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Twin study: genotype-dependent epigenetic factors affecting free thyroxine levels in the normal range. 双胞胎研究：影响正常范围内游离甲状腺素水平的基因型依赖性表观遗传因素。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-02-01 Epub Date: 2024-01-24 DOI: 10.2217/epi-2023-0372
Saki Yoshioka, Yuya Arakawa, Mika Hasegawa, Shiho Kato, Hinako Hashimoto, Saho Mori, Hiromichi Ueda, Mikio Watanabe
{"title":"Twin study: genotype-dependent epigenetic factors affecting free thyroxine levels in the normal range.","authors":"Saki Yoshioka, Yuya Arakawa, Mika Hasegawa, Shiho Kato, Hinako Hashimoto, Saho Mori, Hiromichi Ueda, Mikio Watanabe","doi":"10.2217/epi-2023-0372","DOIUrl":"10.2217/epi-2023-0372","url":null,"abstract":"<p><p><b>Aim:</b> To explore the clinical application of DNA methylation affecting thyroid function, we evaluated the association of DNA methylation with free thyroxine (FT4) and TSH measurements in monozygotic twins. <b>Materials & methods:</b> Discordant pairs for FT4 or TSH levels were examined for the relationship between the within-pair difference of each measurement and the DNA methylation levels using epigenome-wide association studies. The contribution of polymorphisms to the methylation sensitivity was also examined. <b>Results:</b> We found two CpG sites significantly associated with FT4 levels, and also some CpG sites showing significant differences in their methylation levels within FT4-discordant pairs depending on the polymorphism in <i>EPHB2</i>. <b>Conclusion:</b> The FT4 level may be associated with a combination of methylation and polymorphisms in the <i>EPHB2</i> gene.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"147-158"},"PeriodicalIF":3.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139542201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
SET protein as an epigenetics target. 作为表观遗传学靶标的 SET 蛋白。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-02-01 Epub Date: 2023-12-22 DOI: 10.2217/epi-2023-0297
Gabriel da Silva, Thaís Moré Milan, Pablo Shimaoka Chagas, Glauce Lunardelli Trevisan, Camila Lopes Ferraz, Andréia Machado Leopoldino
{"title":"SET protein as an epigenetics target.","authors":"Gabriel da Silva, Thaís Moré Milan, Pablo Shimaoka Chagas, Glauce Lunardelli Trevisan, Camila Lopes Ferraz, Andréia Machado Leopoldino","doi":"10.2217/epi-2023-0297","DOIUrl":"10.2217/epi-2023-0297","url":null,"abstract":"<p><p>The SET gene has four transcripts reported in NCBI, coding two isoforms of SET proteins. The most known function of SET protein is inhibiting protein phosphatase 2A, a tumor suppressor, which has been associated with different biological processes. In this review, our focus was on exploring the other SET functions related to epigenetic mechanisms, which impact cellular migration, cell cycle and apoptosis.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"249-257"},"PeriodicalIF":3.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138828925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
microRNAs and their therapeutic strategy in phase I and phase II clinical trials. I 期和 II 期临床试验中的 microRNAs 及其治疗策略。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-02-01 Epub Date: 2024-02-05 DOI: 10.2217/epi-2023-0363
Ameya Kp, Kumaravel Kaliaperumal, Durairaj Sekar
{"title":"microRNAs and their therapeutic strategy in phase I and phase II clinical trials.","authors":"Ameya Kp, Kumaravel Kaliaperumal, Durairaj Sekar","doi":"10.2217/epi-2023-0363","DOIUrl":"10.2217/epi-2023-0363","url":null,"abstract":"<p><p>miRNAs play a crucial therapeutic role in diseases such as cancer, diabetes and viral infections, with around 1900 identified in the human genome. Some have progressed to clinical trials, and miRNA mimics and miRNA inhibitors are pivotal therapeutic molecules undergoing evaluation. The review delves into various miRNA-associated clinical trials, emphasizing their precision in targeting specific genes, modulating disease pathways and diagnostic potential. This underscores the importance of miRNA therapy, foreseeing innovations in precision medicine techniques for diverse diseases. The future envisions improved delivery systems addressing challenges like immunogenicity and digestion, while a comprehensive miRNA-based omics database could guide the development of tailored antisense miRNAs, further advancing precision medicine strategies.