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Karimi MA, Dadmehr M, Hosseini M, Korouzhdehi B, Oroojalian F. Sensitive detection of methylated DNA and methyltransferase activity based on the lighting up of FAM-labeled DNA quenched fluorescence by gold nanoparticles. RSC Adv 2019; 9:12063-12069. [PMID: 35516994 PMCID: PMC9063544 DOI: 10.1039/c9ra01564g] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/04/2019] [Indexed: 12/27/2022] Open
Abstract
DNA methylation of cytosine bases, which is catalyzed by methyltransferase enzymes, involve biochemical processes that contribute to gene expression and gene regulation in cells. Detection of abnormal patterns of both methylated DNA and methyltransferase enzyme activity at early stages could be considered as promising targets for early cancer diagnosis. In the present study, a novel and facile method is introduced for the sensitive detection of the M.SssI methyltransferase (M.SssI MTase) enzyme and methylated DNA based on the fluorescence recovery of FAM-labeled DNA coupled with gold nanoparticles (AuNPs). Thiol-modified probes were functionalized with AuNPs, which brought the FAM fluorophore into the close proximity of the AuNPs. This led to the overlap between the FAM fluorescence emission and AuNPs absorption spectra, introducing a FRET occurrence and causing fluorescence quenching. The hybridization of the probe and its complementary target provided specific CpG sites for M.SssI MTase enzyme activity. The methylation process gradually converted the quenched FAM fluorophore into an emissive fluorophore upon the addition of the MTase enzyme, and the observed fluorescence recovery proved the efficiency of the assay for the detection of MTase enzyme. The fluorescence intensity showed an increasing trend with M.SssI MTase enzyme activity in the range of 1–8 U mL−1 with a detection limit of 0.14 U mL−1. The addition of methylated ssDNA targets to a ssDNA FAM-labeled probe resulted in a DNA duplex formation, leading to a strong fluorescence signal emission due to the recovery of the fluorophore signal. Conversely, the unmethylated ssDNA target caused no changes in the fluorescence signal. In the presence of methylated DNA targets, the biosensor could specifically recognize it and accordingly trigger the methylated targets through a fluorescence enhancement in the range of 5–100 pM by monitoring the increase in the fluorescence intensity with a detection limit of 2.2 pM. The obtained results showed that the assay could realize the detection of M.SssI MTase and methylated DNA effectively in diluted human serum samples. Human serum conditions showed no significant interference with the assay performance, indicating that the present method has great potential for further application in real samples. A novel method for detection of DNA methylation based on fluorescence recovery of FAM labeled DNA/Au NPs was introduced.![]()
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Affiliation(s)
| | - Mehdi Dadmehr
- Department of Biology
- Payame Noor University
- Tehran
- Iran
| | - Morteza Hosseini
- Department of Life Science Engineering
- Faculty of New Sciences & Technologies
- University of Tehran
- Tehran
- Iran
| | | | - Fatemeh Oroojalian
- Department of Advanced Sciences and Technologies
- School of Medicine
- North Khorasan University of Medical Sciences
- Bojnurd
- Iran
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52
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Joseph DB, Strand DW, Vezina CM. DNA methylation in development and disease: an overview for prostate researchers. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2018; 6:197-218. [PMID: 30697577 PMCID: PMC6334199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/14/2018] [Indexed: 06/09/2023]
Abstract
Epigenetic mechanisms including DNA methylation are critical regulators of organismal development and tissue homeostasis. DNA methylation is the transfer of methyl groups to cytosines, which adds an additional layer of complexity to the genome. DNA methylation marks are recognized by the cellular machinery to regulate transcription. Disruption of DNA methylation with aging or exposure to environmental toxins can change susceptibility to disease or trigger processes that lead to disease. In this review, we provide an overview of the DNA methylation machinery. More specifically, we describe DNA methylation in the context of prostate development, prostate cancer, and benign prostatic hyperplasia (BPH) as well as the impact of dietary and environmental factors on DNA methylation in the prostate.
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Affiliation(s)
- Diya B Joseph
- Department of Comparative Biosciences, University of Wisconsin-MadisonMadison, WI 53706, USA
| | - Douglas W Strand
- Department of Urology, UT Southwestern Medical CenterDallas, TX 75390, USA
| | - Chad M Vezina
- Department of Comparative Biosciences, University of Wisconsin-MadisonMadison, WI 53706, USA
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Lv F, Jin WH, Zhang XL, Wang ZR, Sun AJ. Tamoxifen therapy benefit predictive signature combining with prognostic signature in surgical-only ER-positive breast cancer. J Cell Physiol 2018; 234:11140-11148. [PMID: 30537139 DOI: 10.1002/jcp.27756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/30/2018] [Indexed: 12/18/2022]
Abstract
Tamoxifen treatment is important assistant for estrogen-receptor-positive breast cancer (BRCA) after resection. This study aimed to identify signatures for predicting the prognosis of patients with BRCA after tamoxifen treatment. Data of gene-specific DNA methylation (DM), as well as the corresponding clinical data for the patients with BRCA, were obtained from The Cancer Genome Atlas and followed by systematic bioinformatics analyses. After mapping these DM CPG sites onto genes, we finally obtained 352 relapse-free survival (RFS) associated DM genes, with which 61,776 gene pairs were combined, including 1,614 gene pairs related to RFS. An 11 gene-pair signature was identified to cluster the 189 patients with BRCA into the surgical low-risk group (136 patients) and high-risk group (53 patients). Then, we further identified a tamoxifen-predictive signature that could classify surgical high-risk patients with significant differences on RFS. Combining surgical-only prognostic signature and tamoxifen-predictive signature, patients were clustered into surgical-only low-risk group, tamoxifen nonbenefit group, and tamoxifen benefit group. In conclusion, we identified that the gene pair PDHA2-APRT could serve as a potential prognostic biomarker for patients with BRCA after tamoxifen treatment.
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Affiliation(s)
- Feng Lv
- Department of General Surgery, Affiliated Renhe Hospital of China Three Gorges University, Yichang, Hubei, China
| | - Wei-Hua Jin
- Hubei Three Gorges Polytechnic, Yichang, Hubei, China
| | - Xian-Lin Zhang
- Department of General Surgery, Affiliated Renhe Hospital of China Three Gorges University, Yichang, Hubei, China
| | - Zhong-Rui Wang
- Department of General Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ai-Jun Sun
- Department of General Surgery, Huai'an Second People's Hospital, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
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54
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Zhang H, Wang LJ, Wang L, Chen H, Chen X, Zhang CY. Development of a cascade isothermal amplification approach for the sensitive detection of DNA methyltransferase. J Mater Chem B 2018; 7:157-162. [PMID: 32254960 DOI: 10.1039/c8tb02096e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA methyltransferase (MTase) is an important epigenetic modification enzyme responsible for DNA methylation, and the dysregulation of DNA MTase activity is associated with various diseases in humans. Herein, we take advantage of the DNA lesion repair mechanism in vivo to develop a new fluorescence approach for the specific and sensitive detection of DNA methyltransferase (DNA MTase) on the basis of the DNA lesion repair-directed cascade isothermal amplification. Due to the high amplification efficiency of the uracil repair-mediated exponential isothermal amplification reaction (EXPAR), the efficient cleavage of endonuclease IV (Endo IV)-induced cyclic catalysis, and the low background signal caused by single uracil repair-mediated inhibition of nonspecific amplification, this approach exhibits high sensitivity with a detection limit of 0.014 U mL-1 for pure Dam MTase and 0.61 × 10-6 mg mL-1 for Dam MTase in E. coli cells and it can be further applied for the screening of DNA MTase inhibitors. More importantly, this approach can be applied to detect other DNA MTases by designing appropriate substrates, showing great potential in biomedical research and clinical diagnosis.
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Affiliation(s)
- Huige Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China.
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55
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Zhang Y, Charlton J, Karnik R, Beerman I, Smith ZD, Gu H, Boyle P, Mi X, Clement K, Pop R, Gnirke A, Rossi DJ, Meissner A. Targets and genomic constraints of ectopic Dnmt3b expression. eLife 2018; 7:e40757. [PMID: 30468428 PMCID: PMC6251628 DOI: 10.7554/elife.40757] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/09/2018] [Indexed: 12/19/2022] Open
Abstract
DNA methylation plays an essential role in mammalian genomes and expression of the responsible enzymes is tightly controlled. Deregulation of the de novo DNA methyltransferase DNMT3B is frequently observed across cancer types, yet little is known about its ectopic genomic targets. Here, we used an inducible transgenic mouse model to delineate rules for abnormal DNMT3B targeting, as well as the constraints of its activity across different cell types. Our results explain the preferential susceptibility of certain CpG islands to aberrant methylation and point to transcriptional state and the associated chromatin landscape as the strongest predictors. Although DNA methylation and H3K27me3 are usually non-overlapping at CpG islands, H3K27me3 can transiently co-occur with DNMT3B-induced DNA methylation. Our genome-wide data combined with ultra-deep locus-specific bisulfite sequencing suggest a distributive activity of ectopically expressed Dnmt3b that leads to discordant CpG island hypermethylation and provides new insights for interpreting the cancer methylome.
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Affiliation(s)
- Yingying Zhang
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Jocelyn Charlton
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
- Department of Genome RegulationMax Planck Institute for Molecular GeneticsBerlinGermany
| | - Rahul Karnik
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Isabel Beerman
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
- Department of PediatricsHarvard Medical SchoolMassachusettsUnited States
- Program in Cellular and Molecular Medicine, Division of Hematology/OncologyBoston Children's HospitalMassachusettsUnited States
| | - Zachary D Smith
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Hongcang Gu
- Broad Institute of MIT and HarvardMassachusettsUnited States
| | - Patrick Boyle
- Broad Institute of MIT and HarvardMassachusettsUnited States
| | - Xiaoli Mi
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Kendell Clement
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Ramona Pop
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Andreas Gnirke
- Broad Institute of MIT and HarvardMassachusettsUnited States
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
- Department of PediatricsHarvard Medical SchoolMassachusettsUnited States
- Program in Cellular and Molecular Medicine, Division of Hematology/OncologyBoston Children's HospitalMassachusettsUnited States
| | - Alexander Meissner
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
- Department of Genome RegulationMax Planck Institute for Molecular GeneticsBerlinGermany
- Broad Institute of MIT and HarvardMassachusettsUnited States
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56
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Yang Z, Liu B, Lin T, Zhang Y, Zhang L, Wang M. Multiomics analysis on DNA methylation and the expression of both messenger RNA and microRNA in lung adenocarcinoma. J Cell Physiol 2018; 234:7579-7586. [PMID: 30370535 DOI: 10.1002/jcp.27520] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 09/10/2018] [Indexed: 02/03/2023]
Abstract
Lung adenocarcinoma (LUAD) poses a significant threat to public health worldwide, while the genetic and epigenetic abnormalities involved in the oncogenesis of LUAD remains unknown. This study aimed to identify and validate key genes during the development and progression of LUAD by multiomics analysis. First, Empirical Analysis of Digital Gene Expression Data in R (EdgeR) was used to identify differentially regulated genes between normal samples and LUAD samples. Then significance analysis of microarrays (SAM) was used to identify differentially methylated genes and regulated microRNAs (miRNAs) between normal samples and LUAD samples. Following that, Kyoto Encyclopedia of Genes and Genomes (KEGG)-enrichment analysis was used to analyze the function that these genes enriched in. A total of 4,816 genes, 419 miRNAs, and 4,476 methylated genes that were significantly differentially expressed corresponding to the normal tissues in LUAD were obtained, and some of the pathways these genes enriched in were the same. Moreover, 255 genes differentially methylated and expressed at the same time were also found, and these 255 genes were the target genes of the miRNAs differentially expressed in LUAD. Finally, nine genes (BRCA1, COL1A1, ESR1, FGFR2, HNF4A, IGFBP3, MET, MMP3, and PAK1) network analysis, and two of which were found to be related to the survival of LUAD patients. In summary, a total of nine genes that may play important roles in the development of LUAD were identified, and two (PAK1 and FGFR2) of them can be served as prognostic biomarkers for LUAD patients. The genes found in this study played different roles in the tumor progression of LUAD, indicating these genes may be considered as potential target genes for LUAD treatment.
