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Toward a more holistic approach to the study of exposures and child outcomes. 以更全面的方法研究暴露与儿童结果。
IF 3 4区 医学
Epigenomics Pub Date : 2024-03-14 DOI: 10.2217/epi-2023-0424
Barry M Lester, Marie Camerota, Todd M Everson, Coral L Shuster, Carmen J Marsit
{"title":"Toward a more holistic approach to the study of exposures and child outcomes.","authors":"Barry M Lester, Marie Camerota, Todd M Everson, Coral L Shuster, Carmen J Marsit","doi":"10.2217/epi-2023-0424","DOIUrl":"10.2217/epi-2023-0424","url":null,"abstract":"<p><p><b>Aim:</b> The current work was designed to demonstrate the application of the exposome framework in examining associations between exposures and children's long-term neurodevelopmental and behavioral outcomes. <b>Methods:</b> Longitudinal data were collected from birth through age 6 from 402 preterm infants. Three statistical methods were utilized to demonstrate the exposome framework: exposome-wide association study, cumulative exposure and machine learning models, with and without epigenetic data. <b>Results:</b> Each statistical approach answered a distinct research question regarding the impact of exposures on longitudinal child outcomes. Findings highlight associations between exposures, epigenetics and executive function. <b>Conclusion:</b> Findings demonstrate how an exposome-based approach can be utilized to understand relationships between internal (e.g., DNA methylation) and external (e.g., prenatal risk) exposures and long-term developmental outcomes in preterm children.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11157992/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140119139","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
Predicting locus-specific DNA methylation levels in cancer and paracancer tissues. 预测癌症和癌旁组织中基因座特异性 DNA 甲基化水平
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-03-13 DOI: 10.2217/epi-2023-0114
Shuzheng Zhang, Baoshan Ma, Yu Liu, Yiwen Shen, Di Li, Shuxin Liu, Fengju Song
{"title":"Predicting locus-specific DNA methylation levels in cancer and paracancer tissues.","authors":"Shuzheng Zhang, Baoshan Ma, Yu Liu, Yiwen Shen, Di Li, Shuxin Liu, Fengju Song","doi":"10.2217/epi-2023-0114","DOIUrl":"10.2217/epi-2023-0114","url":null,"abstract":"<p><p><b>Aim:</b> To predict base-resolution DNA methylation in cancerous and paracancerous tissues. <b>Material & methods:</b> We collected six cancer DNA methylation datasets from The Cancer Genome Atlas and five cancer datasets from Gene Expression Omnibus and established machine learning models using paired cancerous and paracancerous tissues. Tenfold cross-validation and independent validation were performed to demonstrate the effectiveness of the proposed method. <b>Results:</b> The developed cross-tissue prediction models can substantially increase the accuracy at more than 68% of CpG sites and contribute to enhancing the statistical power of differential methylation analyses. An XGBoost model leveraging multiple correlating CpGs may elevate the prediction accuracy. <b>Conclusion:</b> This study provides a powerful tool for DNA methylation analysis and has the potential to gain new insights into cancer research from epigenetics.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11158003/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140109702","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
Construction of a prognostic model based on genome-wide methylation analysis of miRNAs for hepatocellular carcinoma. 基于 miRNA 的全基因组甲基化分析构建肝细胞癌的预后模型。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-03-13 DOI: 10.2217/epi-2023-0365
Zhaoqi Shi, Xiaolong Liu, Duguang Li, Xiaoxiao Fan, Lifeng He, Daizhan Zhou, Hui Lin
