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For: Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Briem E, Zhang K, Irizarry RA, Feinberg AP. Increased methylation variation in epigenetic domains across cancer types. Nat Genet 2011;43:768-75. [PMID: 21706001 PMCID: PMC3145050 DOI: 10.1038/ng.865] [Citation(s) in RCA: 780] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 05/25/2011] [Indexed: 02/07/2023]
Number Cited by Other Article(s)
1
Zhang R, Liu H, Bai B, Wang H. Quantification of Epigenetic DNA and RNA Modifications by UHPLC-MS/MS Technologies: New Concepts and New Improvements for the Special Collections. J Sep Sci 2025;48:e70159. [PMID: 40344478 DOI: 10.1002/jssc.70159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2025] [Revised: 03/21/2025] [Accepted: 04/17/2025] [Indexed: 05/11/2025]
2
Haddadin L, Sun X. Stem Cells in Cancer: From Mechanisms to Therapeutic Strategies. Cells 2025;14:538. [PMID: 40214491 PMCID: PMC11988674 DOI: 10.3390/cells14070538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2025] [Revised: 03/23/2025] [Accepted: 04/01/2025] [Indexed: 04/14/2025]  Open
3
Pinto R, Vedeld HM, Lind GE, Jeanmougin M. Unraveling epigenetic heterogeneity across gastrointestinal adenocarcinomas through a standardized analytical framework. Mol Oncol 2025;19:1117-1131. [PMID: 39696831 PMCID: PMC11977639 DOI: 10.1002/1878-0261.13772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 09/30/2024] [Accepted: 10/31/2024] [Indexed: 12/20/2024]  Open
4
Fu Y, Timp W, Sedlazeck FJ. Computational analysis of DNA methylation from long-read sequencing. Nat Rev Genet 2025:10.1038/s41576-025-00822-5. [PMID: 40155770 DOI: 10.1038/s41576-025-00822-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2025] [Indexed: 04/01/2025]
5
Zhou J, Wu Y, Liu H, Tian W, Castanon RG, Bartlett A, Zhang Z, Yao G, Shi D, Clock B, Marcotte S, Nery JR, Liem M, Claffey N, Boggeman L, Barragan C, Drigo RAE, Weimer AK, Shi M, Cooper-Knock J, Zhang S, Snyder MP, Preissl S, Ren B, O’Connor C, Chen S, Luo C, Dixon JR, Ecker JR. Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.23.644697. [PMID: 40196612 PMCID: PMC11974725 DOI: 10.1101/2025.03.23.644697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
6
Colemon A, Romney CV, Jones AD, Bagsby C, Jackson R, Ramanathan S. Interplay Between TGFβ1 Signaling and Cancer-Testis Antigen MAGEB2: A New Thorn in Cancer's Side? Int J Mol Sci 2025;26:2448. [PMID: 40141091 PMCID: PMC11942090 DOI: 10.3390/ijms26062448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2025] [Revised: 03/03/2025] [Accepted: 03/07/2025] [Indexed: 03/28/2025]  Open
7
Margalit S, Tulpová Z, Michaeli Y, Zur T, Deek J, Louzoun-Zada S, Nifker G, Grunwald A, Scher Y, Schütz L, Weinhold E, Gnatek Y, Omer D, Dekel B, Friedman E, Ebenstein Y. Optical genome and epigenome mapping of clear cell renal cell carcinoma. NAR Cancer 2025;7:zcaf008. [PMID: 40061565 PMCID: PMC11886815 DOI: 10.1093/narcan/zcaf008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 02/18/2025] [Accepted: 03/05/2025] [Indexed: 04/02/2025]  Open
8
Li W, Luo P, Chen Q, Cheng L, Gan L, Zhang F, Zhong H, Zheng L, Qian B. Epigenetic modifications in bladder cancer: crosstalk between DNA methylation and miRNAs. Front Immunol 2025;16:1518144. [PMID: 39981244 PMCID: PMC11841399 DOI: 10.3389/fimmu.2025.1518144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Accepted: 01/22/2025] [Indexed: 02/22/2025]  Open
9
Furlano K, Keshavarzian T, Biernath N, Fendler A, de Santis M, Weischenfeldt J, Lupien M. Epigenomics-guided precision oncology: Chromatin variants in prostate tumor evolution. Int J Cancer 2025. [PMID: 39853587 DOI: 10.1002/ijc.35327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 12/17/2024] [Accepted: 01/02/2025] [Indexed: 01/26/2025]
