Analysis of 5-Methylcytosine Regulators and DNA Methylation-Driven Genes in Colon Cancer
Background: Epigenetic-driven events are important molecular mechanisms of carcinogenesis. The 5-methylcytosine (5mC) regulators play important roles in the methylation-driven gene expression. However, the effect of the 5mC regulators on the oncogenic pathways in colon cancer (CC) remains unclear. A...
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| Published in | Frontiers in cell and developmental biology Vol. 9; p. 657092 |
|---|---|
| Main Authors | , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Switzerland
Frontiers Media S.A
31.01.2022
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| Subjects | |
| Online Access | Get full text |
| ISSN | 2296-634X 2296-634X |
| DOI | 10.3389/fcell.2021.657092 |
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| Abstract | Background:
Epigenetic-driven events are important molecular mechanisms of carcinogenesis. The 5-methylcytosine (5mC) regulators play important roles in the methylation-driven gene expression. However, the effect of the 5mC regulators on the oncogenic pathways in colon cancer (CC) remains unclear. Also, the clinical value of such epigenetic-driven events needs further research.
Methods:
The transcriptome and matching epigenetic data were obtained from The Cancer Genome Atlas dataset. The gene set variation analysis identified the oncogenic pathways adjusted by 5mC regulators. The “edgeR” and “methylmix” package identified the differential expression genes of DNA methylation-driven genes. The correlation between 5mC regulators or transcription factors and shortlisted genes was investigated by calculating the Spearman's rank correlation coefficient. Among them, the genes related to diagnosis were screened out based on differential gene expression in extracellular vesicles (EVs) by the “limma” package and histology by immunohistochemistry. Then, a risk signature was constructed by fitting the generalized linear model and validated by the receiver operating characteristic curve.
Results:
MYC targets pathway and phosphatidylinositol-3-kinase–AKT–mammalian target of rapamycin signaling pathway were identified as the hallmark-related pathways associated with 5mC regulators. Also, the P53 pathway was subject to the influence of regulators' expression. A five methylation-driven gene signature (FIRRE, MYBL2, TGFBI, AXIN2, and SLC35D3) was developed as the biomarker for CC diagnosis. Meanwhile, those genes positively related to 5mC regulators and interacted with their relevant or transcription factors.
Conclusion:
In general, 5mC regulators are positively related to each other and DNA methylation-driven genes, with the relationship of multiple active and inhibitory pathways related to cancer. Meanwhile, the signature (FIRRE, MYBL2, TGFBI, AXIN2, and SLC35D3) can prefigure prospective diagnosis in CC. |
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| AbstractList | Background: Epigenetic-driven events are important molecular mechanisms of carcinogenesis. The 5-methylcytosine (5mC) regulators play important roles in the methylation-driven gene expression. However, the effect of the 5mC regulators on the oncogenic pathways in colon cancer (CC) remains unclear. Also, the clinical value of such epigenetic-driven events needs further research.Methods: The transcriptome and matching epigenetic data were obtained from The Cancer Genome Atlas dataset. The gene set variation analysis identified the oncogenic pathways adjusted by 5mC regulators. The “edgeR” and “methylmix” package identified the differential expression genes of DNA methylation-driven genes. The correlation between 5mC regulators or transcription factors and shortlisted genes was investigated by calculating the Spearman's