{"title":"Construction of a prognostic model based on genome-wide methylation analysis of miRNAs for hepatocellular carcinoma.","authors":"Zhaoqi Shi, Xiaolong Liu, Duguang Li, Xiaoxiao Fan, Lifeng He, Daizhan Zhou, Hui Lin","doi":"10.2217/epi-2023-0365","DOIUrl":"10.2217/epi-2023-0365","url":null,"abstract":"<p><p><b>Aim:</b> Using the methylation level of miRNA genes to develop a prognostic model for patients with hepatocellular carcinoma (HCC). <b>Materials & methods:</b> least absolute shrinkage and selection operator and multivariate Cox regression analyses were performed to develop a prognostic model. One miRNA in the model was selected for verification. <b>Results:</b> A prognostic model was developed using eight miRNAs. The areas under the curve for predicting overall survival at 1, 3 and 5 years were 0.75, 0.81 and 0.81. miR-223 was found to be hypomethylated in 160 HCC tissues, and its methylation level was associated with Barcelona Clinic Liver Cancer stages and the prognosis of patients with HCC. <b>Conclusion:</b> The prognostic model based on miRNA methylation levels has the capability to partially forecast the prognosis of patients with HCC.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11160443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140109701","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
Methylation changes of liver DNA during the formation of gallstones. 胆结石形成过程中肝脏 DNA 的甲基化变化
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-03-06 DOI: 10.2217/epi-2023-0391
Junbin Peng, Haojie Li, Fang Tong, Jinlong Hu, Min Li, Gan Chen, Dongquan Liu, Jinshan Liu, Rui Wang, Hongyu Xu, Xuanxuan Li, Xinguo Zhong, Jiaming Yao, Baoqiang Cao
{"title":"Methylation changes of liver DNA during the formation of gallstones.","authors":"Junbin Peng, Haojie Li, Fang Tong, Jinlong Hu, Min Li, Gan Chen, Dongquan Liu, Jinshan Liu, Rui Wang, Hongyu Xu, Xuanxuan Li, Xinguo Zhong, Jiaming Yao, Baoqiang Cao","doi":"10.2217/epi-2023-0391","DOIUrl":"10.2217/epi-2023-0391","url":null,"abstract":"<p><p><b>Aim:</b> To explore the overall methylation changes in liver tissues during the formation of gallstones, as well as the key pathways and genes involved in the process. <b>Methods:</b> Reduced-representation bisulfite sequencing and RNA sequencing were conducted on the liver tissues of mice with gallstones and control normal mice. <b>Results:</b> A total of 8705 differentially methylated regions in CpG and 1410 differentially expressed genes were identified. The joint analysis indicated that aberrant DNA methylation may be associated with dysregulated gene expression in key pathways such as cholesterol metabolism and bile secretion. <b>Conclusion:</b> We propose for the first time that methylation changes in some key pathway genes in liver tissue may be involved in the formation of gallstones.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11160444/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039008","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
Neural tube defects and epigenetics: role of histone post-translational histone modifications. 神经管缺陷与表观遗传学：组蛋白翻译后修饰的作用。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-03-01 Epub Date: 2024-02-27 DOI: 10.2217/epi-2023-0357
Rosa Pardo V, Richard H Finnell, M Elizabeth Ross, Pablo Alarcón, José Suazo
{"title":"Neural tube defects and epigenetics: role of histone post-translational histone modifications.","authors":"Rosa Pardo V, Richard H Finnell, M Elizabeth Ross, Pablo Alarcón, José Suazo","doi":"10.2217/epi-2023-0357","DOIUrl":"10.2217/epi-2023-0357","url":null,"abstract":"<p><p>Neural tube defects (NTDs) are the most common congenital anomalies of the CNS. It is widely appreciated that both genetic and environmental factors contribute to their etiology. The inability to ascribe clear genetic patterns of inheritance to various NTD phenotypes suggests it is possible that epigenetic mechanisms are involved in the etiology of NTDs. In this context, the contribution of DNA methylation as an underlying contributing factor to the etiology of NTDs has been extensively reviewed. Here, an updated accounting of the evidence linking post-translational histone modifications to these birth defects, relying heavily upon studies in humans, and the possible molecular implications inferred from reports based on cellular and animal models, are presented.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"419-426"},"PeriodicalIF":3.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139971500","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
The study of HMOX1 DNA methylation and gene expression and the diagnostic potential of miR-153-3p in preeclampsia. 子痫前期 HMOX1 DNA 甲基化和基因表达的研究以及 miR-153-3p 的诊断潜力。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-03-01 Epub Date: 2024-02-27 DOI: 10.2217/epi-2023-0377
Somayeh Rahimi, Nayebali Rezvani, Saeed Khazayel, Nazanin Jalilian, Ebrahim Shakiba, Fatemeh Khadir, Kheirollah Yari, Zohreh Rahimi