10
Li JS, Riggins K, Yang L, Chen C, Castro P, Alfarkh W, Zarrin-Khameh N, Scheurer ME, Creighton CJ, Musher B, Li W, Shen L. DNA methylation profiling at base-pair resolution reveals unique epigenetic features of early-onset colorectal cancer in underrepresented populations. Clin Epigenetics 2025;17:11. [PMID: 39844333 PMCID: PMC11753045 DOI: 10.1186/s13148-025-01817-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Accepted: 01/10/2025] [Indexed: 01/24/2025]  Open
11
Liu Y, Hrit JA, Chomiak AA, Stransky S, Hoffman JR, Tiedemann RL, Wiseman AK, Kariapper LS, Dickson BM, Worden EJ, Fry CJ, Sidoli S, Rothbart SB. DNA hypomethylation promotes UHRF1-and SUV39H1/H2-dependent crosstalk between H3K18ub and H3K9me3 to reinforce heterochromatin states. Mol Cell 2025;85:394-412.e12. [PMID: 39631394 PMCID: PMC11741932 DOI: 10.1016/j.molcel.2024.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 09/17/2024] [Accepted: 11/07/2024] [Indexed: 12/07/2024]
12
Laisné M, Lupien M, Vallot C. Epigenomic heterogeneity as a source of tumour evolution. Nat Rev Cancer 2025;25:7-26. [PMID: 39414948 DOI: 10.1038/s41568-024-00757-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/16/2024] [Indexed: 10/18/2024]
13
Smith ZD, Hetzel S, Meissner A. DNA methylation in mammalian development and disease. Nat Rev Genet 2025;26:7-30. [PMID: 39134824 DOI: 10.1038/s41576-024-00760-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2024] [Indexed: 12/15/2024]
14
Magnani E, Macchi F, Randic T, Chen C, Madakashira B, Ranjan S, Eski SE, Singh SP, Sadler KC. Epigenetic Disordering Drives Stemness, Senescence Escape and Tumor Heterogeneity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.29.629346. [PMID: 39763773 PMCID: PMC11703240 DOI: 10.1101/2024.12.29.629346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2025]
15
Chu WT, Wang J. Uncovering the lung cancer mechanisms through the chromosome structural ensemble characteristics and nucleation seeds. J Chem Phys 2024;161:225101. [PMID: 39660659 DOI: 10.1063/5.0238929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 11/25/2024] [Indexed: 12/12/2024]  Open
16
Liapodimitri A, Tetens AR, Craig-Schwartz J, Lunsford K, Skalitzky KO, Koldobskiy MA. Progress Toward Epigenetic Targeted Therapies for Childhood Cancer. Cancers (Basel) 2024;16:4149. [PMID: 39766049 PMCID: PMC11674401 DOI: 10.3390/cancers16244149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Revised: 12/09/2024] [Accepted: 12/10/2024] [Indexed: 01/11/2025]  Open
17
Tiedemann R, Hrit J, Du Q, Wiseman A, Eden H, Dickson B, Kong X, Chomiak A, Vaughan R, Tibben B, Hebert J, David Y, Zhou W, Baylin S, Jones P, Clark S, Rothbart S. UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation. Nucleic Acids Res 2024;52:13733-13756. [PMID: 39607687 PMCID: PMC11662662 DOI: 10.1093/nar/gkae1105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 10/04/2024] [Accepted: 10/25/2024] [Indexed: 11/29/2024]  Open
18
Kelly K, Scherer M, Braun MM, Lutsik P, Plass C. EpiCHAOS: a metric to quantify epigenomic heterogeneity in single-cell data. Genome Biol 2024;25:305. [PMID: 39623476 PMCID: PMC11613708 DOI: 10.1186/s13059-024-03446-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 11/26/2024] [Indexed: 12/06/2024]  Open
19
Zhou J, Li D, Xu M, Zhu T, Li Z, Fu Z, Wang M, Li S, Gu D. Interactions between polycyclic aromatic hydrocarbons and genetic variants in the cGAS-STING pathway affect the risk of colorectal cancer. Arch Toxicol 2024;98:4117-4129. [PMID: 39287666 DOI: 10.1007/s00204-024-03862-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 09/05/2024] [Indexed: 09/19/2024]