rank correlation coefficient. Among them, the genes related to diagnosis were screened out based on differential gene expression in extracellular vesicles (EVs) by the “limma” package and histology by immunohistochemistry. Then, a risk signature was constructed by fitting the generalized linear model and validated by the receiver operating characteristic curve.Results: MYC targets pathway and phosphatidylinositol-3-kinase–AKT–mammalian target of rapamycin signaling pathway were identified as the hallmark-related pathways associated with 5mC regulators. Also, the P53 pathway was subject to the influence of regulators' expression. A five methylation-driven gene signature (FIRRE, MYBL2, TGFBI, AXIN2, and SLC35D3) was developed as the biomarker for CC diagnosis. Meanwhile, those genes positively related to 5mC regulators and interacted with their relevant or transcription factors.Conclusion: In general, 5mC regulators are positively related to each other and DNA methylation-driven genes, with the relationship of multiple active and inhibitory pathways related to cancer. Meanwhile, the signature (FIRRE, MYBL2, TGFBI, AXIN2, and SLC35D3) can prefigure prospective diagnosis in CC. Background: Epigenetic-driven events are important molecular mechanisms of carcinogenesis. The 5-methylcytosine (5mC) regulators play important roles in the methylation-driven gene expression. However, the effect of the 5mC regulators on the oncogenic pathways in colon cancer (CC) remains unclear. Also, the clinical value of such epigenetic-driven events needs further research. Methods: The transcriptome and matching epigenetic data were obtained from The Cancer Genome Atlas dataset. The gene set variation analysis identified the oncogenic pathways adjusted by 5mC regulators. The “edgeR” and “methylmix” package identified the differential expression genes of DNA methylation-driven genes. The correlation between 5mC regulators or transcription factors and shortlisted genes was investigated by calculating the Spearman's rank correlation coefficient. Among them, the genes related to diagnosis were screened out based on differential gene expression in extracellular vesicles (EVs) by the “limma” package and histology by immunohistochemistry. Then, a risk signature was constructed by fitting the generalized linear model and validated by the receiver operating characteristic curve. Results: MYC targets pathway and phosphatidylinositol-3-kinase–AKT–mammalian target of rapamycin signaling pathway were identified as the hallmark-related pathways associated with 5mC regulators. Also, the P53 pathway was subject to the influence of regulators' expression. A five methylation-driven gene signature (FIRRE, MYBL2, TGFBI, AXIN2, and SLC35D3) was developed as the biomarker for CC diagnosis. Meanwhile, those genes positively related to 5mC regulators and interacted with their relevant or transcription factors. Conclusion: In general, 5mC regulators are positively related to each other and DNA methylation-driven genes, with the relationship of multiple active and inhibitory pathways related to cancer. Meanwhile, the signature (FIRRE, MYBL2, TGFBI, AXIN2, and SLC35D3) can prefigure prospective diagnosis in CC. Epigenetic-driven events are important molecular mechanisms of carcinogenesis. The 5-methylcytosine (5mC) regulators play important roles in the methylation-driven gene expression. However, the effect of the 5mC regulators on the oncogenic pathways in colon cancer (CC) remains unclear. Also, the clinical value of such epigenetic-driven events needs further research. The transcriptome and matching epigenetic data were obtained from The Cancer Genome Atlas dataset. The gene set variation analysis identified the oncogenic pathways adjusted by 5mC regulators. The "edgeR" and "methylmix" package identified the differential expression genes of DNA methylation-driven genes. The correlation between 5mC regulators or transcription factors and shortlisted genes was investigated by calculating the Spearman's rank correlation coefficient. Among them, the genes related to diagnosis were screened out based on differential gene expression in extracellular vesicles (EVs) by the "limma" package and histology by immunohistochemistry. Then, a risk signature was constructed by fitting the generalized linear model and validated by the receiver operating characteristic curve. MYC targets pathway and phosphatidylinositol-3-kinase-AKT-mammalian target of rapamycin signaling pathway were identified as the hallmark-related pathways associated with 5mC regulators. Also, the P53 pathway was subject to the influence of regulators' expression. A five methylation-driven gene signature (FIRRE, MYBL2, TGFBI, AXIN2, and SLC35D3) was developed as the biomarker for CC diagnosis. Meanwhile, those genes positively related to 5mC regulators and interacted with their relevant or transcription factors. In general, 5mC regulators are positively related to each other and DNA methylation-driven genes, with the relationship of multiple active and inhibitory pathways related to cancer. Meanwhile, the signature (FIRRE, MYBL2, TGFBI, AXIN2, and SLC35D3) can prefigure prospective diagnosis in CC. Background: Epigenetic-driven events are important molecular mechanisms of carcinogenesis. The 5-methylcytosine (5mC) regulators play important roles in the methylation-driven gene expression. However, the effect of the 5mC regulators on the oncogenic pathways in colon cancer (CC) remains unclear. Also, the clinical value of such epigenetic-driven events needs further research. Methods: The transcriptome and matching epigenetic data were obtained from The Cancer Genome Atlas dataset. The gene set variation analysis identified the oncogenic pathways adjusted by 5mC regulators. The "edgeR" and "methylmix" package identified the differential expression genes of DNA methylation-driven genes. The correlation between 5mC regulators or transcription factors and shortlisted genes was investigated by calculating the Spearman's rank correlation coefficient. Among them, the genes related to diagnosis were screened out based on differential gene expression in extracellular vesicles (EVs) by the "limma" package and histology by immunohistochemistry. Then, a risk signature was constructed by fitting the generalized linear model and validated by the receiver operating characteristic curve. Results: MYC targets pathway and phosphatidylinositol-3-kinase-AKT-mammalian target of rapamycin signaling pathway were identified as the hallmark-related pathways associated with 5mC regulators. Also, the P53 pathway was subject to the influence of regulators' expression. A five methylation-driven gene signature (FIRRE, MYBL2, TGFBI, AXIN2, and SLC35D3) was developed as the biomarker for CC diagnosis. Meanwhile, those genes positively related to 5mC regulators and interacted with their relevant or transcription factors. Conclusion: In general, 5mC regulators are positively related to each other and DNA methylation-driven genes, with the relationship of multiple active and inhibitory pathways related to cancer. Meanwhile, the signature (FIRRE, MYBL2, TGFBI, AXIN2, and SLC35D3) can prefigure prospective diagnosis in CC.Background: Epigenetic-driven events are important molecular mechanisms of carcinogenesis. The 5-methylcytosine (5mC) regulators play important roles in the methylation-driven gene expression. However, the effect of the 5mC regulators on the oncogenic pathways in colon cancer (CC) remains unclear. Also, the clinical value of such epigenetic-driven events needs further research. Methods: The transcriptome and matching epigenetic data were obtained from The Cancer Genome Atlas dataset. The gene set variation analysis identified the oncogenic pathways adjusted by 5mC regulators. The "edgeR" and "methylmix" package identified the differential expression genes of DNA methylation-driven genes. The correlation between 5mC regulators or transcription factors and shortlisted genes was investigated by calculating the Spearman's rank correlation coefficient. Among them, the genes related to diagnosis were screened out based on differential gene expression in extracellular vesicles (EVs) by the "limma" package and histology by immunohistochemistry. Then, a risk signature was constructed by fitting the generalized linear model and validated by the receiver operating characteristic curve. Results: MYC targets pathway and phosphatidylinositol-3-kinase-AKT-mammalian target of rapamycin signaling pathway were identified as the hallmark-related pathways associated with 5mC regulators. Also, the P53 pathway was subject to the influence of regulators' expression. A five methylation-driven gene signature (FIRRE, MYBL2, TGFBI, AXIN2, and SLC35D3) was developed as the biomarker for CC diagnosis. Meanwhile, those genes positively related to 5mC regulators and interacted with their relevant or transcription factors. Conclusion: In general, 5mC regulators are positively related to each other and DNA methylation-driven genes, with the relationship of multiple active and inhibitory pathways related to cancer. Meanwhile, the signature (FIRRE, MYBL2, TGFBI, AXIN2, and SLC35D3) can prefigure prospective diagnosis in CC. |
| Author | Du, Cheng Liu, XinLi Wen, Zhikang Li, Jie Fu, Boshi Zhao, Yi Liu, Min Wei, Minjie Li, Mingwei Yang, Meina |
| AuthorAffiliation | 1 Department of Pharmacology , School of Pharmacy , China Medical University , Shenyang , China 4 Department of Digestive Oncology , Cancer Hospital of China Medical University , Shenyang , China 3 Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors , Ministry of Education , China Medical University , Shenyang , China 2 Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation , Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center , Shenyang , China |
| AuthorAffiliation_xml | – name: 2 Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation , Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center , Shenyang , China – name: 1 Department of Pharmacology , School of Pharmacy , China Medical University , Shenyang , China – name: 3 Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors , Ministry of Education , China Medical University , Shenyang , China – name: 4 Department of Digestive Oncology , Cancer Hospital of China Medical University , Shenyang , China |
| Author_xml | – sequence: 1 givenname: Cheng surname: Du fullname: Du, Cheng – sequence: 2 givenname: XinLi surname: Liu fullname: Liu, XinLi – sequence: 3 givenname: Mingwei surname: Li fullname: Li, Mingwei – sequence: 4 givenname: Yi surname: Zhao fullname: Zhao, Yi – sequence: 5 givenname: Jie surname: Li fullname: Li, Jie – sequence: 6 givenname: Zhikang surname: Wen fullname: Wen, Zhikang – sequence: 7 givenname: Min surname: Liu fullname: Liu, Min – sequence: 8 givenname: Meina surname: Yang fullname: Yang, Meina – sequence: 9 givenname: Boshi surname: Fu fullname: Fu, Boshi – sequence: 10 givenname: Minjie surname: Wei fullname: Wei, Minjie |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/35174154$$D View this record in MEDLINE/PubMed |
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| CitedBy_id | crossref_primary_10_3390_ijms25136849 crossref_primary_10_3389_fonc_2024_1335670 crossref_primary_10_1002_ctd2_218 crossref_primary_10_1093_carcin_bgad024 crossref_primary_10_1002_prm2_12108 crossref_primary_10_3390_medicina59050996 |