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Affiliation(s)
- Zhaoyang Yang
- Department of Respiratory Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Bao Liu
- Department of Respiratory Medicine, Harbin Medical University Cancer Hospital, Harbin, China
| | - Tie Lin
- Department of Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yingli Zhang
- Department of Internal Medicine, Harbin Red Cross Center Hospital, Harbin, China
| | - Limin Zhang
- Department of Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Meng Wang
- Department of Respiratory Medicine, Harbin Medical University Cancer Hospital, Harbin, China
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57
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Yang Y, Wang M, Liu B. Exploring and comparing of the gene expression and methylation differences between lung adenocarcinoma and squamous cell carcinoma. J Cell Physiol 2018; 234:4454-4459. [PMID: 30317601 DOI: 10.1002/jcp.27240] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/19/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Yang Yang
- Medical Oncology, Harbin Medical University Cancer Hospital Harbin Heilongjiang China
| | - Meng Wang
- Medical Oncology, Harbin Medical University Cancer Hospital Harbin Heilongjiang China
| | - Bao Liu
- Medical Oncology, Harbin Medical University Cancer Hospital Harbin Heilongjiang China
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58
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Tissue-specific induced DNA methyltransferase 1 (Dnmt1) in endocrine pancreas by RCAS-TVA-based somatic gene transfer system promotes β-cell proliferation. Cancer Gene Ther 2018; 26:94-102. [PMID: 30190513 DOI: 10.1038/s41417-018-0046-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/31/2018] [Accepted: 08/05/2018] [Indexed: 12/13/2022]
Abstract
We reported that inactivation of menin (the protein product of MEN1) increases activity of Dnmt1 and mediates DNA hypermethylation in the development of multiple endocrine neoplasia type 1 (MEN1) syndrome. We have developed a RCAS-TVA-based somatic gene transfer system that enables tissue-specific delivery of Dnmt1 to individual β-cells of the pancreas in a RIP-TVA mouse model. In the present study, we mediated Dnmt1 expression in islet β-cells in RIP-TVA mice by utilizing the RCAS-TVA system to test if the upregulation of Dnmt1 can promote β-cell proliferation. In vitro, we demonstrated that upregulation of Dnmt1 increased β-cell proliferation. In vivo, our results showed that the levels of serum insulin were increased in the RIP-TVA mice with RCASBP-Dnmt1 infection compared with wild-type control mice with RCASBP-Dnmt1 infection. Furthermore, we confirmed that mRNA and protein expression of Dnmt1 as well as Dnmt1 enzyme activity were upregulated in the RIP-TVA mice with RCASBP-Dnmt1 infection compared with wild-type control mice with RCASBP-Dnmt1 infection. Finally, we demonstrated that upregulation of Dnmt1 resulted in hyperplasia through β-cell proliferation. We conclude that the upregulation of Dnmt1 promotes islet β-cell proliferation and targeting Dnmt1 may be a promising therapy for patients suffering from pancreatic neuroendocrine tumors.
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59
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Zheng YF, Lu X, Zhang XY, Guan BG. The landscape of DNA methylation in hepatocellular carcinoma. J Cell Physiol 2018; 234:2631-2638. [PMID: 30145793 DOI: 10.1002/jcp.27077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/28/2018] [Indexed: 12/24/2022]
Abstract
Better understanding of the relationship between changes in the overall methylation status of hepatocellular carcinoma (HCC) and disease progression will help us find good strategies for the early detection and treatment of HCC patients. The purpose of the study was to study the relations between the methylation status changes in HCC patients and progression of the disease to enable early detection and treatment of HCC patients. First, the DNA methylation data of 50 HCC samples and the surrounding normal samples were extracted and the change pattern of methylation status in the DNA promoter region of HCC samples against that of normal samples was studied. Then, some DNA methylation genes that could accurately identify cancer and cancer-adjacent tissues were identified using the k-top scoring pair method. Also, a prognostic signature that could predict the survival of HCC patients was constructed based on the overall survival time and death information of the early HCC patients. Finally, the obtained prognostic signature was verified. In conclusion, this study described the changes in the methylation spectrum during the development of HCC and identified genes associated with HCC progression and prognosis, which may offer new opportunities for the diagnosis and treatment of HCC.
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Affiliation(s)
- Yong-Fa Zheng
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiaojie Lu
- Nanjing Medical University, Nanjing, China
| | - Xiao-Yu Zhang
- Division of Gastrointestinal Surgery, Department of General Surgery, Huai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Bu-Gao Guan
- Department of General Surgery, People's Hospital of Jinhu, Huai'an, China
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60
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Song X, Gong M, Chen Y, Liu H, Zhang J. Nine hub genes as the potential indicator for the clinical outcome of diabetic nephropathy. J Cell Physiol 2018; 234:1461-1468. [PMID: 30078220 DOI: 10.1002/jcp.26958] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 06/13/2018] [Indexed: 01/08/2023]
Abstract
Diabetic nephropathy (DN) is one of the most serious and dangerous chronic complications caused by diabetes mellitus, and the identification and development of novel biomarkers could be beneficial for the diagnosis and prognosis of DN patients. This study focused on researching the differently expressed pattern of the DN samples from glomeruli and tubulointerstitium. Significance analysis of microarrays (SAM) was used to identify differentially regulated genes in 44 microdissected human kidney samples. Functional enrichment analysis was used to analyze the functions these genes are mostly enriched in. Besides, protein-protein interaction (PPI) network was used to select the hub genes that were associated with DN. The gene expression pattern of DN samples from glomeruli and tubulointerstitium was found to be quite different. It showed that the recurrence rate of DN originating from glomeruli and control samples was lower than that from tubulointerstitium and control samples. A total of 332 differentially expressed genes were identified between glomeruli tissues and tubulointerstitium tissues. PPI network analysis was performed on these 332 genes. Finally, nine hub genes were selected as the most potential biomarkers in the occurrence of DN. In conclusion, a total of 332 genes were found to be related to DN, and these genes were found to be mostly enriched in pathways such as immunity, inflammatory, and vascular pathways. Three genes VAV1, LCK, and Plk had the potential to serve as indicators for the occurrence and development of DN in clinical management.
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Affiliation(s)
- Xiaoping Song
- Department of Laboratory, Qingdao Hiser Medical Group, Qingdao, China
| | - Min Gong
- Department of Endocrinology, Qingdao Hiser Medical Group, Qingdao, China
| | - Yanping Chen
- Department of Laboratory, Qingdao Women and Children's Hospital, Qingdao, China
| | - Hui Liu
- Department of Laboratory, Qingdao Women and Children's Hospital, Qingdao, China
| | - Jun Zhang
- Department of Emergency, Qingdao Municipal Hospital East Hospital, Qingdao, China
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61
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Kermani HA, Hosseini M, Miti A, Dadmehr M, Zuccheri G, Hosseinkhani S, Ganjali MR. A colorimetric assay of DNA methyltransferase activity based on peroxidase mimicking of DNA template Ag/Pt bimetallic nanoclusters. Anal Bioanal Chem 2018; 410:4943-4952. [DOI: 10.1007/s00216-018-1143-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/07/2018] [Accepted: 05/14/2018] [Indexed: 01/31/2023]
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Peng WF, Bai F, Shao K, Shen LS, Li HH, Huang S. The key genes underlying pathophysiology association between the type 2-diabetic and colorectal cancer. J Cell Physiol 2018; 233:8551-8557. [PMID: 29319171 DOI: 10.1002/jcp.26440] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/05/2018] [Indexed: 01/05/2023]
Abstract
Although diabetes mellitus (DM) is reported as an independent risk factor for colorectal cancer (CRC) in many researches, the underlying pathophysiology is still unclear. We investigated the differentially expressed genes (DEGs) for the diabetes and CRC to reveal the underlying pathophysiological association between the type 2-diabetic (T2D) and CRC. Gene expression profiles for T2D (GSE55650), CRC (GSE8671), and Metformin treated cell lines (GSE67342) were downloaded from GEO database. The DEGs between T2D samples and their control samples were identified with t-test and variance analysis. After cluster analysis and functional enrichment analysis, protein-protein interaction (PPI) network was constructed to find potential genes for diabetes and CRC in Metformin's treatment. Totally, we identified 583 overlapped genes, 169 common DEGs, and 414 independent DEGs between T2D and CRC samples. The common genes contained 89 up-regulated (DEGs1) and 80 down-regulated genes (DEGs3); and independent DEGs contained 270 down-regulated genes (DEGs4) in diabetes and 144 down-regulated genes (DEGs2) in CRC. In enrichment analysis, the Ribosome pathway was significantly enriched by the independent DEGs. The common genes were mainly enriched in some inflammatory related pathways. Two target genes of Metformin were significantly interacted with six hub genes (HADHB, NDUFS3, TAF1, MYC, HNFF4A, and MAX) with significant changes in expression values (P < 0.05, t-test). To summary, it is suggested that the six hub genes might play important roles in the process of Metformin treatment for diabetes and CRC. However, specific pathology remains to be further studied.
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Affiliation(s)
- Wen-Fang Peng
- Department of Endocrinology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feng Bai
- Department of Endocrinology and Metabolism, Huai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Kan Shao
- Department of Endocrinology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li-Sha Shen
- Department of Endocrinology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui-Hua Li
- Department of Endocrinology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shan Huang
- Department of Endocrinology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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63
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Luo WM, Wang ZY, Zhang X. Identification of four differentially methylated genes as prognostic signatures for stage I lung adenocarcinoma. Cancer Cell Int 2018; 18:60. [PMID: 29713243 PMCID: PMC5909272 DOI: 10.1186/s12935-018-0547-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 03/22/2018] [Indexed: 12/20/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is the main subtype of non-small cell lung cancer with a low survival prognosis. We aimed to generate a prognostic model for the postoperative recurrence of LUAD. Methods The methylated DNA data of LUAD patients were downloaded from the Cancer Genome Atlas (TCGA). The differentially methylated genes were identified and protein–protein interacting network was constructed, with which prognostic signature of this cancer was generated. Survival and functional pathways analysis w used to evaluate the clustering ability of the prognostic signature. Results We identified 151 differentially methylated genes related to relapse-free survival of patients with LUAD. Nine hub genes were identified in PPI network, with which 4 gene pair signature was selected as prognostic signature. The potential functions of 6 genes (JDP2, SERPINA5, PLG, SEMG2, RFX5, and POLR3B) in the 4-gene pair signature were enriched in intracellular protein synthesis and transportation. Conclusion The four gene pair signature can predict the prognosis of patients with stage I LUAD. Our study provides a reference for patients with postoperative adjuvant therapy.