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"259-271"},"PeriodicalIF":3.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139680924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Hypomethylation of Wnt signaling regulator genes in developmental language disorder. 发育性语言障碍中 Wnt 信号调节基因的低甲基化。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-02-01 Epub Date: 2024-01-24 DOI: 10.2217/epi-2023-0345
Mary Iype, Nisha Melempatt, Jesmy James, Sanjeev V Thomas, Ayyappan Anitha
{"title":"Hypomethylation of Wnt signaling regulator genes in developmental language disorder.","authors":"Mary Iype, Nisha Melempatt, Jesmy James, Sanjeev V Thomas, Ayyappan Anitha","doi":"10.2217/epi-2023-0345","DOIUrl":"10.2217/epi-2023-0345","url":null,"abstract":"<p><p><b>Background:</b> Developmental language disorder (DLD) is a neurodevelopmental disorder. Considering the pivotal role of epigenetics in neurodevelopment, we examined any altered DNA methylation between DLD and control subjects. <b>Materials & methods:</b> We looked into genome-wide methylation differences between DLD and control groups. The findings were validated by quantitative PCR (qPCR). <b>Results:</b> In the DLD group, differential methylation of CpG sites was observed in the Wnt signaling regulator genes <i>APCDD1</i>, <i>AMOTL1</i>, <i>LRP5</i>, <i>MARK2</i>, <i>TMEM64</i>, <i>TRABD2B</i>, <i>VEPH1</i> and <i>WNT2B</i>. Hypomethylation of <i>APCDD1</i>, <i>LRP5</i> and <i>WNT2B</i> was confirmed by qPCR. <b>Conclusion:</b> This is the first report associating Wnt signaling with DLD. The findings are relevant in the light of the essential role of Wnt in myelination, and of the altered myelination in DLD.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"137-146"},"PeriodicalIF":3.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139542200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Defining familial longevity and developing a familial longevity score for unbiased epigenetic studies in a birth cohort. 定义家族长寿，为出生队列中无偏见的表观遗传学研究制定家族长寿评分。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-09-12 DOI: 10.1080/17501911.2024.2370760
Jasmin C Pflaum, Vincent D Gaertner, Susanne Brandstetter, Christian Apfelbacher, Michael Melter, Angela Koeninger, Michael Kabesch
{"title":"Defining familial longevity and developing a familial longevity score for unbiased epigenetic studies in a birth cohort.","authors":"Jasmin C Pflaum, Vincent D Gaertner, Susanne Brandstetter, Christian Apfelbacher, Michael Melter, Angela Koeninger, Michael Kabesch","doi":"10.1080/17501911.2024.2370760","DOIUrl":"10.1080/17501911.2024.2370760","url":null,"abstract":"<p><p><b>Aim:</b> Longevity accumulating in families has genetic and epigenetic components. To study early and unbiased epigenetic predictors of longevity prospectively, a birth cohort would be ideal. However, the original family longevity selection score (FLoSS) focuses on populations of elderly only.<b>Methods:</b> In the German birth cohort KUNO-Kids we assessed when information for such scores may be best collected and how to calculate an adapted FLoSS.<b>Results:</b> A total of 551 families contributed to adapted FLoSS, with a mean score of -0.15 (SD 2.33). Adapted FLoSS ≥7 as a marker of exceptional longevity occurred in 3.3% of families, comparable to original FLoSS in elderly.<b>Conclusion:</b> An adapted FLoSS from data collectable postnatally may be a feasible tool to study unbiased epigenetic predictors for longevity.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1149-1158"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457659/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142282447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Epigenomic newborn screening for conditions with intellectual disability and autistic features in Australian newborns. 澳大利亚新生儿智力障碍和自闭症特征的表观基因组学新生儿筛查。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-10-04 DOI: 10.1080/17501911.2024.2402681
