343. [PMID: 31717838 PMCID: PMC6862328 DOI: 10.3390/ijms20215343] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/09/2019] [Accepted: 10/24/2019] [Indexed: 12/29/2022] Open
Abstract
Advances in the study of human DNA methylation variation offer a new avenue for the translation of epigenetic research results to clinical applications. Although current approaches to methylome analysis have been helpful in revealing an epigenetic influence in major human diseases, this type of analysis has proven inadequate for the translation of these advances to clinical diagnostics. As in any clinical test, the use of a methylation signal for diagnostic purposes requires the estimation of an optimal cutoff value for the signal, which is necessary to discriminate a signal induced by a disease state from natural background variation. To address this issue, we propose the application of a fundamental signal detection theory and machine learning approaches. Simulation studies and tests of two available methylome datasets from autism and leukemia patients demonstrate the feasibility of this approach in clinical diagnostics, providing high discriminatory power for the methylation signal induced by disease, as well as high classification performance. Specifically, the analysis of whole biomarker genomic regions could suffice for a diagnostic, markedly decreasing its cost.
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Affiliation(s)
- Robersy Sanchez
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA 16802, USA; (X.Y.); (T.M.)
| | | | | | - Sally A. Mackenzie
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA 16802, USA; (X.Y.); (T.M.)
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8
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Xu Y, Dong Q, Li F, Xu Y, Hu C, Wang J, Shang D, Zheng X, Yang H, Zhang C, Shao M, Meng M, Xiong Z, Li X, Zhang Y. Identifying subpathway signatures for individualized anticancer drug response by integrating multi-omics data. J Transl Med 2019; 17:255. [PMID: 31387579 PMCID: PMC6685260 DOI: 10.1186/s12967-019-2010-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 07/31/2019] [Indexed: 12/19/2022] Open
Abstract
Background Individualized drug response prediction is vital for achieving personalized treatment of cancer and moving precision medicine forward. Large-scale multi-omics profiles provide unprecedented opportunities for precision cancer therapy. Methods In this study, we propose a pipeline to identify subpathway signatures for anticancer drug response of individuals by integrating the comprehensive contributions of multiple genetic and epigenetic (gene expression, copy number variation and DNA methylation) alterations. Results Totally, 46 subpathway signatures associated with individual responses to different anticancer drugs were identified based on five cancer-drug response datasets. We have validated the reliability of subpathway signatures in two independent datasets. Furthermore, we also demonstrated these multi-omics subpathway signatures could significantly improve the performance of anticancer drug response prediction. In-depth analysis of these 46 subpathway signatures uncovered the essential roles of three omics types and the functional associations underlying different anticancer drug responses. Patient stratification based on subpathway signatures involved in anticancer drug response identified subtypes with different clinical outcomes, implying their potential roles as prognostic biomarkers. In addition, a landscape of subpathways associated with cellular responses to 191 anticancer drugs from CellMiner was provided and the mechanism similarity of drug action was accurately unclosed based on these subpathways. Finally, we constructed a user-friendly web interface-CancerDAP (http://bio-bigdata.hrbmu.edu.cn/CancerDAP/) available to explore 2751 subpathways relevant with 191 anticancer drugs response. Conclusions Taken together, our study identified and systematically characterized subpathway signatures for individualized anticancer drug response prediction, which may promote the precise treatment of cancer and the study for molecular mechanisms of drug actions. Electronic supplementary material The online version of this article (10.1186/s12967-019-2010-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanjun Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Qun Dong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Feng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yingqi Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Congxue Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Jingwen Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Desi Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xuan Zheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Haixiu Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Mengting Shao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Mohan Meng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Zhiying Xiong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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9
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Prognostic significance of DNMT3A alterations in Middle Eastern papillary thyroid carcinoma. Eur J Cancer 2019; 117:133-144. [DOI: 10.1016/j.ejca.2019.05.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/16/2019] [Accepted: 05/22/2019] [Indexed: 12/24/2022]
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10
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Zhang K, Li C, Liu J, Tang X, Li Z. DNA methylation alterations as therapeutic prospects in thyroid cancer. J Endocrinol Invest 2019; 42:363-370. [PMID: 29992502 DOI: 10.1007/s40618-018-0922-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/29/2018] [Indexed: 12/31/2022]
Abstract
BACKGROUND Thyroid cancer is one of the most common endocrine malignancies. Although the 10-year survival rate of differentiated thyroid cancer (DTC) is about 90% after conventional treatments, a small proportion of patients still suffer from tumor recurrence or drug resistance. OBJECTIVE This review article summarizes recent researches and clinical trials related to target drugs that reduce mortality in thyroid cancer. METHODS This is a review of the recent literature and clinical trials on the three main aspects including methylation genes in thyroid cancers, the relationship between BRAF mutation and gene methylation, target and dehypermethylation drugs in clinical trials. RESULTS We propose new approaches to treating malignant thyroid cancer, based on advances in understanding the relationship between genetic and epigenetic changes in thyroid cancer. Although the effect of traditional treatment for thyroid cancer is relatively good, a small proportion of patients still suffer from tumor recurrence or drug resistance. Molecular targeted drugs and dehypermethylation drugs have more promising outcomes in aggressive thyroid cancer compared with conventional treatments. CONCLUSION Based on what was discussed in this review, we suggest that integration of epigenetic and targeted therapies into conventional treatments will reduce the occurrence of refractory radioiodine differentiated thyroid cancer and improve the outcomes in aggressive thyroid cancer patients.