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Affiliation(s)
- Wei-Ming Luo
- Department of Radiation Oncology, Shanghai Minhang District Cancer Hospital, 106 Ruili Road, Shanghai, 200240 China
| | - Zheng-Yu Wang
- 2Department of Pharmacy, The Affiliated Huai'an Hospital of Xuzhou Medical University and The Second People's Hospital of Huai'an, 62 South Huai'hai Rode, Huai'an, China
| | - Xin Zhang
- Department of Medical Imaging, The Fourth People's Hospital of Huai'an, Huai'an, Jiangsu China
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64
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Cheng Y, Monteiro C, Matos A, You J, Fraga A, Pereira C, Catalán V, Rodríguez A, Gómez-Ambrosi J, Frühbeck G, Ribeiro R, Hu P. Epigenome-wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity-a pilot study. Clin Epigenetics 2018; 10:54. [PMID: 29692867 PMCID: PMC5904983 DOI: 10.1186/s13148-018-0490-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/05/2018] [Indexed: 12/12/2022] Open
Abstract
Background Periprostatic adipose tissue (PPAT) has been recognized to associate with prostate cancer (PCa) aggressiveness and progression. Here, we sought to investigate whether excess adiposity modulates the methylome of PPAT in PCa patients. DNA methylation profiling was performed in PPAT from obese/overweight (OB/OW, BMI > 25 kg m−2) and normal weight (NW, BMI < 25 kg m−2) PCa patients. Significant differences in methylated CpGs between OB/OW and NW groups were inferred by statistical modeling. Results Five thousand five hundred twenty-six differentially methylated CpGs were identified between OB/OW and NW PCa patients with 90.2% hypermethylated. Four hundred eighty-three of these CpGs were found to be located at both promoters and CpG islands, whereas the representing 412 genes were found to be involved in pluripotency of stem cells, fatty acid metabolism, and many other biological processes; 14 of these genes, particularly FADS1, MOGAT1, and PCYT2, with promoter hypermethylation presented with significantly decreased gene expression in matched samples. Additionally, 38 genes were correlated with antigen processing and presentation of endogenous antigen via MHC class I, which might result in fatty acid accumulation in PPAT and tumor immune evasion. Conclusions Results showed that the whole epigenome methylation profiles of PPAT were significantly different in OB/OW compared to normal weight PCa patients. The epigenetic variation associated with excess adiposity likely resulted in altered lipid metabolism and immune dysregulation, contributing towards unfavorable PCa microenvironment, thus warranting further validation studies in larger samples. Electronic supplementary material The online version of this article (10.1186/s13148-018-0490-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Cheng
- 1Department of Biochemistry and Medical Genetics & Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada.,2Experimental Center, Northwest University for Nationalities, Lanzhou, People's Republic of China
| | - Cátia Monteiro
- 3Molecular Oncology Group, Portuguese Institute of Oncology, Porto, Portugal.,Research Department, Portuguese League Against Cancer-North, Porto, Portugal
| | - Andreia Matos
- 5Laboratory of Genetics and Environmental Health Institute, Faculty of Medicine, University of Lisboa, Lisbon, Portugal.,6Tumor & Microenvironment Interactions, i3S/INEB, Institute for Research and Innovation in Health, and Institute of Biomedical Engineering, University of Porto, Porto, Portugal
| | - Jiaying You
- 1Department of Biochemistry and Medical Genetics & Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada
| | - Avelino Fraga
- 6Tumor & Microenvironment Interactions, i3S/INEB, Institute for Research and Innovation in Health, and Institute of Biomedical Engineering, University of Porto, Porto, Portugal.,7Department of Urology, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - Carina Pereira
- 3Molecular Oncology Group, Portuguese Institute of Oncology, Porto, Portugal.,8CINTESIS, Center for Health Technology and Services Research, Faculty of Medicine, e, University of Porto, Porto, Portugal
| | - Victoria Catalán
- 9Metabolic Research Laboratory, Universidad de Navarra, Pamplona, Spain.,10CIBER Fisiopatología de la Obesidad y Nutricion, Instituto de Salud Carlos III, Madrid, Spain
| | - Amaia Rodríguez
- 9Metabolic Research Laboratory, Universidad de Navarra, Pamplona, Spain.,10CIBER Fisiopatología de la Obesidad y Nutricion, Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Gómez-Ambrosi
- 9Metabolic Research Laboratory, Universidad de Navarra, Pamplona, Spain.,10CIBER Fisiopatología de la Obesidad y Nutricion, Instituto de Salud Carlos III, Madrid, Spain
| | - Gema Frühbeck
- 9Metabolic Research Laboratory, Universidad de Navarra, Pamplona, Spain.,10CIBER Fisiopatología de la Obesidad y Nutricion, Instituto de Salud Carlos III, Madrid, Spain.,11Department of Endocrinology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Ricardo Ribeiro
- 3Molecular Oncology Group, Portuguese Institute of Oncology, Porto, Portugal.,5Laboratory of Genetics and Environmental Health Institute, Faculty of Medicine, University of Lisboa, Lisbon, Portugal.,6Tumor & Microenvironment Interactions, i3S/INEB, Institute for Research and Innovation in Health, and Institute of Biomedical Engineering, University of Porto, Porto, Portugal.,12Department of Clinical Pathology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,13i3S/INEB, Instituto de Investigação e Inovação em Saúde/Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Tumor & Microenvironment Interactions, Rua Alfredo Allen, 208 4200-135 Porto, Portugal
| | - Pingzhao Hu
- 1Department of Biochemistry and Medical Genetics & Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada
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65
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Fadda A, Gentilini D, Moi L, Barault L, Leoni VP, Sulas P, Zorcolo L, Restivo A, Cabras F, Fortunato F, Zavattari C, Varesco L, Gismondi V, De Miglio MR, Scanu AM, Colombi F, Lombardi P, Sarotto I, Loi E, Leone F, Giordano S, Di Nicolantonio F, Columbano A, Zavattari P. Colorectal cancer early methylation alterations affect the crosstalk between cell and surrounding environment, tracing a biomarker signature specific for this tumor. Int J Cancer 2018. [PMID: 29542109 DOI: 10.1002/ijc.31380] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Colorectal cancer (CRC) develops through the accumulation of both genetic and epigenetic alterations. However, while the former are already used as prognostic and predictive biomarkers, the latter are less well characterized. Here, performing global methylation analysis on both CRCs and adenomas by Illumina Infinium HumanMethylation450 Bead Chips, we identified a panel of 74 altered CpG islands, demonstrating that the earliest methylation alterations affect genes coding for proteins involved in the crosstalk between cell and surrounding environment. The panel discriminates CRCs and adenomas from peritumoral and normal mucosa with very high specificity (100%) and sensitivity (99.9%). Interestingly, over 70% of the hypermethylated islands resulted in downregulation of gene expression. To establish the possible usefulness of these non-invasive markers for detection of colon cancer, we selected three biomarkers and identified the presence of altered methylation in stool DNA and plasma cell-free circulating DNA from CRC patients.
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Affiliation(s)
- Antonio Fadda
- Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | - Loredana Moi
- Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Ludovic Barault
- Department of Oncology, University of Torino, Turin, Italy
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Vera Piera Leoni
- Unit of Oncology and Molecular Pathology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Pia Sulas
- Unit of Oncology and Molecular Pathology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Luigi Zorcolo
- Department of Surgery, Colorectal Surgery Center, University of Cagliari, Cagliari, Italy
| | - Angelo Restivo
- Department of Surgery, Colorectal Surgery Center, University of Cagliari, Cagliari, Italy
| | - Francesco Cabras
- Department of Surgery, Colorectal Surgery Center, University of Cagliari, Cagliari, Italy
| | - Federica Fortunato
- Department of Surgery, Colorectal Surgery Center, University of Cagliari, Cagliari, Italy
| | | | - Liliana Varesco
- Unit of Hereditary Cancer, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Viviana Gismondi
- Unit of Hereditary Cancer, IRCCS AOU San Martino-IST, Genoa, Italy
| | | | - Antonio Mario Scanu
- Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | | | | | - Ivana Sarotto
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Eleonora Loi
- Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Francesco Leone
- Department of Oncology, University of Torino, Turin, Italy
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Silvia Giordano
- Department of Oncology, University of Torino, Turin, Italy
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Federica Di Nicolantonio
- Department of Oncology, University of Torino, Turin, Italy
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, Italy
| | - Amedeo Columbano
- Unit of Oncology and Molecular Pathology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Patrizia Zavattari
- Unit of Biology and Genetics, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
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66
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Liu S, Miao C, Liu J, Wang C, Lu X. Four differentially methylated gene pairs to predict the prognosis for early stage hepatocellular carcinoma patients. J Cell Physiol 2018; 233:6583-6590. [DOI: 10.1002/jcp.26256] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/07/2017] [Indexed: 02/03/2023]
Affiliation(s)
- Shaoguang Liu
- Department of Emergency SurgeryGansu Provincial HospitalGansuChina
| | - Changfeng Miao
- Department of General SurgeryGansu Provincial HospitalGansuChina
| | - Juan Liu
- Operating Room, Huai'an Second People's HospitalThe Affiliated Huai'an Hospital of Xuzhou Medical UniversityHuai'anChina
| | - Chang‐Cheng Wang
- Department of GastroenterologyHuai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical UniversityHuai'anJiangsuChina
| | - Xiao‐Jie Lu
- Liver Transplantation CenterThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
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67
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Pan G, Jiang L, Tang J, Guo F. A Novel Computational Method for Detecting DNA Methylation Sites with DNA Sequence Information and Physicochemical Properties. Int J Mol Sci 2018; 19:ijms19020511. [PMID: 29419752 PMCID: PMC5855733 DOI: 10.3390/ijms19020511] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is an important biochemical process, and it has a close connection with many types of cancer. Research about DNA methylation can help us to understand the regulation mechanism and epigenetic reprogramming. Therefore, it becomes very important to recognize the methylation sites in the DNA sequence. In the past several decades, many computational methods—especially machine learning methods—have been developed since the high-throughout sequencing technology became widely used in research and industry. In order to accurately identify whether or not a nucleotide residue is methylated under the specific DNA sequence context, we propose a novel method that overcomes the shortcomings of previous methods for predicting methylation sites. We use k-gram, multivariate mutual information, discrete wavelet transform, and pseudo amino acid composition to extract features, and train a sparse Bayesian learning model to do DNA methylation prediction. Five criteria—area under the receiver operating characteristic curve (AUC), Matthew’s correlation coefficient (MCC), accuracy (ACC), sensitivity (SN), and specificity—are used to evaluate the prediction results of our method. On the benchmark dataset, we could reach 0.8632 on AUC, 0.8017 on ACC, 0.5558 on MCC, and 0.7268 on SN. Additionally, the best results on two scBS-seq profiled mouse embryonic stem cells datasets were 0.8896 and 0.9511 by AUC, respectively. When compared with other outstanding methods, our method surpassed them on the accuracy of prediction. The improvement of AUC by our method compared to other methods was at least 0.0399. For the convenience of other researchers, our code has been uploaded to a file hosting service, and can be downloaded from: https://figshare.com/s/0697b692d802861282d3.
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Affiliation(s)
- Gaofeng Pan
- School of Computer Science and Technology, Tianjin University, Tianjin 300350, China.
- Tianjin University Institute of Computational Biology, Tianjin University, Tianjin 300350, China.
| | - Limin Jiang
- School of Computer Science and Technology, Tianjin University, Tianjin 300350, China.
- Tianjin University Institute of Computational Biology, Tianjin University, Tianjin 300350, China.
| | - Jijun Tang
- School of Computer Science and Technology, Tianjin University, Tianjin 300350, China.
- Tianjin University Institute of Computational Biology, Tianjin University, Tianjin 300350, China.
- Department of Computer Science and Engineering, University of South Carolina, Columbia, SC 29208, USA.
| | - Fei Guo
- School of Computer Science and Technology, Tianjin University, Tianjin 300350, China.
- Tianjin University Institute of Computational Biology, Tianjin University, Tianjin 300350, China.