Mohammed Alshawsh, Melissa Wake, Jozef Gecz, Mark Corbett, Richard Saffery, James Pitt, Ronda Greaves, Katrina Williams, Michael Field, Jeanie Cheong, Minh Bui, Sheena Arora, Simon Sadedin, Sebastian Lunke, Meg Wall, David J Amor, David E Godler
{"title":"Epigenomic newborn screening for conditions with intellectual disability and autistic features in Australian newborns.","authors":"Mohammed Alshawsh, Melissa Wake, Jozef Gecz, Mark Corbett, Richard Saffery, James Pitt, Ronda Greaves, Katrina Williams, Michael Field, Jeanie Cheong, Minh Bui, Sheena Arora, Simon Sadedin, Sebastian Lunke, Meg Wall, David J Amor, David E Godler","doi":"10.1080/17501911.2024.2402681","DOIUrl":"10.1080/17501911.2024.2402681","url":null,"abstract":"<p><p>This study describes a protocol to assess a novel workflow called Epi-Genomic Newborn Screening (EpiGNs) on 100,000 infants from the state of Victoria, Australia. The workflow uses a first-tier screening approach called methylation-specific quantitative melt analysis (MS-QMA), followed by second and third tier testing including targeted methylation and copy number variation analyzes with droplet digital PCR, EpiTYPER system and low-coverage whole genome sequencing. EpiGNs utilizes only two 3.2 mm newborn blood spot punches to screen for genetic conditions, including fragile X syndrome, Prader-Willi syndrome, Angelman syndrome, Dup15q syndrome and sex chromosome aneuploidies. The program aims to: identify clinically actionable methylation screening thresholds for the first-tier screen and estimate prevalence for the conditions screened.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1203-1214"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11487350/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
circ_0006988 promotes gastric cancer cell proliferation, migration and invasion through miRNA-92a-2-5p/TFAP4 axis. circ_0006988通过miRNA-92a-2-5p/TFAP4轴促进胃癌细胞增殖、迁移和侵袭。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-10-14 DOI: 10.1080/17501911.2024.2410697
Yalin Mu, Juan Lu, Kai Yue, Shuoxin Yin, Ru Zhang, Chenghui Zhang
{"title":"circ_0006988 promotes gastric cancer cell proliferation, migration and invasion through miRNA-92a-2-5p/TFAP4 axis.","authors":"Yalin Mu, Juan Lu, Kai Yue, Shuoxin Yin, Ru Zhang, Chenghui Zhang","doi":"10.1080/17501911.2024.2410697","DOIUrl":"10.1080/17501911.2024.2410697","url":null,"abstract":"<p><p><b>Aim:</b> To explore precise function and underlying mechanism of circ_0006988 in gastric cancer (GC).<b>Materials & methods:</b> GC tissues were collected clinically, and GC cells were purchased from the company. Quantitative real-time polymerase chain reaction and western blot were used to detect mRNA and protein expression. Functional analysis was performed through CCK-8, Transwell and scratch experiment. Binding relationship was validated through dual luciferase reporter and RNA immunoprecipitation assays. HGC-27 cells were subcutaneously injected into mice to construct a xenograft tumor model.<b>Results:</b> In GC tissues and cells, circ_0006988 overexpressed, promoting proliferation, migration and invasion. MiRNA-92a-2-5p downregulation or <i>TFAP4</i> overexpression weakened effects of circ_0006988 silencing on GC progression.<b>Conclusion:</b> circ_0006988 facilitates GC development through miRNA-92a-2-5p/TFAP4 axis.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1287-1299"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11534138/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142461102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Epigenome-850K-wide profiling reveals peripheral blood differential methylation in term low birth weight. 表观基因组-850K全谱分析揭示了足月低体重儿的外周血甲基化差异。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-07-03 DOI: 10.1080/17501911.2024.2358744