20
Lu S, Zheng Z, Zhu C. Histone methyltransferase WHSC1 cooperate with YBX1 promote glioblastoma progression via regulating PLK1 expression. Cell Signal 2024;124:111471. [PMID: 39406278 DOI: 10.1016/j.cellsig.2024.111471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 10/03/2024] [Accepted: 10/12/2024] [Indexed: 10/22/2024]
21
Balaramane D, Spill Y, Weber M, Bardet A. MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylated regions from whole-genome datasets. Nucleic Acids Res 2024;52:e98. [PMID: 39420630 PMCID: PMC11602171 DOI: 10.1093/nar/gkae880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/13/2024] [Accepted: 09/30/2024] [Indexed: 10/19/2024]  Open
22
Köhnke T, Karigane D, Hilgart E, Fan AC, Kayamori K, Miyauchi M, Collins CT, Suchy FP, Rangavajhula A, Feng Y, Nakauchi Y, Martinez-Montes E, Fowler JL, Loh KM, Nakauchi H, Koldobskiy MA, Feinberg AP, Majeti R. DNMT3AR882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.26.620318. [PMID: 39553934 PMCID: PMC11565803 DOI: 10.1101/2024.10.26.620318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
23
Grisolia P, Tufano R, Iannarone C, De Falco A, Carlino F, Graziano C, Addeo R, Scrima M, Caraglia F, Ceccarelli A, Nuzzo PV, Cossu AM, Forte S, Giuffrida R, Orditura M, Caraglia M, Ceccarelli M. Differential methylation of circulating free DNA assessed through cfMeDiP as a new tool for breast cancer diagnosis and detection of BRCA1/2 mutation. J Transl Med 2024;22:938. [PMID: 39407254 PMCID: PMC11476115 DOI: 10.1186/s12967-024-05734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 10/05/2024] [Indexed: 10/20/2024]  Open
24
Li Y, Li W, Deng J, Yin M. PER3 promoter hypermethylation correlates to the progression of pan-cancer. Clin Epigenetics 2024;16:140. [PMID: 39402618 PMCID: PMC11476066 DOI: 10.1186/s13148-024-01760-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Accepted: 10/07/2024] [Indexed: 10/19/2024]  Open
25
Tokairin K, Ito M, Lee AG, Teo M, He S, Cheng MY, Steinberg GK. Genome-Wide DNA Methylation Profiling Reveals Low Methylation Variability in Moyamoya Disease. Transl Stroke Res 2024:10.1007/s12975-024-01299-w. [PMID: 39356405 DOI: 10.1007/s12975-024-01299-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 08/13/2024] [Accepted: 09/09/2024] [Indexed: 10/03/2024]
26
Zhao K, Oualkacha K, Zeng Y, Shen C, Klein K, Lakhal-Chaieb L, Labbe A, Pastinen T, Hudson M, Colmegna I, Bernatsky S, Greenwood CMT. Addressing dispersion in mis-measured multivariate binomial outcomes: A novel statistical approach for detecting differentially methylated regions in bisulfite sequencing data. Stat Med 2024;43:3899-3920. [PMID: 38932470 DOI: 10.1002/sim.10149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 04/13/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
27
Zhang J, Xu L, Yan X, Hu J, Gao X, Zhao H, Geng M, Wang N, Hu S. Multiomics and machine learning-based analysis of pancancer pseudouridine modifications. Discov Oncol 2024;15:361. [PMID: 39162904 PMCID: PMC11335713 DOI: 10.1007/s12672-024-01093-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 06/12/2024] [Indexed: 08/21/2024]  Open
28
Górczak K, Burzykowski T, Claesen J. A varying-coefficient model for the analysis of methylation sequencing data. Comput Biol Chem 2024;111:108094. [PMID: 38781748 DOI: 10.1016/j.compbiolchem.2024.108094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
29
Xiong HY, Wyns A, Campenhout JV, Hendrix J, De Bruyne E, Godderis L, Schabrun S, Nijs J, Polli A. Epigenetic Landscapes of Pain: DNA Methylation Dynamics in Chronic Pain. Int J Mol Sci 2024;25:8324. [PMID: 39125894 PMCID: PMC11312850 DOI: 10.3390/ijms25158324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/19/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024]  Open