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68
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Qiu WR, Xiao X, Xu ZC, Chou KC. iPhos-PseEn: identifying phosphorylation sites in proteins by fusing different pseudo components into an ensemble classifier. Oncotarget 2018; 7:51270-51283. [PMID: 27323404 PMCID: PMC5239474 DOI: 10.18632/oncotarget.9987] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/23/2016] [Indexed: 11/26/2022] Open
Abstract
Protein phosphorylation is a posttranslational modification (PTM or PTLM), where a phosphoryl group is added to the residue(s) of a protein molecule. The most commonly phosphorylated amino acids occur at serine (S), threonine (T), and tyrosine (Y). Protein phosphorylation plays a significant role in a wide range of cellular processes; meanwhile its dysregulation is also involved with many diseases. Therefore, from the angles of both basic research and drug development, we are facing a challenging problem: for an uncharacterized protein sequence containing many residues of S, T, or Y, which ones can be phosphorylated, and which ones cannot? To address this problem, we have developed a predictor called iPhos-PseEn by fusing four different pseudo component approaches (amino acids’ disorder scores, nearest neighbor scores, occurrence frequencies, and position weights) into an ensemble classifier via a voting system. Rigorous cross-validations indicated that the proposed predictor remarkably outperformed its existing counterparts. For the convenience of most experimental scientists, a user-friendly web-server for iPhos-PseEn has been established at http://www.jci-bioinfo.cn/iPhos-PseEn, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.
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Affiliation(s)
- Wang-Ren Qiu
- Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, China.,Department of Computer Science and Bond Life Science Center, University of Missouri, Columbia, MO, USA
| | - Xuan Xiao
- Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, China.,Gordon Life Science Institute, Boston, MA, USA
| | - Zhao-Chun Xu
- Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, China
| | - Kuo-Chen Chou
- Gordon Life Science Institute, Boston, MA, USA.,Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.,Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
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69
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Wang LH, Huang J, Wu CR, Huang LY, Cui J, Xing ZZ, Zhao CY. Downregulation of miR‑29b targets DNMT3b to suppress cellular apoptosis and enhance proliferation in pancreatic cancer. Mol Med Rep 2018; 17:2113-2120. [PMID: 29207141 PMCID: PMC5783451 DOI: 10.3892/mmr.2017.8145] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 05/19/2017] [Indexed: 12/16/2022] Open
Abstract
As one of the most aggressive types of tumor, pancreatic cancer is a principal cause of tumor‑associated mortality. Negative associations between microRNA‑29 (miR‑29) and DNA methyltransferases (DNMT) 3a and 3b have been demonstrated to be associated with the carcinogenesis of a number of types of cancer; however, this has not been completely elucidated in pancreatic cancer. In the present study, pancreatic cancer tissues (n=15) and corresponding paracancerous tissues (n=15) were obtained and the results of reverse transcription‑quantitative polymerase chain reaction analysis indicated decreased expression of miR‑29b and enhanced mRNA expression of DNMT3b in pancreatic cancer tissues, compared with the corresponding paracancerous tissues. Increased protein expression of DNMT3b was demonstrated by western blotting and immunohistochemistry. In addition, the negative association between miR‑29b and DNMT3b was noted in pancreatic cancer tissues, and luciferase reporter assays confirmed that miR‑29b was able to directly target DNMT3b in vitro. Notably, miR‑29b overexpression was able to decrease cell viability and to promote the apoptosis by targeting DNMT3b, and the knockdown of DNMT3b exhibited consistent results in vitro and in vivo. The results of the present study suggested that miR‑29b, as a tumor suppressor, may be a novel target for the development of treatments for pancreatic cancer.
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Affiliation(s)
- Li-Hua Wang
- Department of Gastroenterology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Ju Huang
- Department of Queen Mary University, Medical College of Nanchang University, Nanchang, Jiangxi 330038, P.R. China
| | - Cheng-Rong Wu
- Department of Gastroenterology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Liu-Ye Huang
- Department of Gastroenterology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Jun Cui
- Department of Gastroenterology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Zhi-Zhi Xing
- Department of Gastroenterology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Chun-Yu Zhao
- Department of Gastroenterology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
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70
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DNA methylation profile is associated with the osteogenic potential of three distinct human odontogenic stem cells. Signal Transduct Target Ther 2018. [PMID: 29527327 PMCID: PMC5837092 DOI: 10.1038/s41392-017-0001-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Among the various sources of human autologous stem cells, stem cells isolated from dental tissues exhibit excellent properties in tissue engineering and regenerative medicine. However, the distinct potential of these odontogenic cell lines remains unclear. In this study, we analyzed DNA methylation patterns to determine whether specific differences existed among three different odontogenic cell types. Using the HumanMethylation450 Beadchip, the whole genomes of human dental pulp stem cells (DPSCs), periodontal ligament stem cells (PDLSCs), and dental follicle progenitor cells (DFPCs) were compared. Then, the osteogenic potential of these cells was evaluated both in vitro and in vivo, and the methylation levels of certain genes related to bone formation differed among the three cell lines. P values less than 0.05 were considered to indicate statistical significance. The three cell types showed highly similar DNA methylation patterns, although specific differences were identified. Gene ontology analysis revealed that one of the most significantly different gene categories was related to bone formation. Thus, expression of cell surface epitopes and osteogenic-related transcription factors as well as the bone formation capacity were compared. The results showed that compared with DFPCs and DPSCs, PDLSCs had higher transcription levels of osteogenic-related factors, a higher in vitro osteogenic potential, and an increased new bone formation capacity in vivo. In conclusion, the results of this study suggested that the differential DNA methylation profiles could be related to the osteogenic potential of these human odontogenic cell populations. Additionally, the increased osteogenic potential of PDLSCs might aid researchers or clinicians in making better choices regarding tissue regeneration and clinical therapies.
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71
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Jia J, Liu Z, Xiao X, Liu B, Chou KC. iCar-PseCp: identify carbonylation sites in proteins by Monte Carlo sampling and incorporating sequence coupled effects into general PseAAC. Oncotarget 2018; 7:34558-70. [PMID: 27153555 PMCID: PMC5085176 DOI: 10.18632/oncotarget.9148] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 04/09/2016] [Indexed: 01/22/2023] Open
Abstract
Carbonylation is a posttranslational modification (PTM or PTLM), where a carbonyl group is added to lysine (K), proline (P), arginine (R), and threonine (T) residue of a protein molecule. Carbonylation plays an important role in orchestrating various biological processes but it is also associated with many diseases such as diabetes, chronic lung disease, Parkinson's disease, Alzheimer's disease, chronic renal failure, and sepsis. Therefore, from the angles of both basic research and drug development, we are facing a challenging problem: for an uncharacterized protein sequence containing many residues of K, P, R, or T, which ones can be carbonylated, and which ones cannot? To address this problem, we have developed a predictor called iCar-PseCp by incorporating the sequence-coupled information into the general pseudo amino acid composition, and balancing out skewed training dataset by Monte Carlo sampling to expand positive subset. Rigorous target cross-validations on a same set of carbonylation-known proteins indicated that the new predictor remarkably outperformed its existing counterparts. For the convenience of most experimental scientists, a user-friendly web-server for iCar-PseCp has been established at http://www.jci-bioinfo.cn/iCar-PseCp, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved. It has not escaped our notice that the formulation and approach presented here can also be used to analyze many other problems in computational proteomics.
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Affiliation(s)
- Jianhua Jia
- Computer Department, Jing-De-Zhen Ceramic Institute, Jing-De-Zhen 333403 China.,Gordon Life Science Institute, Boston, MA 02478, USA
| | - Zi Liu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Xuan Xiao
- Computer Department, Jing-De-Zhen Ceramic Institute, Jing-De-Zhen 333403 China.,Gordon Life Science Institute, Boston, MA 02478, USA
| | - Bingxiang Liu
- Computer Department, Jing-De-Zhen Ceramic Institute, Jing-De-Zhen 333403 China
| | - Kuo-Chen Chou
- Gordon Life Science Institute, Boston, MA 02478, USA.,Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia
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72
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Yuan Z, Sánchez Claros C, Suzuki M, Maggi EC, Kaner JD, Kinstlinger N, Gorecka J, Quinn TJ, Geha R, Corn A, Pastoriza J, Jing Q, Adem A, Wu H, Alemu G, Du YC, Zheng D, Greally JM, Libutti SK. Loss of MEN1 activates DNMT1 implicating DNA hypermethylation as a driver of MEN1 tumorigenesis. Oncotarget 2017; 7:12633-50. [PMID: 26871472 PMCID: PMC4914310 DOI: 10.18632/oncotarget.7279] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/24/2016] [Indexed: 12/12/2022] Open
Abstract
Multiple endocrine neoplasia type 1 (MEN1) syndrome results from mutations in the MEN1 gene and causes tumor formation via largely unknown mechanisms. Using a novel genome-wide methylation analysis, we studied tissues from MEN1-parathyroid tumors, Men1 knockout (KO) mice, and Men1 null mouse embryonic fibroblast (MEF) cell lines. We demonstrated that inactivation of menin (the protein product of MEN1) increases activity of DNA (cytosine-5)-methyltransferase 1 (DNMT1) by activating retinoblastoma-binding protein 5 (Rbbp5). The increased activity of DNMT1 mediates global DNA hypermethylation, which results in aberrant activation of the Wnt/β-catenin signaling pathway through inactivation of Sox regulatory genes. Our study provides important insights into the role of menin in DNA methylation and its impact on the pathogenesis of MEN1 tumor development.
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Affiliation(s)
- Ziqiang Yuan
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Masako Suzuki
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Elaine C Maggi
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Justin D Kaner
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Noah Kinstlinger
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jolanta Gorecka
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Thomas J Quinn
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Rula Geha
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Amanda Corn
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jessica Pastoriza
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Qiang Jing
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Asha Adem
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Hao Wu
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Girum Alemu
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yi-Chieh Du
- Department of Pathology and Lab Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
| | - John M Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Steven K Libutti
- Department of Surgery, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
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73
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Promoter DNA methylation analysis reveals a novel diagnostic CpG-based biomarker and RAB25 hypermethylation in clear cell renel cell carcinoma. Sci Rep 2017; 7:14200. [PMID: 29079774 PMCID: PMC5660223 DOI: 10.1038/s41598-017-14314-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/05/2017] [Indexed: 01/20/2023] Open
Abstract
Clear-cell renal cell carcinoma (ccRCC) is a common aggressive urinary malignant tumor that cannot be easily diagnosed at an early stage. The DNA methylation occurs within promoter before precancerous lesion plays a pivotal role that could help us in diagnosing and understanding ccRCC. In this study, based on a whole-genome promoter DNA methylation profiling, we used shrunken centroids classifier method to identify a CpG-based biomarker that is capable of differentiating between ccRCC tumor and adjacent tissues. The biomarker was validated in 19 ccRCCs and three public datasets. We found that both CYP4B1 and RAB25 are downregulated with promoter hypermethylation and CA9 is upregulated with promoter hypomethylation, and we validated their mRNA differential expressions in 19 ccRCCs and 10 GEO datasets. We further confirmed that hypermethylated RAB25 is inversely correlated with its mRNA level. Log-rank test showed that ccRCC patients with low levels of CA9 promoter methylation had a higher survival rate. This reveals clinically a potential biomarker for use in early detection for ccRCC, and provides a better understanding of carcinogenesis.