Jing Liu, Qi Sun, Die Liu, Haixiao Liang, Yuanmei Chen, Fang Ye, Qi Zhang
{"title":"Epigenome-850K-wide profiling reveals peripheral blood differential methylation in term low birth weight.","authors":"Jing Liu, Qi Sun, Die Liu, Haixiao Liang, Yuanmei Chen, Fang Ye, Qi Zhang","doi":"10.1080/17501911.2024.2358744","DOIUrl":"10.1080/17501911.2024.2358744","url":null,"abstract":"<p><p><b>Aim:</b> We investigate the genome-wide DNA methylation (DNAm) patterns of term low birth weight (TLBW) neonates.<b>Methods:</b> In the discovery phase, we assayed 32 samples (TLBW/control:16/16) using the EPIC 850k BeadChip Array. Targeted pyrosequencing of in 60 samples (TLBW/control:28/32) using targeted pyrosequencing during the replication phase.<b>Results:</b> The 850K array identified TLBW-associated 144 differentially methylated positions (DMPs) and 149 DMRs. Nearly 77% DMPs exhibited hypomethylation, located in the opensea and gene body regions. The most significantly enriched pathway in KEGG is sphingolipid metabolism (hsa00600), and the genes <i>GALC</i> and <i>SGMS1</i> related to this pathway both show hypomethylation.<b>Conclusion:</b> Our analysis provides evidence of genome-wide DNAm alterations in TLBW. Further investigations are needed to elucidate the functional significance of these DNAm changes.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"821-833"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11370964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141491381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Matched analysis of detailed peripheral blood and tumor immune microenvironment profiles in bladder cancer. 膀胱癌外周血和肿瘤免疫微环境详细图谱的匹配分析。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-01-15 DOI: 10.2217/epi-2023-0358
Ji-Qing Chen, Lucas A Salas, John K Wiencke, Devin C Koestler, Annette M Molinaro, Angeline S Andrew, John D Seigne, Margaret R Karagas, Karl T Kelsey, Brock C Christensen
{"title":"Matched analysis of detailed peripheral blood and tumor immune microenvironment profiles in bladder cancer.","authors":"Ji-Qing Chen, Lucas A Salas, John K Wiencke, Devin C Koestler, Annette M Molinaro, Angeline S Andrew, John D Seigne, Margaret R Karagas, Karl T Kelsey, Brock C Christensen","doi":"10.2217/epi-2023-0358","DOIUrl":"10.2217/epi-2023-0358","url":null,"abstract":"<p><p><b>Background:</b> Bladder cancer and therapy responses hinge on immune profiles in the tumor microenvironment (TME) and blood, yet studies linking tumor-infiltrating immune cells to peripheral immune profiles are limited. <b>Methods:</b> DNA methylation cytometry quantified TME and matched peripheral blood immune cell proportions. With tumor immune profile data as the input, subjects were grouped by immune infiltration status and consensus clustering. <b>Results:</b> Immune hot and cold groups had different immune compositions in the TME but not in circulating blood. Two clusters of patients identified with consensus clustering had different immune compositions not only in the TME but also in blood. <b>Conclusion:</b> Detailed immune profiling via methylation cytometry reveals the significance of understanding tumor and systemic immune relationships in cancer patients.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"41-56"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10804212/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139466496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Decoding the year of 2023: welcome to the 16th Volume of Epigenomics. 解码2023年:欢迎阅读第16卷表观基因组学。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2023-11-27 DOI: 10.2217/epi-2023-0394
Man-Hong Leung
{"title":"Decoding the year of 2023: welcome to the 16th Volume of <i>Epigenomics</i>.","authors":"Man-Hong Leung","doi":"10.2217/epi-2023-0394","DOIUrl":"10.2217/epi-2023-0394","url":null,"abstract":"","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1-4"},"PeriodicalIF":3.8,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138440433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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