| Cites_doi | 10.1371/journal.pone.0229007 10.1073/pnas.1521230113 10.1038/npp.2012.112 10.1073/pnas.1703577114 10.1016/j.omtn.2021.08.017 10.3322/caac.21654 10.1093/bioinformatics/btp616 10.1016/j.cell.2007.01.029 10.7150/ijbs.41587 10.1126/science.1170116 10.1093/bioinformatics/bty156 10.1186/1471-2105-14-7 10.7150/thno.51507 10.1016/j.pharmthera.2017.11.002 10.1177/1947601911418499 10.1101/gr.239244.118 10.7150/thno.13438 10.1093/bioinformatics/bti623 10.1016/j.jhep.2017.12.018 10.1186/s40364-017-0081-z 10.4137/CIN.S13495 10.1016/j.bioactmat.2021.07.017 10.4049/jimmunol.0900970 10.1172/JCI129317 10.1021/acsnano.1c06429 10.1016/j.ygeno.2021.04.035 10.7150/thno.58385 10.1093/nar/gkv007 10.1038/ncb3094 10.1053/j.gastro.2021.08.054 10.1016/j.addr.2021.114032 10.3109/10408363.2015.1092496 10.1186/s13045-020-00854-w 10.1038/s41467-019-09984-3 10.1073/pnas.1415301111 10.1053/j.gastro.2021.01.028 10.1159/000151708 10.1038/nrg2341 10.1038/onc.2013.560 10.1186/s13059-015-0618-0 10.1016/j.stem.2019.11.012 10.1126/science.aat6806 10.1089/omi.2011.0118 10.1038/s41588-018-0073-4 10.1080/20013078.2018.1535750 10.7554/eLife.39944 10.1093/carcin/bgz199 10.3892/ijo.2015.3263 10.1146/annurev-pathol-011110-130235 |
| ContentType | Journal Article |
| Copyright | Copyright © 2022 Du, Liu, Li, Zhao, Li, Wen, Liu, Yang, Fu and Wei. Copyright © 2022 Du, Liu, Li, Zhao, Li, Wen, Liu, Yang, Fu and Wei. 2022 Du, Liu, Li, Zhao, Li, Wen, Liu, Yang, Fu and Wei |
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| Keywords | diagnosis biomarker colon cancer methylation-driven gene 5mC regulators |
| Language | English |
| License | Copyright © 2022 Du, Liu, Li, Zhao, Li, Wen, Liu, Yang, Fu and Wei. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 These authors have contributed equally to this work and share the first authorship Baozhen Zhang, Peking University Cancer Hospital, China Edited by: Lucas Treps, Centre de Recherche en Cancérologie et Immunologie Nantes Angers (CRCINA), France Reviewed by: Hamid Zand, National Nutrition and Food Technology Research Institute, Iran This article was submitted to Molecular and Cellular Oncology, a section of the journal Frontiers in Cell and Developmental Biology |
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| References | Hanzelmann (B12) 2013; 14 Hu (B15) 2014; 13 Yu (B48) 2012; 16 Robinson (B33) 2010; 26 Chen (B7) 2020; 13 Hao (B13) 2017; 114 Mayakonda (B24) 2018; 28 Siegel (B34) 2021; 71 Ritchie (B32) 2015; 43 Poh (B29) 2016; 6 Bai (B2) 2020; 16 Jones (B16) 2007; 128 Ren (B30) 2015; 5 Olsson (B27) 2020; 15 Souren (B36) 2019; 10 Li (B19) 2020; 41 Abitbol (B1) 2018; 68 Thery (B41) 2018; 7 Zhang (B49) 2017; 5 Moore (B26) 2013; 38 Cai (B4) 2021; 161 Zhou (B50) 2018; 50 Suzuki (B38) 2008; 9 Sun (B37) 2021; 11 Yang (B47) 2015; 16 Luo (B22) 2018; 361 Fong (B10) 2015; 17 Cedoz (B5) 2018; 34 Bestor (B3) 2015; 112 Webber (B42) 2015; 34 Xu (B46) 2019; 129 Fearon (B9) 2011; 6 Wieckowski (B43) 2009; 183 Syed (B39) 2020; 26 Parry (B28) 2011; 2 Martin (B23) 2008; 75 Chen (B6) 2021; 179 Ren (B31) 2016; 48 Wu (B44) 2021; 15 Meehan (B25) 2016; 53 Li (B20) 2021; 113 Tahiliani (B40) 2009; 324 Sing (B35) 2005; 21 Ginder (B11) 2018; 184 Li (B21) 2021; 26 Xiao (B45) 2022; 9 Hayata (B14) 2021; 160 Chiavarina (B8) 2021; 11 Kim (B17) 2018; 7 Kowal (B18) 2016; 113 |