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74
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Matsuura T, Miyazaki S, Miyazaki T, Tashiro F, Miyazaki JI. Zfp296 negatively regulates H3K9 methylation in embryonic development as a component of heterochromatin. Sci Rep 2017; 7:12462. [PMID: 28963472 PMCID: PMC5622089 DOI: 10.1038/s41598-017-12772-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/14/2017] [Indexed: 12/20/2022] Open
Abstract
The Cys2/His2-type zinc finger protein Zfp296 has been implicated in stem cell pluripotency and tumor pathogenesis. However, its mechanisms remain elusive. Here, we demonstrated that a Zfp296 deficiency in mice impairs germ-cell development and embryonic growth. Zfp296 was intracellularly localized to heterochromatin in embryos. A GST-Zfp296 pull-down experiment using ES cell nuclear extract followed by LC-MS/MS showed that Zfp296 interacts with component proteins of heterochromatin (such as HP1, Dnmt1, Dnmt3b, and ATRX) and the NuRD complex. We focused on H3K9 methylation as a hallmark of heterochromatin, and found that Zfp296 overexpression in cultured cells reduces the Suv39h1-mediated H3K9 methylation. Consistent with this finding, in Zfp296 -/- mouse embryos, we observed a global increase in H3K9 methylation in a developmental stage-dependent manner, and showed, by ChIP-qPCR, that the H3K9me3 levels at major satellite repeats were elevated in Zfp296 -/- embryos. Our results demonstrate that Zfp296 is a component of heterochromatin that affects embryonic development by negatively regulating H3K9 methylation.
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Affiliation(s)
- Takumi Matsuura
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Osaka, Japan
| | - Satsuki Miyazaki
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Osaka, Japan
| | - Tatsushi Miyazaki
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Osaka, Japan
| | - Fumi Tashiro
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Osaka, Japan
| | - Jun-Ichi Miyazaki
- Division of Stem Cell Regulation Research, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Osaka, Japan.
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75
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Mah KM, Weiner JA. Regulation of Wnt signaling by protocadherins. Semin Cell Dev Biol 2017; 69:158-171. [PMID: 28774578 PMCID: PMC5586504 DOI: 10.1016/j.semcdb.2017.07.043] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 07/21/2017] [Accepted: 07/28/2017] [Indexed: 12/23/2022]
Abstract
The ∼70 protocadherins comprise the largest group within the cadherin superfamily. Their diversity, the complexity of the mechanisms through which their genes are regulated, and their many critical functions in nervous system development have engendered a growing interest in elucidating the intracellular signaling pathways through which they act. Recently, multiple protocadherins across several subfamilies have been implicated as modulators of Wnt signaling pathways, and through this as potential tumor suppressors. Here, we review the extant data on the regulation by protocadherins of Wnt signaling pathways and components, and highlight some key unanswered questions that could shape future research.
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Affiliation(s)
- Kar Men Mah
- Department of Biology, The University of Iowa, Iowa City, IA, USA.
| | - Joshua A Weiner
- Department of Biology, The University of Iowa, Iowa City, IA, USA; Department of Psychiatry, The University of Iowa, Iowa City, IA, USA; Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA, USA.
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76
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MicroRNA-1301 suppresses tumor cell migration and invasion by targeting the p53/UBE4B pathway in multiple human cancer cells. Cancer Lett 2017; 401:20-32. [DOI: 10.1016/j.canlet.2017.04.038] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/21/2017] [Accepted: 04/26/2017] [Indexed: 11/20/2022]
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77
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Zhang C, Wang X, Li X, Zhao N, Wang Y, Han X, Ci C, Zhang J, Li M, Zhang Y. The landscape of DNA methylation-mediated regulation of long non-coding RNAs in breast cancer. Oncotarget 2017; 8:51134-51150. [PMID: 28881636 PMCID: PMC5584237 DOI: 10.18632/oncotarget.17705] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/24/2017] [Indexed: 12/22/2022] Open
Abstract
Although systematic studies have identified a host of long non-coding RNAs (lncRNAs) which are involved in breast cancer, the knowledge about the methyla-tion-mediated dysregulation of those lncRNAs remains limited. Here, we integrated multi-omics data to analyze the methylated alteration of lncRNAs in breast invasive carcinoma (BRCA). We found that lncRNAs showed diverse methylation patterns on promoter regions in BRCA. LncRNAs were divided into two categories and four subcategories based on their promoter methylation patterns and expression levels be-tween tumor and normal samples. Through cis-regulatory analysis and gene ontology network, abnormally methylated lncRNAs were identified to be associated with can-cer regulation, proliferation or expression of transcription factors. Competing endog-enous RNA network and functional enrichment analysis of abnormally methylated lncRNAs showed that lncRNAs with different methylation patterns were involved in several hallmarks and KEGG pathways of cancers significantly. Finally, survival analysis based on mRNA modules in networks revealed that lncRNAs silenced by high methylation were associated with prognosis significantly in BRCA. This study enhances the understanding of aberrantly methylated patterns of lncRNAs and pro-vides a novel insight for identifying cancer biomarkers and potential therapeutic tar-gets in breast cancer.
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Affiliation(s)
- Chunlong Zhang
- Department of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163000, China
| | - Xinyu Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xuecang Li
- Department of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163000, China
| | - Ning Zhao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150081, China
| | - Yihan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xiaole Han
- Department of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163000, China
| | - Ce Ci
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Jian Zhang
- Department of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163000, China
| | - Meng Li
- Department of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163000, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
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78
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Wang Q, Pan M, Wei J, Liu X, Wang F. Evaluation of DNA Methyltransferase Activity and Inhibition via Isothermal Enzyme-Free Concatenated Hybridization Chain Reaction. ACS Sens 2017; 2:932-939. [PMID: 28750535 DOI: 10.1021/acssensors.7b00168] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Methyltransferase (MTase)-catalyzed DNA methylation plays a vital role in the biological epigenetic processes of key diseases and has attracted increasing attention, making the amplified detection of MTase activity of great significance in clinical disease diagnosis and treatment. Herein, we developed an isothermal, enzyme-free, and autonomous strategy for analyzing MTase activity based on concatenated hybridization chain reaction (C-HCR)-mediated Förster resonance energy transfer (FRET). In a typical C-HCR procedure without MTase (Dam), Y-shaped initiator DNA activates upstream HCR-1 to assemble a double-stranded DNA (dsDNA) copolymeric nanowire consisting of multiple tandem DNA trigger units that motivate downstream HCR-2 to successively bring a fluorophore donor/acceptor (FAM/TAMRA) pair into close proximity, leading to the generation of an amplified FRET readout signal. The target Dam MTase and auxiliary DpnI endonuclease can sequentially and specifically recognize/methylate and cleave the Y-shaped initiator oligonucleotide, respectively, and thus prohibit the C-HCR process and FRET signal generation, resulting in the construction of a signal-on sensing platform for MTase assay. Our proposed isothermal enzyme-free C-HCR amplification approach was further utilized for screening MTase inhibitors. Furthermore, the proposed C-HCR approach can be easily adapted for probing other different MTases and for screening the corresponding inhibitors just by changing the recognition sequence of Y-shaped initiator DNA through a "plug-and-play" format. It provides a versatile and robust tool for highly sensitive detection of various biotransformations and thus holds great promise in clinical assessment and diagnosis.
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Affiliation(s)
- Qing Wang
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Min Pan
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Jie Wei
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Xiaoqing Liu
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
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79
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Hsu W, Mercado AT, Hsiao G, Yeh JM, Chen CY. Detection and discrimination of maintenance and de novo CpG methylation events using MethylBreak. Biosens Bioelectron 2017; 91:658-663. [PMID: 28110250 DOI: 10.1016/j.bios.2017.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/23/2016] [Accepted: 01/13/2017] [Indexed: 11/28/2022]
Abstract
Understanding the principles governing the establishment and maintenance activities of DNA methyltransferases (DNMTs) can help in the development of predictive biomarkers associated with genetic disorders and diseases. A detection system was developed that distinguishes and quantifies methylation events using methylation-sensitive endonucleases and molecular beacon technology. MethylBreak (MB) is a 22-mer oligonucleotide with one hemimethylated and two unmethylated CpG sites, which are also recognition sites for Sau96I and SacII, and is attached to a fluorophore and a quencher. Maintenance methylation was quantified by fluorescence emission due to the digestion of SacII when the hemimethylated CpG site is methylated, which inhibits Sau96I cleavage. The signal difference between SacII digestion of both MB substrate and maintenance methylated MB corresponds to de novo methylation event. Our technology successfully discriminated and measured both methylation activities at different concentrations of MB and achieved a high correlation coefficient of R2=0.997. Additionally, MB was effectively applied to normal and cancer cell lines and in the analysis of enzymatic kinetics and RNA inhibition of recombinant human DNMT1.
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Affiliation(s)
- William Hsu
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320, Taiwan
| | - Augustus T Mercado
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320, Taiwan; Department of Chemistry, Chung Yuan Christian University, Chung-Li 320, Taiwan
| | - George Hsiao
- Graduate Institute of Medical Sciences and Department of Pharmacology, Taipei Medical University, 250 Wu-Hsing Street, Taipei 110-31, Taiwan
| | - Jui-Ming Yeh
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 320, Taiwan; Center for Nanotechnology and Institute of Biomedical Technology, Chung Yuan Christian University, Chung-Li 320, Taiwan.
| | - Chung-Yung Chen
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320, Taiwan; Center for Nanotechnology and Institute of Biomedical Technology, Chung Yuan Christian University, Chung-Li 320, Taiwan.
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80
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Kirby MK, Ramaker RC, Roberts BS, Lasseigne BN, Gunther DS, Burwell TC, Davis NS, Gulzar ZG, Absher DM, Cooper SJ, Brooks JD, Myers RM. Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns. BMC Cancer 2017; 17:273. [PMID: 28412973 PMCID: PMC5392915 DOI: 10.1186/s12885-017-3252-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/01/2017] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Current diagnostic tools for prostate cancer lack specificity and sensitivity for detecting very early lesions. DNA methylation is a stable genomic modification that is detectable in peripheral patient fluids such as urine and blood plasma that could serve as a non-invasive diagnostic biomarker for prostate cancer. METHODS We measured genome-wide DNA methylation patterns in 73 clinically annotated fresh-frozen prostate cancers and 63 benign-adjacent prostate tissues using the Illumina Infinium HumanMethylation450 BeadChip array. We overlaid the most significantly differentially methylated sites in the genome with transcription factor binding sites measured by the Encyclopedia of DNA Elements consortium. We used logistic regression and receiver operating characteristic curves to assess the performance of candidate diagnostic models. RESULTS We identified methylation patterns that have a high predictive power for distinguishing malignant prostate tissue from benign-adjacent prostate tissue, and these methylation signatures were validated using data from The Cancer Genome Atlas Project. Furthermore, by overlaying ENCODE transcription factor binding data, we observed an enrichment of enhancer of zeste homolog 2 binding in gene regulatory regions with higher DNA methylation in malignant prostate tissues. CONCLUSIONS DNA methylation patterns are greatly altered in prostate cancer tissue in comparison to benign-adjacent tissue. We have discovered patterns of DNA methylation marks that can distinguish prostate cancers with high specificity and sensitivity in multiple patient tissue cohorts, and we have identified transcription factors binding in these differentially methylated regions that may play important roles in prostate cancer development.