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Affiliation(s)
- K Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
- Institute of Clinical Pharmacology, Central South University and Hunan Key Laboratory of Pharmacogenetics, Xiangya Road #110, Changsha, 410078, Hunan, People's Republic of China
| | - C Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
- Institute of Clinical Pharmacology, Central South University and Hunan Key Laboratory of Pharmacogenetics, Xiangya Road #110, Changsha, 410078, Hunan, People's Republic of China
- Department of Pharmacy, ZhuZhou Central Hospital, ZhuZhou, 410078, People's Republic of China
| | - J Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
- Institute of Clinical Pharmacology, Central South University and Hunan Key Laboratory of Pharmacogenetics, Xiangya Road #110, Changsha, 410078, Hunan, People's Republic of China
| | - X Tang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
- Institute of Clinical Pharmacology, Central South University and Hunan Key Laboratory of Pharmacogenetics, Xiangya Road #110, Changsha, 410078, Hunan, People's Republic of China
- Department of Center for ADR monitoring of Hubei, Wuhan, 430071, People's Republic of China
| | - Z Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.
- Institute of Clinical Pharmacology, Central South University and Hunan Key Laboratory of Pharmacogenetics, Xiangya Road #110, Changsha, 410078, Hunan, People's Republic of China.
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11
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Wang S, Chen L, Wang Q, He Z, Chen S, Zhang H, Li H, Guo P, Li Q, Zhang R, Xing X, Zeng X, Lin W, Xiao Y, Dong G, Ma L, Gurram N, Zhang A, Chen W, Li D. Strain differences between CD-1 and C57BL/6 mice in expression of metabolic enzymes and DNA methylation modifications of the primary hepatocytes. Toxicology 2018; 412:19-28. [PMID: 30503582 DOI: 10.1016/j.tox.2018.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/23/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
Abstract
Primary mouse hepatocyte cultures are widely used in toxicological and pharmacological studies. However, the strain differences in alterations of metabolic enzymes and the regulation of gene expression in response to different stimuli remains unclear. To address this issue, we examined the expression of metabolic enzymes and the regulatory role of DNA methylation in the primary hepatocytes of two mouse strains, CD-1 and C57BL/6. Primary culture of mouse hepatocytes was established using collagen sandwich configuration. Analysis of gene expression of 24 phase I, 18 phase II, and 6 phase III metabolic enzymes on 4 consecutive days after cell seeding revealed that the basal levels of most enzymes in primary cultured hepatocytes differed greatly between the two mouse strains. However, the dynamic changes in most genes were identical between the two strains. In addition, treatment with 3-methylcholanthrene, phenobarbital, and rifampin led to the induction of cytochrome P-450 (cyp) 1a1 and cyp1a2, cyp2b10, cyp3a11. However, induction varied in degree between the two types of primary hepatocytes. The dynamic changes in global DNA methylation and the expression of DNA methylation regulatory factors of the two mouse strains were similar. Of the genes down-regulated over the culture period, hypermethylation of cyp2e1 gene appeared in both mouse strains and led to a suppression of gene expression. Taken together, these results demonstrate that the expression of metabolic enzymes and the response to agonists in primary hepatocytes differ between CD-1 and C57BL/6 mouse strains. Epigenetic regulation might be involved in the suppression of cyp 450s' expression.