| References_xml | – volume: 15 start-page: e0229007 year: 2020 ident: B27 article-title: Allocating Colorectal Cancer Patients to Different Risk Categories by Using a Five-Biomarker mRNA Combination in Lymph Node Analysis publication-title: PLoS One doi: 10.1371/journal.pone.0229007 – volume: 113 start-page: E968 year: 2016 ident: B18 article-title: Proteomic Comparison Defines Novel Markers to Characterize Heterogeneous Populations of Extracellular Vesicle Subtypes publication-title: Proc. Natl. Acad. Sci. U S A. doi: 10.1073/pnas.1521230113 – volume: 38 start-page: 23 year: 2013 ident: B26 article-title: DNA Methylation and its Basic Function publication-title: Neuropsychopharmacology doi: 10.1038/npp.2012.112 – volume: 114 start-page: 7414 year: 2017 ident: B13 article-title: DNA Methylation Markers for Diagnosis and Prognosis of Common Cancers publication-title: Proc. Natl. Acad. Sci. U S A. doi: 10.1073/pnas.1703577114 – volume: 5 start-page: 1542 year: 2015 ident: B30 article-title: MYBL2 Is an Independent Prognostic Marker that Has Tumor-Promoting Functions in Colorectal Cancer publication-title: Am. J. Cancer Res. – volume: 26 start-page: 488 year: 2021 ident: B21 article-title: Circulating EVs Long RNA-Based Subtyping and Deconvolution Enable Prediction of Immunogenic Signatures and Clinical Outcome for PDAC publication-title: Mol. Ther. Nucleic Acids doi: 10.1016/j.omtn.2021.08.017 – volume: 71 start-page: 7 year: 2021 ident: B34 article-title: Cancer Statistics, 2021 publication-title: CA Cancer J. Clin. doi: 10.3322/caac.21654 – volume: 26 start-page: 139 year: 2010 ident: B33 article-title: edgeR: a Bioconductor Package for Differential Expression Analysis of Digital Gene Expression Data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp616 – volume: 128 start-page: 683 year: 2007 ident: B16 article-title: The Epigenomics of Cancer publication-title: Cell doi: 10.1016/j.cell.2007.01.029 – volume: 16 start-page: 1153 year: 2020 ident: B2 article-title: Development and Validation of a Prognostic Nomogram for Gastric Cancer Based on DNA Methylation-Driven Differentially Expressed Genes publication-title: Int. J. Biol. Sci. doi: 10.7150/ijbs.41587 – volume: 324 start-page: 930 year: 2009 ident: B40 article-title: Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1 publication-title: Science doi: 10.1126/science.1170116 – volume: 34 start-page: 3044 year: 2018 ident: B5 article-title: MethylMix 2.0: an R Package for Identifying DNA Methylation Genes publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty156 – volume: 14 start-page: 7 year: 2013 ident: B12 article-title: GSVA: Gene Set Variation Analysis for Microarray and RNA-Seq Data publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-14-7 – volume: 11 start-page: 1626 year: 2021 ident: B8 article-title: Metastatic Colorectal Cancer Cells Maintain the TGFbeta Program and Use TGFBI to Fuel Angiogenesis publication-title: Theranostics doi: 10.7150/thno.51507 – volume: 184 start-page: 98 year: 2018 ident: B11 article-title: Readers of DNA Methylation, the MBD Family as Potential Therapeutic Targets publication-title: Pharmacol. Ther. doi: 10.1016/j.pharmthera.2017.11.002 – volume: 2 start-page: 618 year: 2011 ident: B28 article-title: The Roles of the Methyl-CpG Binding Proteins in Cancer publication-title: Genes Cancer doi: 10.1177/1947601911418499 – volume: 28 start-page: 1747 year: 2018 ident: B24 article-title: Maftools: Efficient and Comprehensive Analysis of Somatic Variants in Cancer publication-title: Genome Res. doi: 10.1101/gr.239244.118 – volume: 6 start-page: 369 year: 2016 ident: B29 article-title: DNA Methyltransferase Activity Assays: Advances and Challenges publication-title: Theranostics doi: 10.7150/thno.13438 – volume: 21 start-page: 3940 year: 2005 ident: B35 article-title: ROCR: Visualizing Classifier Performance in R publication-title: Bioinformatics doi: 10.1093/bioinformatics/bti623 – volume: 68 start-page: 1203 year: 2018 ident: B1 article-title: AXIN Deficiency in Human and Mouse Hepatocytes Induces Hepatocellular Carcinoma in the Absence of Beta-Catenin Activation publication-title: J. Hepatol. doi: 10.1016/j.jhep.2017.12.018 – volume: 5 start-page: 1 year: 2017 ident: B49 