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Affiliation(s)
- Marie K. Kirby
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Present Address: TRM Oncology, 5901-C Peachtree Dunwoody Rd, Suite 200, Atlanta, GA 30328 USA
| | - Ryne C. Ramaker
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Department of Genetics, Kaul Human Genetics Building, Suite 230, 720 20th Street South, Birmingham, AL 35294 USA
| | - Brian S. Roberts
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | | | - David S. Gunther
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Present Address: University of Southern California, University Park, Los Angeles, CA 90089 USA
| | - Todd C. Burwell
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Present Address: Boeing Co., 499 Boeing Blvd, SW, Huntsville, AL 35824 USA
| | - Nicholas S. Davis
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
- Present Address: Duke University, 101 Science Drive, Durham, NC 27708 USA
| | - Zulfiqar G. Gulzar
- Department of Urology, Stanford University Medical Center, Room S287, 300 Pasteur Drive, Stanford, CA 94305-5118 USA
- Present Address: NuGEN technologies, 201 Industrial Rd #310, San Carlos, CA 94070 USA
| | - Devin M. Absher
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | - Sara J. Cooper
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | - James D. Brooks
- Department of Urology, Stanford University Medical Center, Room S287, 300 Pasteur Drive, Stanford, CA 94305-5118 USA
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
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81
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Tang Y, Jiang S, Gu Y, Li W, Mo Z, Huang Y, Li T, Hu Y. Promoter DNA methylation analysis reveals a combined diagnosis of CpG-based biomarker for prostate cancer. Oncotarget 2017; 8:58199-58209. [PMID: 28938548 PMCID: PMC5601644 DOI: 10.18632/oncotarget.16437] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/28/2017] [Indexed: 01/08/2023] Open
Abstract
Background Prostate cancer (PCa) is the most common tumor in elderly men. However, the specificity and sensitivity of serum prostate-specific antigen levels in PCa diagnosis are controversial. This study aims to reveal a novel diagnosis biomarker in PCa. Materials and Methods The differential methylated CpG sites between 423 primary PCa and 39 adjacent samples from The Cancer Genome Atlas (TCGA) on Illumina HumanMethylation 450 platform were analyzed. The diagnostic methylation markers were mined using the Prediction Analysis of Microarrays package in Bioconductor. Then, the Gene Expression Omnibus data was used for verification. Pyrosequencing was applied to improve methylation levels of five CpGs (cg06363129, cg08843517, cg05385513, cg07220448 and cg11417025). Results The area under curve of receiver operating characteristic of eight diagnostic methylation CpGs (cg06363129, cg08843517, cg03576469, cg05385513, cg07220448, cg11417025, cg20883831, and cg23824801) in TCGA data ranged from 0.910 to 0.939. Except for cg20883831 and cg23824801, the correlations between methylation levels of six other sites and their expressions in patients were significant (r > 0.5 and P < 0.001). The methylation level of cg06363129 was significantly different between the groups of Gleason Score (GS) = 7 and GS ≥ 8 (P < 0.05). Pyrosequencing in our samples confirmed that four diagnostic methylation sites (cg06363129, cg08843517, cg05385513, and cg11417025) had high diagnostic efficacy. Conclusions The combined diagnosis of four methylation CpGs sites (cg06363129, cg08843517, cg05385513, and cg11417025) in the gene promoter has high tissue specificity and diagnostic efficacy for PCa. Results revealed a novel potential biomarker for prostate cancer diagnosis.
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Affiliation(s)
- Yuanyuan Tang
- Guangxi Reproductive Medical Research Center, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Shusuan Jiang
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Yinmin Gu
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Weidong Li
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Zengnan Mo
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China.,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Yuanjie Huang
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Tianyu Li
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China.,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Yanling Hu
- Life Sciences Institute, Guangxi Medical University, Nanning, Guangxi 530021, China.,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, China.,Guangxi Colleges and Universities Key Laboratory of Biological Molecular Medicine Research, Guangxi Medical University, Nanning, Guangxi 530021, China
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82
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Zhang W, Xu J. DNA methyltransferases and their roles in tumorigenesis. Biomark Res 2017; 5:1. [PMID: 28127428 PMCID: PMC5251331 DOI: 10.1186/s40364-017-0081-z] [Citation(s) in RCA: 225] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/03/2017] [Indexed: 01/13/2023] Open
Abstract
DNA methylation plays an important role in gene expression, chromatin stability, and genetic imprinting. In mammals, DNA methylation patterns are written and regulated by DNA methyltransferases (DNMTs), including DNMT1, DNMT3A and DNMT3B. Recent emerging evidence shows that defects in DNMTs are involved in tumor transformation and progression, thus indicating that epigenetic disruptions caused by DNMT abnormalities are associated with tumorigenesis. Herein, we review the latest findings related to DNMT alterations in cancer cells and discuss the contributions of these effects to oncogenic phenotypes.
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Affiliation(s)
- Wu Zhang
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital affiliated to Shanghai Jiao-Tong University School of Medicine, 197 Rui Jin Er Road, 200025 Shanghai, China
| | - Jie Xu
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital affiliated to Shanghai Jiao-Tong University School of Medicine, 197 Rui Jin Er Road, 200025 Shanghai, China
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83
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Yates C, Long MD, Campbell MJ, Sucheston-Campbell L. miRNAs as drivers of TMPRSS2-ERG negative prostate tumors in African American men. FRONT BIOSCI-LANDMRK 2017; 22:212-229. [PMID: 27814612 PMCID: PMC5858730 DOI: 10.2741/4482] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
African Americans (AAs) who have PCa typically have more aggressive disease and make up a disproportionate number of the disease deaths, relative to European Americans (EAs). TMPRSS2 translocations, a common event in EA patients, are exploited in diagnostic and prognostic settings, whereas they are diminished in frequency in AA men. Thus, these patients with TMPRSS2 fusion-negative disease represent an under-investigated patient group. We propose that epigenetic events are a significant and alternative driver of aggressive disease in fusion-negative PCa. To reveal epigenetically governed microRNAs (miRNAs) that are enriched in fusion-negative disease and associated with aggressive in AA PCa, we leveraged both our experimental evidence and publically available data. These analyses identified 18 miRNAs that are differentially altered in fusion-negative disease, associated with DNA CpG methylation, and implicated in aggressive and AA PCas. Understanding the relationships between miRNA expression, upstream epigenetic regulation by DNA methylation, and downstream regulation of mRNA targets in fusion negative disease is imperative to understanding the biological basis of the racial health disparity in PCa.
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Affiliation(s)
- Clayton Yates
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL 36088
| | - Mark D Long
- Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263
| | - Moray J Campbell
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL 36088,
| | - Lara Sucheston-Campbell
- Cancer Prevention and Control, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263
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84
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Jiang B, Wei Y, Xu J, Yuan R, Xiang Y. Coupling hybridization chain reaction with DNAzyme recycling for enzyme-free and dual amplified sensitive fluorescent detection of methyltransferase activity. Anal Chim Acta 2017; 949:83-88. [DOI: 10.1016/j.aca.2016.11.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/27/2016] [Accepted: 11/05/2016] [Indexed: 12/20/2022]
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85
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Skorodumova LO, Babalyan KA, Sultanov R, Vasiliev AO, Govorov AV, Pushkar DY, Prilepskaya EA, Danilenko SA, Generozov EV, Larin AK, Kostryukova ES, Sharova EI. [GSTP1, APC and RASSF1 gene methylation in prostate cancer samples: comparative analysis of MS-HRM method and Infinium HumanMethylation450 BeadChip beadchiparray diagnostic value]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2016; 62:708-714. [PMID: 28026816 DOI: 10.18097/pbmc20166206708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
There is a clear need in molecular markers for prostate cancer (PC) risk stratification. Alteration of DNA methylation is one of processes that occur during ÐÑ progression. Methylation-sensitive PCR with high resolution melting curve analysis (MS-HRM) can be used for gene methylation analysis in routine laboratory practice. This method requires very small amounts of DNA for analysis. Numerous results have been accumulated on DNA methylation in PC samples analyzed by the Infinium HumanMethylation450 BeadChip (HM450). However, the consistency of MS-HRM results with chip hybridization results has not been examined yet. The aim of this study was to assess the consistency of results of GSTP1, APC and RASSF1 gene methylation analysis in ÐÑ biopsy samples obtained by MS-HRM and chip hybridization. The methylation levels of each gene determined by MS-HRM were statistically different in the group of PC tissue samples and the samples without signs of tumor growth. Chip hybridization data analysis confirmed the results obtained with the MS-HRM. Differences in methylation levels between tumor tissue and histologically intact tissue of each sample determined by MS-HRM and chip hybridization, were consistent with each other. Thus, we showed that the assessment of GSTP1, APC and RASSF1 gene methylation analysis using MS-HRM is suitable for the design of laboratory assays that will differentiate the PC tissue from the tissue without signs of tumor growth.
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Affiliation(s)
- L O Skorodumova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - K A Babalyan
- Moscow Institute of Physics and Technology, Dolgoprudniy, Moscow Region, Russia
| | - R Sultanov
- Moscow Institute of Physics and Technology, Dolgoprudniy, Moscow Region, Russia
| | - A O Vasiliev
- Moscow State Medical Stomatological University, Moscow, Russia
| | - A V Govorov
- Moscow State Medical Stomatological University, Moscow, Russia
| | - D Y Pushkar
- Moscow State Medical Stomatological University, Moscow, Russia
| | - E A Prilepskaya
- Moscow State Medical Stomatological University, Moscow, Russia
| | - S A Danilenko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - E V Generozov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - A K Larin
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - E S Kostryukova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia; Moscow Institute of Physics and Technology, Dolgoprudniy, Moscow Region, Russia
| | - E I Sharova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
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86
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Wu C, Jin X, Yang J, Yang Y, He Y, Ding L, Pan Y, Chen S, Jiang J, Huang H. Inhibition of EZH2 by chemo- and radiotherapy agents and small molecule inhibitors induces cell death in castration-resistant prostate cancer. Oncotarget 2016; 7:3440-52. [PMID: 26657505 PMCID: PMC4823118 DOI: 10.18632/oncotarget.6497] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 11/16/2015] [Indexed: 12/16/2022] Open
Abstract
Androgen deprivation therapy is the mainstay of treatment of advanced prostate cancer (PCa). However, a significant portion of patients experience disease relapse and tumors ultimately evolve into castration resistant prostate cancer (CRPC), for which there is no cure in the clinic. The Polycomb protein enhancer of zeste homolog 2 (EZH2) is frequently overexpressed in CRPC. It is unclear whether EZH2 can be a therapeutic target in CRPC. Here, we demonstrated that chemo- and radiotherapy agents such as camptothecin (CPT) and γ irradiation decrease EZH2 expression in various PCa cell lines. We provided evidence that functional p53 and RB proteins are required for CPT- and irradiation-induced downregulation of EZH2 in CRPC cells. We demonstrated that EZH2-specific small molecule inhibitors mitigate CRPC cell growth. We further showed that the EZH2 inhibitor GSK126 inhibits both Polycomb-dependent and -independent functions of EZH2 in PCa cells. Importantly, we found that inhibition of EZH2 by genetic and pharmacological means sensitizes CRPC cells to CPT-induced apoptotic death and growth inhibition in culture and in mice. Our data suggest that concomitant administration of small molecule inhibitors of EZH2 may significantly increase the anti-tumor efficacy of conventional chemo- and radiotherapies in CRPC.
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Affiliation(s)
- Changping Wu
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China
| | - Xin Jin
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Jing Yang
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China.,Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Yinhui Yang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Yundong He
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Liya Ding
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Yunqian Pan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Shuai Chen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, China
| | - Jingting Jiang
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.,Department of Urology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.,Mayo Clinic Cancer Center, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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87
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Epigenetic events in male common urogenital organs cancer. JOURNAL OF CANCER RESEARCH AND PRACTICE 2016. [DOI: 10.1016/j.jcrpr.2016.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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88
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Zhang H, Yang Y, Dong H, Cai C. A superstructure-based electrochemical assay for signal-amplified detection of DNA methyltransferase activity. Biosens Bioelectron 2016; 86:927-932. [DOI: 10.1016/j.bios.2016.07.103] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/11/2016] [Accepted: 07/28/2016] [Indexed: 12/12/2022]
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89
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Chen C, Peng H, Huang X, Zhao M, Li Z, Yin N, Wang X, Yu F, Yin B, Yuan Y, Lu Q. Genome-wide profiling of DNA methylation and gene expression in esophageal squamous cell carcinoma. Oncotarget 2016; 7:4507-21. [PMID: 26683359 PMCID: PMC4826222 DOI: 10.18632/oncotarget.6607] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/26/2015] [Indexed: 01/02/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is the leading cause of cancer-related death worldwide. Previous studies have suggested that DNA methylation involved in the development of ESCC. However, the precise mechanisms underlying the regulation and maintenance of the methylome as well as their relationship with ESCC remain poorly understood. Herein, we used methylated DNA immunoprecipitation sequencing (MeDIP-Seq) and RNA-Seq to investigate whole-genome DNA methylation patterns and the genome expression profiles in ESCC samples. The results of MeDIP-Seq analyses identified differentially methylated regions (DMRs) covering almost the entire genome with sufficient depth and high resolution. The gene ontology (GO) analysis showed that the DMRs related genes belonged to several different ontological domains, such as cell cycle, adhesion, proliferation and apoptosis. The RNA-Seq analysis identified a total of 6150 differentially expressed genes (3423 up-regulated and 2727 down-regulated). The significant GO terms showed that these genes belonged to several molecular functions and biological pathways. Moreover, the bisulfite-sequencing of genes MLH1, CDH5, TWIST1 and CDX1 confirmed the methylation status identified by MeDIP-Seq. And the mRNA expression levels of MLH1, TWIST1 and CDX1 were consistent with their DNA methylation profiles. The DMR region of MLH1 was found to correlate with survival. The identification of whole-genome DNA methylation patterns and gene expression profiles in ESCC provides new insight into the carcinogenesis of ESCC and represents a promising avenue through which to investigate novel therapeutic targets.