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Affiliation(s)
- Shan Wang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Liping Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Qing Wang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Zhini He
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Shen Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Haiyan Zhang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Huiyao Li
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Ping Guo
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Qiong Li
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Rui Zhang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xiumei Xing
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xiaowen Zeng
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Weiwei Lin
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yongmei Xiao
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Guanghui Dong
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Lu Ma
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, China
| | - Namratha Gurram
- School of Public Health, State University of New York at Albany, One University Place, Rensselaer, NY, USA
| | - Aihua Zhang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, China
| | - Wen Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Daochuan Li
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China.
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12
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Garafutdinov RR, Galimova AA, Sakhabutdinova AR. The influence of CpG (5'-d(CpG)-3' dinucleotides) methylation on ultrasonic DNA fragmentation. J Biomol Struct Dyn 2018; 37:3877-3886. [PMID: 30351231 DOI: 10.1080/07391102.2018.1533888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
DNA methylation is an important way of gene regulation. The variety of methods for DNA methylation analysis based on chemical modification or enzyme digestion has been proposed. However, DNA is able to undergo transformations under physical power. Here, we report that the cytosine methylation in CpG dinucleotides determines the difference in fragmentation rate of methylated and unmethylated DNA under sonication. We found that at the beginning of sonication, methylated DNAs are degraded faster than unmethylated one, and the difference in fragmentation degree can be evaluated with high reliability by quantitative polymerase chain reaction (qPCR). The optimal parameters that provide the greatest difference in amount of amplifiable DNA targets corresponding to fragmentation degree are the following: moderate amplicon size (about 150-250 bp), medium CpG sparseness (one CpG dinucleotide per ∼12-14 nucleotides of the chain), and short sonication time (less than 5 min). Along with CpG, the CpA and CpT contents of amplified regions should be taken into account for proper DNA fragmentation by ultrasound as well. The obtained data could be used for elaboration of a method for comparative methylation testing, when there is no need to detect methylation of certain CpG dinucleotides. This method will be simple (can be used by any technician familiar with PCR), low cost (no need to use an expensive reagents), and fast (only brief DNA sonication and conventional qPCR are carried out). Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravil R Garafutdinov
- a Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences , Ufa , Bashkortostan , Russia
| | - Aizilya A Galimova
- a Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences , Ufa , Bashkortostan , Russia
| | - Assol R Sakhabutdinova
- a Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences , Ufa , Bashkortostan , Russia
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13
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Zhang Y, Zhang T, Chen Y. Comprehensive Analysis of Gene Expression Profiles and DNA Methylome reveals Oas1, Ppie, Polr2g as Pathogenic Target Genes of Gestational Diabetes Mellitus. Sci Rep 2018; 8:16244. [PMID: 30389953 PMCID: PMC6215015 DOI: 10.1038/s41598-018-34292-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 10/01/2018] [Indexed: 12/25/2022] Open
Abstract
Gestational Diabetes Mellitus (GDM) has a high incidence of pregnancy, which seriously affects the life quality of pregnant women and fetal health. DNA methylation is one of the most important epigenetic modification that can regulate the gene expression level, and thus affect the occurrence of various diseases. Increasing evidence has shown that gene expression changes caused by DNA methylation play an important role in metabolic diseases. Here we explored the mechanisms and biological processes that affect the occurrence and development of GDM through analyzing the gene expression profiles and DNA methylation data of GDM. We detected 24,577 differential CpG sites mapping to 9339 genes (DMGs, differential methylation gene) and 931 differential expressed genes (DEGs) between normal samples and GDM samples. GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis of 326 overlapping genes between DMGs and DEGs showed obvious enrichment in terms related to metabolic disorders and immune responses. We identified Oas1, Ppie, Polr2g as possible pathogenic target genes of GDM by combining protein-protein interaction analysis. Our study provides possible targets for early diagnosis of GDM and information for clinical prevention of abnormal fetal development and type 2 diabetes.
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Affiliation(s)
- Yan Zhang
- Department of Obstetrics & Gynecology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, P. R. China
| | - Tiancheng Zhang
- Key Lab of Reproduction Regulation of NPFPC-Shanghai Institute of Planned Parenthood Research (SIPPR), Fudan University Reproduction and Development Institution, Shanghai, China
| | - Yunyan Chen
- Department of Obstetrics & Gynecology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, P. R. China.