30
Bai X, Yao HC, Wu B, Liu LR, Ding YY, Xiao CL. DeepBAM: a high-accuracy single-molecule CpG methylation detection tool for Oxford nanopore sequencing. Brief Bioinform 2024;25:bbae413. [PMID: 39177264 PMCID: PMC11342253 DOI: 10.1093/bib/bbae413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 07/29/2024] [Accepted: 08/05/2024] [Indexed: 08/24/2024]  Open
31
Cucoreanu C, Tigu AB, Nistor M, Moldovan RC, Pralea IE, Iacobescu M, Iuga CA, Szabo R, Dindelegan GC, Ciuce C. Epigenetic and Molecular Alterations in Obesity: Linking CRP and DNA Methylation to Systemic Inflammation. Curr Issues Mol Biol 2024;46:7430-7446. [PMID: 39057082 PMCID: PMC11275580 DOI: 10.3390/cimb46070441] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024]  Open
32
Ao X, Parisien M, Fillingim RB, Ohrbach R, Slade GD, Diatchenko L, Smith SB. Whole-genome methylation profiling reveals regions associated with painful temporomandibular disorders and active recovery processes. Pain 2024;165:1060-1073. [PMID: 38015635 PMCID: PMC11018476 DOI: 10.1097/j.pain.0000000000003104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 08/24/2023] [Indexed: 11/30/2023]
33
Lee MK, Azizgolshani N, Zhang Z, Perreard L, Kolling FW, Nguyen LN, Zanazzi GJ, Salas LA, Christensen BC. Associations in cell type-specific hydroxymethylation and transcriptional alterations of pediatric central nervous system tumors. Nat Commun 2024;15:3635. [PMID: 38688903 PMCID: PMC11061294 DOI: 10.1038/s41467-024-47943-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024]  Open
34
Teschendorff AE. On epigenetic stochasticity, entropy and cancer risk. Philos Trans R Soc Lond B Biol Sci 2024;379:20230054. [PMID: 38432318 PMCID: PMC10909509 DOI: 10.1098/rstb.2023.0054] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 09/26/2023] [Indexed: 03/05/2024]  Open
35
Toh H, Sasaki H. Spatiotemporal DNA methylation dynamics shape megabase-scale methylome landscapes. Life Sci Alliance 2024;7:e202302403. [PMID: 38233073 PMCID: PMC10794778 DOI: 10.26508/lsa.202302403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 01/19/2024]  Open
36
Zhang S, Ma B, Liu Y, Shen Y, Li D, Liu S, Song F. Predicting locus-specific DNA methylation levels in cancer and paracancer tissues. Epigenomics 2024;16:549-570. [PMID: 38477028 PMCID: PMC11158003 DOI: 10.2217/epi-2023-0114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 02/20/2024] [Indexed: 03/14/2024]  Open
37
Taglini F, Kafetzopoulos I, Rolls W, Musialik KI, Lee HY, Zhang Y, Marenda M, Kerr L, Finan H, Rubio-Ramon C, Gautier P, Wapenaar H, Kumar D, Davidson-Smith H, Wills J, Murphy LC, Wheeler A, Wilson MD, Sproul D. DNMT3B PWWP mutations cause hypermethylation of heterochromatin. EMBO Rep 2024;25:1130-1155. [PMID: 38291337 PMCID: PMC7615734 DOI: 10.1038/s44319-024-00061-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024]  Open
38
Tiedemann RL, Hrit J, Du Q, Wiseman AK, Eden HE, Dickson BM, Kong X, Chomiak AA, Vaughan RM, Hebert JM, David Y, Zhou W, Baylin SB, Jones PA, Clark SJ, Rothbart SB. UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580169. [PMID: 38405904 PMCID: PMC10888769 DOI: 10.1101/2024.02.13.580169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
39
Gu M, Ren B, Fang Y, Ren J, Liu X, Wang X, Zhou F, Xiao R, Luo X, You L, Zhao Y. Epigenetic regulation in cancer. MedComm (Beijing) 2024;5:e495. [PMID: 38374872 PMCID: PMC10876210 DOI: 10.1002/mco2.495] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/21/2024]  Open
40