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Affiliation(s)
- Chen Chen
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Hao Peng
- Department of Thoracic and Cardiovascular Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, P.R. China
| | - Xiaojie Huang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Ming Zhao
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Zhi Li
- Beijing Genomics Institute at Shenzhen, Shenzhen, P.R. China
| | - Ni Yin
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Fenglei Yu
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Bangliang Yin
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Yunchang Yuan
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
| | - Qianjin Lu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, P.R. China
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90
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Dietary Flavones as Dual Inhibitors of DNA Methyltransferases and Histone Methyltransferases. PLoS One 2016; 11:e0162956. [PMID: 27658199 PMCID: PMC5033486 DOI: 10.1371/journal.pone.0162956] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/31/2016] [Indexed: 12/14/2022] Open
Abstract
Methylation of DNA and histone proteins are mutually involved in the epigenetic regulation of gene expression mediated by DNA methyltransferases (DNMTs) and histone methyltransferases (HMTs). DNMTs methylate cytosine residues within gene promoters, whereas HMTs catalyze the transfer of methyl groups to lysine and arginine residues of histone proteins, thus causing chromatin condensation and transcriptional repression, which play an important role in the pathogenesis of cancer. The potential reversibility of epigenetic alterations has encouraged the development of dual pharmacologic inhibitors of DNA and histone methylation as anticancer therapeutics. Dietary flavones can affect epigenetic modifications that accumulate over time and have shown anticancer properties, which are undefined. Through DNA binding and in silico protein-ligand docking studies with plant flavones viz. Apigenin, Chrysin and Luteolin, the effect of flavones on DNA and histone methylation was assessed. Spectroscopic analysis of flavones with calf-thymus DNA revealed intercalation as the dominant binding mode, with specific binding to a GC-rich sequence in the DNA duplex. A virtual screening approach using a model of the catalytic site of DNMT and EZH2 demonstrated that plant flavones are tethered at both ends inside the catalytic pocket of DNMT and EZH2 by means of hydrogen bonding. Epigenetic studies performed with flavones exhibited a decrease in DNMT enzyme activity and a reversal of the hypermethylation of cytosine bases in the DNA and prevented cytosine methylation in the GC-rich promoter sequence incubated with the M.SssI enzyme. Furthermore, a marked decrease in HMT activity and a decrease in EZH2 protein expression and trimethylation of H3K27 were noted in histones isolated from cancer cells treated with plant flavones. Our results suggest that dietary flavones can alter DNMT and HMT activities and the methylation of DNA and histone proteins that regulate epigenetic modifications, thus providing a significant anticancer effect by altering epigenetic processes involved in the development of cancer.
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91
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Corbin JM, Ruiz-Echevarría MJ. One-Carbon Metabolism in Prostate Cancer: The Role of Androgen Signaling. Int J Mol Sci 2016; 17:E1208. [PMID: 27472325 PMCID: PMC5000606 DOI: 10.3390/ijms17081208] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 07/16/2016] [Accepted: 07/18/2016] [Indexed: 01/06/2023] Open
Abstract
Cancer cell metabolism differs significantly from the metabolism of non-transformed cells. This altered metabolic reprogramming mediates changes in the uptake and use of nutrients that permit high rates of proliferation, growth, and survival. The androgen receptor (AR) plays an essential role in the establishment and progression of prostate cancer (PCa), and in the metabolic adaptation that takes place during this progression. In its role as a transcription factor, the AR directly affects the expression of several effectors and regulators of essential catabolic and biosynthetic pathways. Indirectly, as a modulator of the one-carbon metabolism, the AR can affect epigenetic processes, DNA metabolism, and redox balance, all of which are important factors in tumorigenesis. In this review, we focus on the role of AR-signaling on one-carbon metabolism in tumorigenesis. Clinical implications of one-carbon metabolism and AR-targeted therapies for PCa are discussed in this context.
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Affiliation(s)
- Joshua M Corbin
- Department of Pathology, Oklahoma University Health Sciences Center, Oklahoma City, OK 73104, USA.
| | - Maria J Ruiz-Echevarría
- Department of Pathology, Oklahoma University Health Sciences Center and Stephenson Cancer Center, Oklahoma City, OK 73104, USA.
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92
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Labib M, Sargent EH, Kelley SO. Electrochemical Methods for the Analysis of Clinically Relevant Biomolecules. Chem Rev 2016; 116:9001-90. [DOI: 10.1021/acs.chemrev.6b00220] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Mahmoud Labib
- Department
of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | | | - Shana O. Kelley
- Department
of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2, Canada
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Canada
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93
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Chang HF, Wu CC, Sun CA, Chu CM, Lin FG, Hsieh JF, Hsu CH, Huang CH, Yang T, Tsai YM, Kuan JC, Chou YC. Clinical stage and risk of recurrence and mortality: interaction of DNA methylation factors in patients with colorectal cancer. J Investig Med 2016; 64:1200-7. [PMID: 27296458 DOI: 10.1136/jim-2016-000086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2016] [Indexed: 12/12/2022]
Abstract
Aberrant DNA methylation plays a crucial role in cancer development; however, prospective evidence of an interaction between molecular biomarkers and cancer staging for predicting the prognosis of colorectal cancer (CRC) is still limited. We examined DNA methylation in tumors and adjacent normal tissues from patients who underwent CRC surgical resection, and evaluated the interaction between cancer staging (advanced vs local) and DNA methylation to predict the prognosis of CRC. We recruited 132 patients with CRC from Tri-Service General Hospital in Taiwan and used the candidate gene approach to select 3 tumor suppressor genes involved in carcinogenesis pathways. ORs and 95% CIs were computed using logistic regression analyses while adjusting for potential covariates. Advanced cancer stage was correlated with cancer recurrence (OR 7.22, 95% CI 2.82 to 18.45; p<0.001). In addition, after stratification by promoter methylation in 3 combined genes in the matched normal tissues, we observed a joint effect after adjusting for sex, age at surgery, and adjuvant chemotherapy, yielding a significant OR of 20.35 (95% CI 4.16 to 99.57; p<0.001). DNA methylation status would significantly increase the recurrence risk of CRC with a significant impact on joint effect between DNA methylation and clinical stage, particularly in matched normal tissues. This was attributed to molecular changes that could not be examined on the basis of clinical pathology. Our interaction results may serve as a reference marker for evaluating the risk of recurrence in future studies.
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Affiliation(s)
- Hsien-Feng Chang
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Chang-Chieh Wu
- Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chien-An Sun
- Department of Public Health, College of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan
| | - Chi-Ming Chu
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Fu-Gong Lin
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Jih-Fu Hsieh
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Hsiung Hsu
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Chi-Hua Huang
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Tsan Yang
- Department of Health Business Administration, Meiho University, Pingtung, Taiwan
| | - Yang-Ming Tsai
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
| | - Jen-Chun Kuan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Yu-Ching Chou
- School of Public Health, National Defense Medical Center, Taipei, Taiwan
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94
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Yang Q, Mas A, Diamond MP, Al-Hendy A. The Mechanism and Function of Epigenetics in Uterine Leiomyoma Development. Reprod Sci 2016; 23:163-75. [PMID: 25922306 PMCID: PMC5933172 DOI: 10.1177/1933719115584449] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Uterine leiomyomas, also known as uterine fibroids, are the most common pelvic tumors, occurring in nearly 70% of all reproductive-aged women and are the leading indication for hysterectomy worldwide. The development of uterine leiomyomas involve a complex and heterogeneous constellation of hormones, growth factors, stem cells, genetic, and epigenetic abnormalities. An increasing body of evidence emphasizes the important contribution of epigenetics in the pathogenesis of leiomyomas. Genome-wide methylation analysis demonstrates that a subset of estrogen receptor (ER) response genes exhibit abnormal hypermethylation levels that are inversely correlated with their RNA expression. Several tumor suppressor genes, including Kruppel-like factor 11 (KLF11), deleted in lung and esophageal cancer 1 (DLEC1), keratin 19 (KRT19), and death-associated protein kinase 1 (DAPK1) also display higher hypermethylation levels in leiomyomas when compared to adjacent normal tissues. The important role of active DNA demethylation was recently identified with regard to the ten-eleven translocation protein 1 and ten-eleven translocation protein 3-mediated elevated levels of 5-hydroxymethylcytosine in leiomyoma. In addition, both histone deacetylase and histone methyltransferase are reported to be involved in the biology of leiomyomas. A number of deregulated microRNAs have been identified in leiomyomas, leading to an altered expression of their targets. More recently, the existence of side population (SP) cells with characteristics of tumor-initiating cells have been characterized in leiomyomas. These SP cells exhibit a tumorigenic capacity in immunodeficient mice when exposed to 17β-estradiol and progesterone, giving rise to fibroid-like tissue in vivo. These new findings will likely enhance our understanding of the crucial role epigenetics plays in the pathogenesis of uterine leiomyomas as well as point the way to novel therapeutic options.
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Affiliation(s)
- Qiwei Yang
- Division of Translation Research, Department of Obstetrics and Gynecology, Georgia Regents University, Medical College of Georgia, Augusta, GA, USA
| | - Aymara Mas
- Division of Translation Research, Department of Obstetrics and Gynecology, Georgia Regents University, Medical College of Georgia, Augusta, GA, USA
| | - Michael P Diamond
- Division of Translation Research, Department of Obstetrics and Gynecology, Georgia Regents University, Medical College of Georgia, Augusta, GA, USA
| | - Ayman Al-Hendy
- Division of Translation Research, Department of Obstetrics and Gynecology, Georgia Regents University, Medical College of Georgia, Augusta, GA, USA
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95
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Abstract
Prostate cancer (PCa) is the most common male malignancy and the second highest cause of cancer-related mortality in United States. MicroRNAs (miRNAs) are small non-coding RNAs that represent a new mechanism to regulate mRNA post-transcriptionally. It is involved in diverse physiological and pathophysiological process. Dysregulation of miRNAs has been associated with the multistep progression of PCa from prostatic intraepithelial neoplasia (PIN), localized adenocarcinoma to metastatic castration-resistance PCa (CRPC). Identification of unique miRNA could provide new biomarkers for PCa and develop into therapeutic strategies. In this review, we will summarize a broad spectrum of both tumor suppressive and oncogenic miRNAs, and their mechanisms contribute to prostate carcinogenesis.