{"title":"The study of <i>HMOX1</i> DNA methylation and gene expression and the diagnostic potential of <i>miR-153-3p</i> in preeclampsia.","authors":"Somayeh Rahimi, Nayebali Rezvani, Saeed Khazayel, Nazanin Jalilian, Ebrahim Shakiba, Fatemeh Khadir, Kheirollah Yari, Zohreh Rahimi","doi":"10.2217/epi-2023-0377","DOIUrl":"10.2217/epi-2023-0377","url":null,"abstract":"<p><p><b>Background:</b> The objective was to elucidate the potential epigenetic regulatory mechanism in <i>HMOX1</i> expression in preeclampsia. <b>Materials & methods:</b> <i>HMOX1</i> promoter DNA methylation was evaluated in the placental tissue and blood of preeclamptic and normotensive pregnant women. <i>HMOX1</i> and <i>miR-153-3p</i> gene expression were assessed in placental tissue and peripheral blood mononuclear cells (PBMCs). Related microarray datasets in the Gene Expression Omnibus database were also analyzed. <b>Results:</b> In placental tissue, despite <i>HMOX1</i> expression downregulation, there was no significant change in <i>HMOX1</i> methylation. In PBMCs, there was no significant alteration in <i>HMOX1</i> expression, while hypomethylation was observed in blood. The <i>miR-153-3p</i> expression increased in the placental tissue and in the PBMCs of preeclampsia. <b>Conclusion:</b> DNA methylation does not affect <i>HMOX1</i> expression, while <i>miR-153-3p</i> might be a biomarker for preeclampsia.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"389-401"},"PeriodicalIF":3.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139971501","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
Epigenetic disruption of histone deacetylase-2 accelerated apoptotic signaling and retarded malignancy in gastric cells. 组蛋白去乙酰化酶-2的表观遗传学破坏加速了胃细胞的凋亡信号转导并延缓了其恶变。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-03-01 Epub Date: 2024-02-15 DOI: 10.2217/epi-2023-0350
Sayedeh Azimeh Hosseini, Mahdi Ghatrehsamani, Hajar Yaghoobi, Fatemeh Elahian, Seyed Abbas Mirzaei
{"title":"Epigenetic disruption of histone deacetylase-2 accelerated apoptotic signaling and retarded malignancy in gastric cells.","authors":"Sayedeh Azimeh Hosseini, Mahdi Ghatrehsamani, Hajar Yaghoobi, Fatemeh Elahian, Seyed Abbas Mirzaei","doi":"10.2217/epi-2023-0350","DOIUrl":"10.2217/epi-2023-0350","url":null,"abstract":"<p><p><b>Background:</b> The objective of this research was to determine whether HDAC2 function is associated with gastric cancer progression. <b>Methods:</b> HDAC2 was knocked out in EPG85.257 cells using CRISPR/Cas9 and tumorigenesis pathways were evaluated. <b>Results:</b> Cell proliferation, colony formation, wound healing and transwell invasion were inhibited in ΔHDAC2:EPG85.257 cells. Quantitative analyses revealed a significant downregulation of MMP1, p53, Bax, MAPK1, MAPK3, pro-Caspase3, ERK1/2, p-ERK1/2, AKT1/2/3, p-AKT1/2/3, p-NF-κB (p65), Twist, Snail and p-FAK transcripts/proteins, while SIRT1, PTEN, p21 and Caspase3 were upregulated in ΔHDAC2:EPG85.257 cells. <b>Conclusion:</b> These results indicated that HDAC2 enhanced migration, colony formation and transmigration ability. HDAC2 inhibition may improve gastric cancer chemotherapy pathways.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"277-292"},"PeriodicalIF":3.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139734834","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
Alteration of DNA methyltransferases by eribulin elicits broad DNA methylation changes with potential therapeutic implications for triple-negative breast cancer. 艾瑞布林对DNA甲基转移酶的改变引起了广泛的DNA甲基化变化，对三阴性乳腺癌具有潜在的治疗意义。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-03-01 Epub Date: 2024-02-15 DOI: 10.2217/epi-2023-0339
Meisam Bagheri, Min Kyung Lee, Kristen E Muller, Todd W Miller, Diwakar R Pattabiraman, Brock C Christensen
