EpigenomicsPub Date : 2024-02-01Epub Date: 2023-12-19DOI: 10.2217/epi-2023-0279
Madia Lozupone, Vincenzo Solfrizzi, Rodolfo Sardone, Vittorio Dibello, Fabio Castellana, Roberta Zupo, Luisa Lampignano, Ilaria Bortone, Antonio Daniele, Francesco Panza
{"title":"The epigenetics of frailty.","authors":"Madia Lozupone, Vincenzo Solfrizzi, Rodolfo Sardone, Vittorio Dibello, Fabio Castellana, Roberta Zupo, Luisa Lampignano, Ilaria Bortone, Antonio Daniele, Francesco Panza","doi":"10.2217/epi-2023-0279","DOIUrl":"10.2217/epi-2023-0279","url":null,"abstract":"<p><p>The conceptual change of frailty, from a physical to a biopsychosocial phenotype, expanded the field of frailty, including social and behavioral domains with critical interaction between different frailty models. Environmental exposures - including physical exercise, psychosocial factors and diet - may play a role in the frailty pathophysiology. Complex underlying mechanisms involve the progressive interactions of genetics with epigenetics and of multimorbidity with environmental factors. Here we review the literature on possible mechanisms explaining the association between epigenetic hallmarks (i.e., global DNA methylation, DNA methylation age acceleration and microRNAs) and frailty, considered as biomarkers of aging. Frailty could be considered the result of environmental epigenetic factors on biological aging, caused by conflicting DNA methylation age and chronological age.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"189-202"},"PeriodicalIF":3.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138799266","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}
EpigenomicsPub Date : 2024-02-01Epub Date: 2024-02-06DOI: 10.2217/epi-2023-0100
Jun Li, Pei-Ting Li, Wei Wu, Bo-Ni Ding, Yan-Guang Wen, Hai-Lin Cai, Shuang-Xi Liu, Tao Hong, Jian-Fei Zhang, Jian-Da Zhou, Li-Yuan Qian, Juan Du
{"title":"POU2F2-mediated upregulation of lncRNA <i>PTPRG-AS1</i> inhibits ferroptosis in breast cancer via miR-376c-3p/SLC7A11 axis.","authors":"Jun Li, Pei-Ting Li, Wei Wu, Bo-Ni Ding, Yan-Guang Wen, Hai-Lin Cai, Shuang-Xi Liu, Tao Hong, Jian-Fei Zhang, Jian-Da Zhou, Li-Yuan Qian, Juan Du","doi":"10.2217/epi-2023-0100","DOIUrl":"10.2217/epi-2023-0100","url":null,"abstract":"<p><p><b>Background:</b> Triple-negative breast cancer (TNBC) is a subtype of BC with high rates of mortality. The mechanism of <i>PTPRG-AS1</i> in ferroptosis of TNBC was investigated. <b>Methods:</b> Chromatin immunoprecipitation and dual-luciferase reporter assays were used to measure intermolecular relationships. MTT and colony formation assays detected cell viability and proliferation. Kits detected Fe<sup>2+</sup> and reactive oxygen species levels. The role of PTPRG-AS1 in tumor growth was analyzed <i>in vivo</i>. <b>Results:</b> <i>PTPRG-AS1</i> was increased in TNBC tissues and cells. <i>PTPRG-AS1</i> silencing increased the reduction of glutathione and GPX4, increased Fe<sup>2+</sup> and reactive oxygen species in erastin-treated cells and inhibited proliferation. POU2F2 transcriptionally upregulated <i>PTPRG-AS1</i>. <i>PTPRG-AS1</i> targeted miR-376c-3p to upregulate <i>SLC7A11</i>. <i>PTPRG-AS1</i> knockdown suppressed tumor growth <i>in vivo</i>. <b>Conclusion:</b> POU2F2 transcriptionally activates <i>PTPRG-AS1</i> to modulate ferroptosis and proliferation by miR-376c-3p/SLC7A11, promoting TNBC.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"215-231"},"PeriodicalIF":3.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691541","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}
EpigenomicsPub Date : 2024-02-01Epub Date: 2024-02-12DOI: 10.2217/epi-2023-0406
Jing Hua, Miaomiao Chu, Chaohui Wang, Hangfan Zhang, Jing Luan, Yifei Zhang, Qiang Li, Taiwu Xiao, Chuansheng Zhu, Xuan Li, Bo Fu
{"title":"Digital PCR-based <i>GRHL2</i> methylation testing in acute myeloid leukemia: diagnosis, prognosis and monitoring.","authors":"Jing Hua, Miaomiao Chu, Chaohui Wang, Hangfan Zhang, Jing Luan, Yifei Zhang, Qiang Li, Taiwu Xiao, Chuansheng Zhu, Xuan Li, Bo Fu","doi":"10.2217/epi-2023-0406","DOIUrl":"10.2217/epi-2023-0406","url":null,"abstract":"<p><p><b>Background:</b> Acute myeloid leukemia (AML) is a challenging disease with high rates of recurrence. The role of the cancer-related gene <i>GRHL2</i> in AML has not been widely studied. <b>Methods:</b> Peripheral blood samples were collected from 73 AML patients and 68 healthy controls. Droplet digital PCR was used to detect <i>GRHL2</i> methylation levels to explore the value of <i>GRHL2</i> methylation in the diagnosis, treatment response and prognosis of AML. <b>Result:</b> <i>GRHL2</i> methylation was significantly increased in AML patients (p < 0.01), with high diagnostic accuracy (area under the curve: 0.848; p < 0.001). <i>GRHL2</i> methylation was correlated with chemotherapy response (p < 0.05) and is an independent prognostic factor for AML (p < 0.05). <b>Conclusion:</b> <i>GRHL2</i> methylation is expected to serve as a biomarker for diagnosing AML patients and predicting prognosis.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"233-247"},"PeriodicalIF":3.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139722175","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}
{"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}
EpigenomicsPub Date : 2024-02-01Epub Date: 2023-12-22DOI: 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}
EpigenomicsPub Date : 2024-02-01Epub Date: 2024-02-05DOI: 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}
EpigenomicsPub Date : 2024-02-01Epub Date: 2024-01-24DOI: 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}
EpigenomicsPub Date : 2024-01-01Epub Date: 2024-09-12DOI: 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}
EpigenomicsPub Date : 2024-01-01Epub Date: 2024-10-04DOI: 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}
EpigenomicsPub Date : 2024-01-01Epub Date: 2024-10-14DOI: 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}