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Affiliation(s)
- U-Ging Lo
- Departments of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Diane Yang
- Departments of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jer-Tsong Hsieh
- Departments of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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96
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Poh WJ, Wee CPP, Gao Z. DNA Methyltransferase Activity Assays: Advances and Challenges. Am J Cancer Res 2016; 6:369-91. [PMID: 26909112 PMCID: PMC4737724 DOI: 10.7150/thno.13438] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/12/2015] [Indexed: 12/28/2022] Open
Abstract
DNA methyltransferases (MTases), a family of enzymes that catalyse the methylation of DNA, have a profound effect on gene regulation. A large body of evidence has indicated that DNA MTase is potentially a predictive biomarker closely associated with genetic disorders and genetic diseases like cancer. Given the attention bestowed onto DNA MTases in molecular biology and medicine, highly sensitive detection of DNA MTase activity is essential in determining gene regulation, epigenetic modification, clinical diagnosis and therapeutics. Conventional techniques such as isotope labelling are effective, but they often require laborious sample preparation, isotope labelling, sophisticated equipment and large amounts of DNA, rendering them unsuitable for uses at point-of-care. Simple, portable, highly sensitive and low-cost assays are urgently needed for DNA MTase activity screening. In most recent technological advances, many alternative DNA MTase activity assays such as fluorescent, electrochemical, colorimetric and chemiluminescent assays have been proposed. In addition, many of them are coupled with nanomaterials and/or enzymes to significantly enhance their sensitivity. Herein we review the progress in the development of DNA MTase activity assays with an emphasis on assay mechanism and performance with some discussion on challenges and perspectives. It is hoped that this article will provide a broad coverage of DNA MTase activity assays and their latest developments and open new perspectives toward the development of DNA MTase activity assays with much improved performance for uses in molecular biology and clinical practice.
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97
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Iglesias-Gato D, Wikström P, Tyanova S, Lavallee C, Thysell E, Carlsson J, Hägglöf C, Cox J, Andrén O, Stattin P, Egevad L, Widmark A, Bjartell A, Collins CC, Bergh A, Geiger T, Mann M, Flores-Morales A. The Proteome of Primary Prostate Cancer. Eur Urol 2015; 69:942-52. [PMID: 26651926 DOI: 10.1016/j.eururo.2015.10.053] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/29/2015] [Indexed: 12/15/2022]
Abstract
BACKGROUND Clinical management of the prostate needs improved prognostic tests and treatment strategies. Because proteins are the ultimate effectors of most cellular reactions, are targets for drug actions and constitute potential biomarkers; a quantitative systemic overview of the proteome changes occurring during prostate cancer (PCa) initiation and progression can result in clinically relevant discoveries. OBJECTIVES To study cellular processes altered in PCa using system-wide quantitative analysis of changes in protein expression in clinical samples and to identify prognostic biomarkers for disease aggressiveness. DESIGN, SETTING, AND PARTICIPANTS Mass spectrometry was used for genome-scale quantitative proteomic profiling of 28 prostate tumors (Gleason score 6-9) and neighboring nonmalignant tissue in eight cases, obtained from formalin-fixed paraffin-embedded prostatectomy samples. Two independent cohorts of PCa patients (summing 752 cases) managed by expectancy were used for immunohistochemical evaluation of proneuropeptide-Y (pro-NPY) as a prognostic biomarker. RESULTS AND LIMITATIONS Over 9000 proteins were identified as expressed in the human prostate. Tumor tissue exhibited elevated expression of proteins involved in multiple anabolic processes including fatty acid and protein synthesis, ribosomal biogenesis and protein secretion but no overt evidence of increased proliferation was observed. Tumors also showed increased levels of mitochondrial proteins, which was associated with elevated oxidative phosphorylation capacity measured in situ. Molecular analysis indicated that some of the proteins overexpressed in tumors, such as carnitine palmitoyltransferase 2 (CPT2, fatty acid transporter), coatomer protein complex, subunit alpha (COPA, vesicle secretion), and mitogen- and stress-activated protein kinase 1 and 2 (MSK1/2, protein kinase) regulate the proliferation of PCa cells. Additionally, pro-NPY was found overexpressed in PCa (5-fold, p<0.05), but largely absent in other solid tumor types. Pro-NPY expression, alone or in combination with the ERG status of the tumor, was associated with an increased risk of PCa specific mortality, especially in patients with Gleason score ≤ 7 tumors. CONCLUSIONS This study represents the first system-wide quantitative analysis of proteome changes associated to localized prostate cancer and as such constitutes a valuable resource for understanding the complex metabolic changes occurring in this disease. We also demonstrated that pro-NPY, a protein that showed differential expression between high and low risk tumors in our proteomic analysis, is also a PCa specific prognostic biomarker associated with increased risk for disease specific death in patients carrying low risk tumors. PATIENT SUMMARY The identification of proteins whose expression change in prostate cancer provides novel mechanistic information related to the disease etiology. We hope that future studies will prove the value of this proteome dataset for development of novel therapies and biomarkers.
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Affiliation(s)
- Diego Iglesias-Gato
- IVS, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Centre for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; Danish Cancer Society, Copenhagen, Denmark.
| | - Pernilla Wikström
- Department of Medical Biosciences, Pathology, Umea University, Umea, Sweden
| | - Stefka Tyanova
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Charlotte Lavallee
- IVS, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Centre for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; Danish Cancer Society, Copenhagen, Denmark
| | - Elin Thysell
- Department of Medical Biosciences, Pathology, Umea University, Umea, Sweden
| | - Jessica Carlsson
- School of Health and Medical Sciences, Department of Urology, University of Örebro, Sweden
| | - Christina Hägglöf
- Department of Medical Biosciences, Pathology, Umea University, Umea, Sweden
| | - Jürgen Cox
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Ove Andrén
- School of Health and Medical Sciences, Department of Urology, University of Örebro, Sweden
| | - Pär Stattin
- Departments of Surgery and Perioperative Sciences, Umea University, Umea, Sweden
| | - Lars Egevad
- Section of Urology, Department of Surgical Science, Karolinska Institutet, Stockholm, Sweden
| | - Anders Widmark
- Department of Radiation Sciences, Oncology, Umea University, Umea, Sweden
| | - Anders Bjartell
- Department of Translational Medicine, Division of Urological Cancers, University of Lund, Lund, Sweden
| | - Colin C Collins
- Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anders Bergh
- Department of Medical Biosciences, Pathology, Umea University, Umea, Sweden
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Matthias Mann
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Amilcar Flores-Morales
- IVS, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Centre for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; Danish Cancer Society, Copenhagen, Denmark.
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98
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Geybels MS, Zhao S, Wong CJ, Bibikova M, Klotzle B, Wu M, Ostrander EA, Fan JB, Feng Z, Stanford JL. Epigenomic profiling of DNA methylation in paired prostate cancer versus adjacent benign tissue. Prostate 2015; 75:1941-50. [PMID: 26383847 PMCID: PMC4928710 DOI: 10.1002/pros.23093] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/31/2015] [Indexed: 01/16/2023]
Abstract
BACKGROUND Aberrant DNA methylation may promote prostate carcinogenesis. We investigated epigenome-wide DNA methylation profiles in prostate cancer (PCa) compared to adjacent benign tissue to identify differentially methylated CpG sites. METHODS The study included paired PCa and adjacent benign tissue samples from 20 radical prostatectomy patients. Epigenetic profiling was done using the Infinium HumanMethylation450 BeadChip. Linear models that accounted for the paired study design and False Discovery Rate Q-values were used to evaluate differential CpG methylation. mRNA expression levels of the genes with the most differentially methylated CpG sites were analyzed. RESULTS In total, 2,040 differentially methylated CpG sites were identified in PCa versus adjacent benign tissue (Q-value < 0.001), the majority of which were hypermethylated (n = 1,946; 95%). DNA methylation profiles accurately distinguished between PCa and benign tissue samples. Twenty-seven top-ranked hypermethylated CpGs had a mean methylation difference of at least 40% between tissue types, which included 25 CpGs in 17 genes. Furthermore, for 10 genes over 50% of promoter region CpGs were hypermethylated in PCa versus benign tissue. The top-ranked differentially methylated genes included three genes that were associated with both promoter hypermethylation and reduced gene expression: SCGB3A1, HIF3A, and AOX1. Analysis of The Cancer Genome Atlas (TCGA) data provided confirmatory evidence for our findings. CONCLUSIONS This study of PCa versus adjacent benign tissue showed many differentially methylated CpGs and regions in and outside gene promoter regions, which may potentially be used for the development of future epigenetic-based diagnostic tests or as therapeutic targets.
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Affiliation(s)
- Milan S. Geybels
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Shanshan Zhao
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
- National Institute of Environmental Health Sciences, Biostatistics & Computational Biology Branch, North Carolina
| | - Chao-Jen Wong
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | | | - Michael Wu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Elaine A. Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | | | | | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
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99
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Bhasin JM, Lee BH, Matkin L, Taylor MG, Hu B, Xu Y, Magi-Galluzzi C, Klein EA, Ting AH. Methylome-wide Sequencing Detects DNA Hypermethylation Distinguishing Indolent from Aggressive Prostate Cancer. Cell Rep 2015; 13:2135-46. [PMID: 26628371 DOI: 10.1016/j.celrep.2015.10.078] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 09/10/2015] [Accepted: 10/28/2015] [Indexed: 01/12/2023] Open
Abstract
A critical need in understanding the biology of prostate cancer is characterizing the molecular differences between indolent and aggressive cases. Because DNA methylation can capture the regulatory state of tumors, we analyzed differential methylation patterns genome-wide among benign prostatic tissue and low-grade and high-grade prostate cancer and found extensive, focal hypermethylation regions unique to high-grade disease. These hypermethylation regions occurred not only in the promoters of genes but also in gene bodies and at intergenic regions that are enriched for DNA-protein binding sites. Integration with existing RNA-sequencing (RNA-seq) and survival data revealed regions where DNA methylation correlates with reduced gene expression associated with poor outcome. Regions specific to aggressive disease are proximal to genes with distinct functions from regions shared by indolent and aggressive disease. Our compendium of methylation changes reveals crucial molecular distinctions between indolent and aggressive prostate cancer.
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Affiliation(s)
- Jeffrey M Bhasin
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Byron H Lee
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Lars Matkin
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Margaret G Taylor
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Bo Hu
- Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Cristina Magi-Galluzzi
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Angela H Ting
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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100
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Gross AM, Kreisberg JF, Ideker T. Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types. PLoS One 2015; 10:e0142618. [PMID: 26555223 PMCID: PMC4640835 DOI: 10.1371/journal.pone.0142618] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/23/2015] [Indexed: 12/21/2022] Open
Abstract
To identify the transcriptional regulatory changes that are most widespread in solid tumors, we performed a pan-cancer analysis using over 600 pairs of tumors and adjacent normal tissues profiled in The Cancer Genome Atlas (TCGA). Frequency of upregulation was calculated across mRNA expression levels, microRNA expression levels and CpG methylation sites and is provided here as a resource. Frequent tumor-associated alterations were identified using a simple statistical approach. Many of the identified changes were consistent with the increased rate of cell division in cancer, such as the overexpression of cell cycle genes and hypermethylation of PRC2 binding sites. However, we also identified proliferation-independent alterations, which highlight novel pathways essential to tumor formation. Nearly all of the GABA receptors are frequently downregulated, with the gene encoding the delta subunit (GABRD) strongly upregulated as the notable exception. Metabolic genes are also frequently downregulated, particularly alcohol dehydrogenases and others consistent with the decreased role of oxidative phosphorylation in cancerous cells. Alterations in the composition of GABA receptors and metabolism may play a key role in the differentiation of cancer cells, independent of proliferation.
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Affiliation(s)
- Andrew M. Gross
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California, United States of America
| | - Jason F. Kreisberg
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Trey Ideker
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California, United States of America
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
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