{"title":"Alteration of DNA methyltransferases by eribulin elicits broad DNA methylation changes with potential therapeutic implications for triple-negative breast cancer.","authors":"Meisam Bagheri, Min Kyung Lee, Kristen E Muller, Todd W Miller, Diwakar R Pattabiraman, Brock C Christensen","doi":"10.2217/epi-2023-0339","DOIUrl":"10.2217/epi-2023-0339","url":null,"abstract":"<p><p><b>Background:</b> Triple-negative breast cancer (TNBC) is an aggressive disease with limited treatment options. Eribulin, a chemotherapeutic drug, induces epigenetic changes in cancer cells, suggesting a unique mechanism of action. <b>Materials & methods:</b> MDA-MB 231 cells were treated with eribulin and paclitaxel, and the samples from 53 patients treated with neoadjuvant eribulin were compared with those from 14 patients who received the standard-of-care treatment using immunohistochemistry. <b>Results:</b> Eribulin treatment caused significant DNA methylation changes in drug-tolerant persister TNBC cells, and it also elicited changes in the expression levels of epigenetic modifiers (DNMT1, TET1, DNMT3A/B) <i>in vitro</i> and in primary TNBC tumors. <b>Conclusion:</b> These findings provide new insights into eribulin's mechanism of action and potential biomarkers for predicting TNBC treatment response.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"293-308"},"PeriodicalIF":3.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10910603/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139734833","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
Fatty acid metabolism-related lncRNA prognostic signature for serous ovarian carcinoma. 浆液性卵巢癌脂肪酸代谢相关lncRNA预后特征
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-03-01 Epub Date: 2024-02-15 DOI: 10.2217/epi-2023-0388
Lele Ye, Zhuofeng Jiang, Mengxia Zheng, Kan Pan, Jingru Lian, Bing Ju, Xuefei Liu, Sangsang Tang, Gangqiang Guo, Songfa Zhang, Xin Hong, Weiguo Lu
{"title":"Fatty acid metabolism-related lncRNA prognostic signature for serous ovarian carcinoma.","authors":"Lele Ye, Zhuofeng Jiang, Mengxia Zheng, Kan Pan, Jingru Lian, Bing Ju, Xuefei Liu, Sangsang Tang, Gangqiang Guo, Songfa Zhang, Xin Hong, Weiguo Lu","doi":"10.2217/epi-2023-0388","DOIUrl":"10.2217/epi-2023-0388","url":null,"abstract":"<p><p><b>Background:</b> To explore the role of fatty acid metabolism (FAM)-related lncRNAs in the prognosis and antitumor immunity of serous ovarian cancer (SOC). <b>Materials & methods:</b> A SOC FAM-related lncRNA risk model was developed and evaluated by a series of analyses. Additional immune-related analyses were performed to further assess the associations between immune state, tumor microenvironment and the prognostic risk model. <b>Results:</b> Five lncRNAs associated with the FAM genes were found and used to create a predictive risk model. The patients with a low-risk profile exhibited favorable prognostic outcomes. <b>Conclusion:</b> The established prognostic risk model exhibits better predictive capabilities for the prognosis of patients with SOC and offers novel potential therapy targets for SOC.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"309-329"},"PeriodicalIF":3.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139734835","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
DNMT3L interacts with Piwi and modulates the expression of piRNAs in transgenic Drosophila. DNMT3L 与 Piwi 相互作用并调节转基因果蝇中 piRNA 的表达。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-03-01 Epub Date: 2024-03-05 DOI: 10.2217/epi-2023-0405
Ramisetti Rajeev, Rakesh K Mishra, Sanjeev Khosla
{"title":"DNMT3L interacts with Piwi and modulates the expression of piRNAs in transgenic <i>Drosophila</i>.","authors":"Ramisetti Rajeev, Rakesh K Mishra, Sanjeev Khosla","doi":"10.2217/epi-2023-0405","DOIUrl":"10.2217/epi-2023-0405","url":null,"abstract":"<p><p><b>Aim:</b> To explore the role of Piwi protein and piRNAs in DNMT3L-mediated epigenetic inheritance. <b>Materials & methods:</b> Transgenic <i>Drosophila</i> were used to examine the effect of ectopically expressed DNMT3L on the profile of piRNAs by sequencing of small RNAs. <b>Results & conclusion:</b> Our previous work showed accumulation and inheritance of epimutations across multiple generations in transgenic DNMT3L <i>Drosophila</i>. Here, we show interaction of DNMT3L with Piwi and a significant alteration in the piRNA profile across multiple generations in transgenic <i>Drosophila</i>. In the light of its interaction with histone H1, we propose that in addition to its role of modulating core histone modifications, DNMT3L allows for inheritance of epigenetic information through its collaboration with Piwi, piRNAs and histone H1.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"375-388"},"PeriodicalIF":3.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140027808","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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