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Chondrou V, Stavrou EF, Markopoulos G, Kouraklis-Symeonidis A, Fotopoulos V, Symeonidis A, Vlachaki E, Chalkia P, Patrinos GP, Papachatzopoulou A, Sgourou A. Impact of ZBTB7A hypomethylation and expression patterns on treatment response to hydroxyurea. Hum Genomics 2018; 12:45. [PMID: 30285874 PMCID: PMC6167880 DOI: 10.1186/s40246-018-0177-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/11/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND We aimed to clarify the emerging epigenetic landscape in a group of genes classified as "modifier genes" of the β-type globin genes (HBB cluster), known to operate in trans to accomplish the two natural developmental switches in globin expression, from embryonic to fetal during the first trimester of conception and from fetal to adult around the time of birth. The epigenetic alterations were determined in adult sickle cell anemia (SCA) homozygotes and SCA/β-thalassemia compound heterozygotes of Greek origin, who are under hydroxyurea (HU) treatment. Patients were distinguished in HU responders and HU non-responders (those not benefited from the HU) and both, and in vivo and in vitro approaches were implemented. RESULTS We examined the CpG islands' DNA methylation profile of BCL11A, KLF1, MYB, MAP3K5, SIN3A, ZBTB7A, and GATA2, along with γ-globin and LRF/ZBTB7A expression levels. In vitro treatment of hematopoietic stem cells (HSCs) with HU induced a significant DNA hypomethylation pattern in ZBTB7A (p*, 0.04) and GATA2 (p*, 0.03) CpGs exclusively in the HU non-responders. Also, this group of patients exhibited significantly elevated baseline methylation patterns in ZBTB7A, before the HU treatment, compared to HU responders (p*, 0.019) and to control group of healthy individuals (p*, 0.021), which resembles a potential epigenetic barrier for the γ-globin expression. γ-Globin expression in vitro matched with detected HbF levels during patients' monitoring tests (in vivo) under HU treatment, implying a good reproducibility of the in vitro HU epigenetic effect. LRF/ZBTB7A expression was elevated only in the HU non-responders under the influence of HU. CONCLUSIONS This is one of the very first pharmacoepigenomic studies indicating that the hypomethylation of ZBTB7A during HU treatment enhances the LRF expression, which by its turn suppresses the HbF resumption in the HU non-responders. Its role as an epigenetic regulator of hemoglobin switching is also supported by the wide distribution of ZBTB7A-binding sites within the 5' CpG sequences of all studied human HBB cluster "modifier genes." Also, the baseline methylation level of selective CpGs in ZBTB7A and GATA2 could be an indicator of the negative HU response among the β-type hemoglobinopathy patients.
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Affiliation(s)
- Vasiliki Chondrou
- School of Science and Technology, Biology Laboratory, Hellenic Open University, Patras, Greece
| | - Eleana F Stavrou
- School of Science and Technology, Biology Laboratory, Hellenic Open University, Patras, Greece
| | - Georgios Markopoulos
- Faculty of Medicine, Biology Laboratory, University of Ioannina, Ioannina, Greece
| | - Alexandra Kouraklis-Symeonidis
- Thalassemia and Hemoglobinopathies Unit, Hematology Division, Department of Internal Medicine, General University Hospital of Patras, Patras, Greece
| | - Vasilios Fotopoulos
- School of Science and Technology, Digital Systems and Media Computing Laboratory, Hellenic Open University, Patras, Greece
| | - Argiris Symeonidis
- Medical School, Hematology Division, Department of Internal Medicine, University of Patras, Patras, Greece
| | - Efthymia Vlachaki
- Thalassemia Unit, "Hippokrateio" General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Panagiota Chalkia
- Thalassemia and Sickle Cell Unit, AHEPA University General Hospital of Thessaloniki, Thessaloniki, Greece
| | - George P Patrinos
- School of Health Sciences, Department of Pharmacy, Laboratory of Pharmacogenomics and Individualized Therapy, University of Patras, Patras, Greece
| | | | - Argyro Sgourou
- School of Science and Technology, Biology Laboratory, Hellenic Open University, Patras, Greece.