article-title: DNA Methyltransferases and Their Roles in Tumorigenesis publication-title: Biomark Res. doi: 10.1186/s40364-017-0081-z – volume: 13 start-page: 13 year: 2014 ident: B15 article-title: OmicCircos: A Simple-To-Use R Package for the Circular Visualization of Multidimensional Omics Data publication-title: Cancer Inform. doi: 10.4137/CIN.S13495 – volume: 9 start-page: 373 year: 2022 ident: B45 article-title: Targeting central Nervous System Extracellular Vesicles Enhanced Triiodothyronine Remyelination Effect on Experimental Autoimmune Encephalomyelitis publication-title: Bioact Mater. doi: 10.1016/j.bioactmat.2021.07.017 – volume: 183 start-page: 3720 year: 2009 ident: B43 article-title: Tumor-derived Microvesicles Promote Regulatory T Cell Expansion and Induce Apoptosis in Tumor-Reactive Activated CD8+ T Lymphocytes publication-title: J. Immunol. doi: 10.4049/jimmunol.0900970 – volume: 129 start-page: 4316 year: 2019 ident: B46 article-title: Tumor Suppressor TET2 Promotes Cancer Immunity and Immunotherapy Efficacy publication-title: J. Clin. Invest. doi: 10.1172/JCI129317 – volume: 15 start-page: 19522 year: 2021 ident: B44 article-title: Ratiometric 3D DNA Machine Combined with Machine Learning Algorithm for Ultrasensitive and High-Precision Screening of Early Urinary Diseases publication-title: ACS Nano doi: 10.1021/acsnano.1c06429 – volume: 113 start-page: 2032 year: 2021 ident: B20 article-title: A Ten-Gene Methylation Signature as a Novel Biomarker for Improving Prediction of Prognosis and Indicating Gene Targets in Endometrial Cancer publication-title: Genomics doi: 10.1016/j.ygeno.2021.04.035 – volume: 11 start-page: 5346 year: 2021 ident: B37 article-title: An Integrated Epigenomic-Transcriptomic Landscape of Lung Cancer Reveals Novel Methylation Driver Genes of Diagnostic and Therapeutic Relevance publication-title: Theranostics doi: 10.7150/thno.58385 – volume: 43 start-page: e47 year: 2015 ident: B32 article-title: Limma powers Differential Expression Analyses for RNA-Sequencing and Microarray Studies publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkv007 – volume: 17 start-page: 183 year: 2015 ident: B10 article-title: Breast-cancer-secreted miR-122 Reprograms Glucose Metabolism in Premetastatic Niche to Promote Metastasis publication-title: Nat. Cell Biol doi: 10.1038/ncb3094 – volume: 161 start-page: 2053 year: 2021 ident: B4 article-title: A Multilocus Blood-Based Assay Targeting Circulating Tumor DNA Methylation Enables Early Detection and Early Relapse Prediction of Colorectal Cancer publication-title: Gastroenterology doi: 10.1053/j.gastro.2021.08.054 – volume: 179 start-page: 114032 year: 2021 ident: B6 article-title: Cellular Transformers for Targeted Therapy publication-title: Adv. Drug Deliv. Rev. doi: 10.1016/j.addr.2021.114032 – volume: 53 start-page: 121 year: 2016 ident: B25 article-title: The Contribution of Tumour-Derived Exosomes to the Hallmarks of Cancer publication-title: Crit. Rev. Clin. Lab. Sci. doi: 10.3109/10408363.2015.1092496 – volume: 13 start-page: 22 year: 2020 ident: B7 article-title: Identification of Cross-Talk between M(6)A and 5mC Regulators Associated with Onco-Immunogenic Features and Prognosis across 33 Cancer Types publication-title: J. Hematol. Oncol. doi: 10.1186/s13045-020-00854-w – volume: 10 start-page: 2094 year: 2019 ident: B36 article-title: DNA Methylation Signatures of Monozygotic Twins Clinically Discordant for Multiple Sclerosis publication-title: Nat. Commun. doi: 10.1038/s41467-019-09984-3 – volume: 112 start-page: 6796 year: 2015 ident: B3 article-title: Notes on the Role of Dynamic DNA Methylation in Mammalian Development publication-title: Proc. Natl. Acad. Sci. U S A. doi: 10.1073/pnas.1415301111 – volume: 160 start-page: 2133 year: 2021 ident: B14 