Gao Y, Zhou N, Liu J. Ovarian Cancer Diagnosis and Prognosis Based on Cell-Free DNA Methylation. Cancer Control 2024;31:10732748241255548. [PMID: 38764160 PMCID: PMC11104031 DOI: 10.1177/10732748241255548] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/12/2024] [Accepted: 04/30/2024] [Indexed: 05/21/2024]  Open
41
Verdikt R, Thienpont B. Epigenetic remodelling under hypoxia. Semin Cancer Biol 2024;98:1-10. [PMID: 38029868 DOI: 10.1016/j.semcancer.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
42
Guo J, Zhao M, Chen C, Wang F, Chen Z. A laser-induced graphene-based electrochemical immunosensor for nucleic acid methylation detection. Analyst 2023;149:137-147. [PMID: 37986634 DOI: 10.1039/d3an01628e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
43
Xue X, Wang Z, Wang Y, Zhou X. Disease Diagnosis Based on Nucleic Acid Modifications. ACS Chem Biol 2023;18:2114-2127. [PMID: 37527510 DOI: 10.1021/acschembio.3c00251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
44
Ashouri A, Zhang C, Gaiti F. Decoding Cancer Evolution: Integrating Genetic and Non-Genetic Insights. Genes (Basel) 2023;14:1856. [PMID: 37895205 PMCID: PMC10606072 DOI: 10.3390/genes14101856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023]  Open
45
Liang WW, Lu RJH, Jayasinghe RG, Foltz SM, Porta-Pardo E, Geffen Y, Wendl MC, Lazcano R, Kolodziejczak I, Song Y, Govindan A, Demicco EG, Li X, Li Y, Sethuraman S, Payne SH, Fenyö D, Rodriguez H, Wiznerowicz M, Shen H, Mani DR, Rodland KD, Lazar AJ, Robles AI, Ding L. Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin. Cancer Cell 2023;41:1567-1585.e7. [PMID: 37582362 PMCID: PMC11613269 DOI: 10.1016/j.ccell.2023.07.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 05/30/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
46
Okletey J, Angelis D, Jones TM, Montagna C, Spiliotis ET. An oncogenic isoform of septin 9 promotes the formation of juxtanuclear invadopodia by reducing nuclear deformability. Cell Rep 2023;42:112893. [PMID: 37516960 PMCID: PMC10530659 DOI: 10.1016/j.celrep.2023.112893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/17/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023]  Open
47
Zheng Y, Ziman B, Ho AS, Sinha UK, Xu LY, Li EM, Koeffler HP, Berman BP, Lin DC. Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation. Genome Biol 2023;24:193. [PMID: 37620896 PMCID: PMC10463844 DOI: 10.1186/s13059-023-03035-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]  Open
48
Jeong S, Cho S, Yang SK, Oh SA, Kang YK. Parallel shift of DNA methylation and gene expression toward the mean in mouse spleen with aging. Aging (Albany NY) 2023;15:6690-6709. [PMID: 37494662 PMCID: PMC10415566 DOI: 10.18632/aging.204903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/06/2023] [Indexed: 07/28/2023]
49
Guo H, Vuille JA, Wittner BS, Lachtara EM, Hou Y, Lin M, Zhao T, Raman AT, Russell HC, Reeves BA, Pleskow HM, Wu CL, Gnirke A, Meissner A, Efstathiou JA, Lee RJ, Toner M, Aryee MJ, Lawrence MS, Miyamoto DT, Maheswaran S, Haber DA. DNA hypomethylation silences anti-tumor immune genes in early prostate cancer and CTCs. Cell 2023;186:2765-2782.e28. [PMID: 37327786 PMCID: PMC10436379 DOI: 10.1016/j.cell.2023.05.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/09/2023] [Accepted: 05/17/2023] [Indexed: 06/18/2023]
50
Okletey J, Angelis D, Jones TM, Montagna C, Spiliotis ET. An oncogenic isoform of septin 9 promotes the formation of juxtanuclear invadopodia by reducing nuclear deformability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.18.545473. [PMID: 37398172 PMCID: PMC10312791 DOI: 10.1101/2023.06.18.545473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
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