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15
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Chen YH, Zeng WJ, Wen ZP, Cheng Q, Chen XP. Under explored epigenetic modulators: role in glioma chemotherapy. Eur J Pharmacol 2018; 833:201-209. [PMID: 29864410 DOI: 10.1016/j.ejphar.2018.05.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 05/31/2018] [Accepted: 05/31/2018] [Indexed: 12/15/2022]
Abstract
Patients with somatic mutations of epigenetic regulators are characterized by aberrant chromatin modification patterns. Recent mechanistic studies pairing chemical tool compounds and deep-sequencing technology have greatly broadened our understanding of epigenetic regulation in glioma progression and underpinned alternative treatment of epigenetic inhibitors. However, the effect of most inhibitors is condition-dependent, and the overall results of clinical trials still have not been applied to patients. There is an intense need to develop more potent and specific compounds as well as identify the population who may achieve clinical benefits. Besides, combination therapy with conventional therapeutics is another alternative strategy. In this review, we summarize well-characterized chemical probes in glioma research and clinical translation. We also discuss the target population and combination of therapy regimens of various agents. In a holistic sense, we try to provide guidance for selecting targeted chemical probes and pave the way for personalized rational therapy.
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Affiliation(s)
- Yan-Hong Chen
- Department of Clinical pharmacology, Xiangya Hospital, Central South University, Changsha 410078, China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, China
| | - Wen-Jing Zeng
- Department of Clinical pharmacology, Xiangya Hospital, Central South University, Changsha 410078, China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, China
| | - Zhi-Peng Wen
- Department of Clinical pharmacology, Xiangya Hospital, Central South University, Changsha 410078, China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, China
| | - Quan Cheng
- Department of Clinical pharmacology, Xiangya Hospital, Central South University, Changsha 410078, China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, China
| | - Xiao-Ping Chen
- Department of Clinical pharmacology, Xiangya Hospital, Central South University, Changsha 410078, China; Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, China.
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16
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Konstantinidou MK, Karaglani M, Panagopoulou M, Fiska A, Chatzaki E. Are the Origins of Precision Medicine Found in the Corpus Hippocraticum? Mol Diagn Ther 2017; 21:601-606. [DOI: 10.1007/s40291-017-0291-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Oliva D, Nilsson M, Andersson BÅ, Sharp L, Lewin F, Laytragoon-Lewin N. Single nucleotide polymorphisms might influence chemotherapy induced nausea in women with breast cancer. Clin Transl Radiat Oncol 2016; 2:1-6. [PMID: 29657992 PMCID: PMC5893496 DOI: 10.1016/j.ctro.2016.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/29/2016] [Accepted: 12/04/2016] [Indexed: 11/27/2022] Open
Abstract
Background Women receiving FEC (5 fluorouracil, epirubicin and cyclophosphamide) chemotherapy (CT) for breast cancer (BC) often experience side effects such as nausea and vomiting. Individual variations of side effects occur in patients despite similar cancer therapy. The purpose of this study was to investigate a possible genetic background as a predictor for individual variations in nausea induced by CT. Methods 114 women were included in the study. All women received adjuvant CT for BC. Self-reported nausea and vomiting was recorded in a structured diary over ten days following treatment. Blood samples were collected before the treatment and used for the detection of 48 single nucleotide polymorphisms (SNPs) in 43 genes. SNPs from each individual woman were analyzed for their relation to the patient-reported frequency and intensity of nausea and vomiting. Results Eighty-four percent (n = 96) of the women reported acute or delayed nausea or combined nausea and vomiting during the ten days following CT. Three out of the forty-eight SNPs in the following genes: FAS/CD95, RB1/LPAR6 and CCL2 were found to be associated with a risk of nausea. Conclusion SNPs in the FAS/CD95, RB1/LPAR6 and CCL2 genes were found to be associated with nausea among women treated with adjuvant FEC for BC. SNPs analysis is fast and cost effective and can be done prior to any cancer therapy. The association between individual SNPs and severe side effects from FEC may contribute to a more personalized care of patients with BC.