article-title: Axin2(+) Peribiliary Glands in the Periampullary Region Generate Biliary Epithelial Stem Cells that Give Rise to Ampullary Carcinoma publication-title: Gastroenterology doi: 10.1053/j.gastro.2021.01.028 – volume: 75 start-page: 281 year: 2008 ident: B23 article-title: MBD2-mediated Transcriptional Repression of the p14ARF Tumor Suppressor Gene in Human colon Cancer Cells publication-title: Pathobiology doi: 10.1159/000151708 – volume: 9 start-page: 465 year: 2008 ident: B38 article-title: DNA Methylation Landscapes: Provocative Insights from Epigenomics publication-title: Nat. Rev. Genet. doi: 10.1038/nrg2341 – volume: 34 start-page: 290 year: 2015 ident: B42 article-title: Differentiation of Tumour-Promoting Stromal Myofibroblasts by Cancer Exosomes publication-title: Oncogene doi: 10.1038/onc.2013.560 – volume: 16 start-page: 52 year: 2015 ident: B47 article-title: The lncRNA Firre Anchors the Inactive X Chromosome to the Nucleolus by Binding CTCF and Maintains H3K27me3 Methylation publication-title: Genome Biol. doi: 10.1186/s13059-015-0618-0 – volume: 26 start-page: 64 year: 2020 ident: B39 article-title: Endometrial Axin2(+) Cells Drive Epithelial Homeostasis, Regeneration, and Cancer Following Oncogenic Transformation publication-title: Cell Stem Cell doi: 10.1016/j.stem.2019.11.012 – volume: 361 start-page: 1336 year: 2018 ident: B22 article-title: Dynamic DNA Methylation: In the Right Place at the Right Time publication-title: Science doi: 10.1126/science.aat6806 – volume: 16 start-page: 284 year: 2012 ident: B48 article-title: clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters publication-title: OMICS doi: 10.1089/omi.2011.0118 – volume: 50 start-page: 591 year: 2018 ident: B50 article-title: DNA Methylation Loss in Late-Replicating Domains Is Linked to Mitotic Cell Division publication-title: Nat. Genet. doi: 10.1038/s41588-018-0073-4 – volume: 7 start-page: 1535750 year: 2018 ident: B41 article-title: Minimal Information for Studies of Extracellular Vesicles 2018 (MISEV2018): a Position Statement of the International Society for Extracellular Vesicles and Update of the MISEV2014 Guidelines publication-title: J. Extracell Vesicles doi: 10.1080/20013078.2018.1535750 – volume: 7 year: 2018 ident: B17 article-title: Replication Study: Melanoma Exosomes Educate Bone Marrow Progenitor Cells toward a Pro-metastatic Phenotype through publication-title: MET. Elife. doi: 10.7554/eLife.39944 – volume: 41 start-page: 235 year: 2020 ident: B19 article-title: Temporal DNA Methylation Pattern and Targeted Therapy in Colitis-Associated Cancer publication-title: Carcinogenesis doi: 10.1093/carcin/bgz199 – volume: 48 start-page: 690 year: 2016 ident: B31 article-title: Identifying Molecular Subtypes in Human colon Cancer Using Gene Expression and DNA Methylation Microarray Data publication-title: Int. J. Oncol. doi: 10.3892/ijo.2015.3263 – volume: 6 start-page: 479 year: 2011 ident: B9 article-title: Molecular Genetics of Colorectal Cancer publication-title: Annu. Rev. Pathol. doi: 10.1146/annurev-pathol-011110-130235 |
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Epigenetic-driven events are important molecular mechanisms of carcinogenesis. The 5-methylcytosine (5mC) regulators play important roles in the... Epigenetic-driven events are important molecular mechanisms of carcinogenesis. The 5-methylcytosine (5mC) regulators play important roles in the... Background: Epigenetic-driven events are important molecular mechanisms of carcinogenesis. The 5-methylcytosine (5mC) regulators play important roles in the... |
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| Title | Analysis of 5-Methylcytosine Regulators and DNA Methylation-Driven Genes in Colon Cancer |
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