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Affiliation(s)
- Delmy Oliva
- Department of Oncology, Ryhov County Hospital, SE-551 85 Jönköping, Sweden.,Linköpings University, Department of Clinical and Experimental Medicine, Oncology, SE-581 85 Linköping, Sweden
| | - Mats Nilsson
- Futurum - The Academy for Healthcare, Region Jönköping County, SE-551 85 Jönköping, Sweden
| | - Bengt-Åke Andersson
- Linköpings University, Department of Clinical and Experimental Medicine, Oncology, SE-581 85 Linköping, Sweden.,Division of Medical Diagnostics, Region Jönköping County, SE-551 85 Jönköping, Sweden
| | - Lena Sharp
- Regional Cancer Centre, Stockholm-Gotland, SE-10239 Stockholm, Sweden.,Karolinska Institutet, Department of Learning, Informatics Management and Ethics, SE-171 77 Stockholm, Sweden
| | - Freddi Lewin
- Department of Oncology, Ryhov County Hospital, SE-551 85 Jönköping, Sweden.,Linköpings University, Department of Clinical and Experimental Medicine, Oncology, SE-581 85 Linköping, Sweden
| | - Nongnit Laytragoon-Lewin
- Linköpings University, Department of Clinical and Experimental Medicine, Oncology, SE-581 85 Linköping, Sweden.,Division of Medical Diagnostics, Region Jönköping County, SE-551 85 Jönköping, Sweden
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18
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Chambliss AB, Chan DW. Precision medicine: from pharmacogenomics to pharmacoproteomics. Clin Proteomics 2016; 13:25. [PMID: 27708556 PMCID: PMC5037608 DOI: 10.1186/s12014-016-9127-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/17/2016] [Indexed: 12/31/2022] Open
Abstract
Disease progression and drug response may vary significantly from patient to patient. Fortunately, the rapid development of high-throughput ‘omics’ technologies has allowed for the identification of potential biomarkers that may aid in the understanding of the heterogeneities in disease development and treatment outcomes. However, mechanistic gaps remain when the genome or the proteome are investigated independently in response to drug treatment. In this article, we discuss the current status of pharmacogenomics in precision medicine and highlight the needs for concordant analysis at the proteome and metabolome levels via the more recently-evolved fields of pharmacoproteomics, toxicoproteomics, and pharmacometabolomics. Integrated ‘omics’ investigations will be critical in piecing together targetable mechanisms of action for both drug development and monitoring of therapy in order to fully apply precision medicine to the clinic.
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Affiliation(s)
- Allison B Chambliss
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA ; Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033 USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
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19
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Ahmad A. Epigenetics in Personalized Management of Lung Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 890:111-22. [PMID: 26703801 DOI: 10.1007/978-3-319-24932-2_6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In last several years, the focus on the origin and progression of human cancers has shifted from genetic to epigenetic regulation, with particular attention to methylation and acetylation events that have profound effect on the eventual expression of oncogenes and the suppression of tumor suppressors. A few drugs targeting these epigenetic changes have already been approved for treatment, albeit not for lung cancer. With the recent advances in the push towards personalized therapy, questions have been asked about the possible targeting of epigenetic events for personalized lung cancer therapy. Some progress has been made but a lot needs to be done. In this chapter, a succinct review of these topics is provided.
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Affiliation(s)
- Aamir Ahmad
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA.
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20
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Lv JF, Hu L, Zhuo W, Zhang CM, Zhou HH, Fan L. Epigenetic alternations and cancer chemotherapy response. Cancer Chemother Pharmacol 2015; 77:673-84. [DOI: 10.1007/s00280-015-2951-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/17/2015] [Indexed: 12/29/2022]
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21
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Seripa D, Panza F, Daragjati J, Paroni G, Pilotto A. Measuring pharmacogenetics in special groups: geriatrics. Expert Opin Drug Metab Toxicol 2015; 11:1073-88. [PMID: 25990744 DOI: 10.1517/17425255.2015.1041919] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The cytochrome P450 (CYP) enzymes oxidize about 80% of the most commonly used drugs. Older patients form a very interesting clinical group in which an increased prevalence of adverse drug reactions (ADRs) and therapeutic failures (TFs) is observed. Might CYP drug metabolism change with age, and justify the differences in drug response observed in a geriatric setting? AREAS COVERED A complete overview of the CYP pharmacogenetics with a focus on the epigenetic CYP gene regulation by DNA methylation in the context of advancing age, in which DNA methylation might change. EXPERT OPINION Responder phenotypes consist of a continuum spanning from ADRs to TFs, with the best responders at the midpoint. CYP genetics is the basis of this continuum on which environmental and physiological factors act, modeling the phenotype observed in clinical practice. Physiological age-related changes in DNA methylation, the main epigenetic mechanisms regulating gene expression in humans, results in a physiological decrease in CYP gene expression with advancing age. This may be one of the physiological changes that, together with increased drug use, contributed to the higher prevalence of ADRs and TFs observed in the geriatric setting, thus, making geriatrics a special group for pharmacogenetics.
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Affiliation(s)
- Davide Seripa
- IRCCS Casa Sollievo della Sofferenza, Geriatric Unit and Gerontology-Geriatrics Research Laboratory, Department of Medical Sciences , San Giovanni Rotondo, Foggia , Italy
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