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A review of single-cell transcriptomics and epigenomics studies in maternal and child health. 母婴健康中的单细胞转录组学和表观基因组学研究综述。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-05-06 DOI: 10.1080/17501911.2024.2343276
Chang Shu, Kelly Street, Carrie V Breton, Theresa M Bastain, Melissa L Wilson
{"title":"A review of single-cell transcriptomics and epigenomics studies in maternal and child health.","authors":"Chang Shu, Kelly Street, Carrie V Breton, Theresa M Bastain, Melissa L Wilson","doi":"10.1080/17501911.2024.2343276","DOIUrl":"10.1080/17501911.2024.2343276","url":null,"abstract":"<p><p>Single-cell sequencing technologies enhance our understanding of cellular dynamics throughout pregnancy. We outlined the workflow of single-cell sequencing techniques and reviewed single-cell studies in maternal and child health. We conducted a literature review of single cell studies on maternal and child health using PubMed. We summarized the findings from 16 single-cell atlases of the human and mammalian placenta across gestational stages and 31 single-cell studies on maternal exposures and complications including infection, obesity, diet, gestational diabetes, pre-eclampsia, environmental exposure and preterm birth. Single-cell studies provides insights on novel cell types in placenta and cell type-specific marks associated with maternal exposures and complications.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"775-793"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11318716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140852302","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
The fate and function of non-coding RNAs during necroptosis. 坏死过程中非编码 RNA 的命运和功能
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-06-17 DOI: 10.1080/17501911.2024.2354653
Esra Bozgeyik, Alperen Elek, Zekihan Gocer, Ibrahim Bozgeyik
{"title":"The fate and function of non-coding RNAs during necroptosis.","authors":"Esra Bozgeyik, Alperen Elek, Zekihan Gocer, Ibrahim Bozgeyik","doi":"10.1080/17501911.2024.2354653","DOIUrl":"10.1080/17501911.2024.2354653","url":null,"abstract":"<p><p>Necroptosis is a novel form of cell death which is activated when apoptotic cell death signals are disrupted. Accumulating body of observations suggests that noncoding RNAs, which are the lately discovered mystery of the human genome, are significantly associated with necroptotic signaling circuitry. The fate and function of miRNAs have been well documented in human disease, especially cancer. Recently, lncRNAs have gained much attention due to their diverse regulatory functions. Although available studies are currently based on bioinformatic analysis, predicted interactions desires further attention, as these hold significant promise and should not be overlooked. In the light of these, here we comprehensively review and discuss noncoding RNA molecules that play significant roles during execution of necroptotic cell death.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"901-915"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11370912/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141330599","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
Novel insights into sevoflurane-induced developmental neurotoxicity mechanisms. 七氟醚诱导发育神经毒性机制的新见解
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-09-24 DOI: 10.1080/17501911.2024.2395250
Tingting Gao, Zeqing Huang
{"title":"Novel insights into sevoflurane-induced developmental neurotoxicity mechanisms.","authors":"Tingting Gao, Zeqing Huang","doi":"10.1080/17501911.2024.2395250","DOIUrl":"10.1080/17501911.2024.2395250","url":null,"abstract":"<p><p><b>Aim:</b> This study explores Sevoflurane (Sevo)-induced neurotoxicity mechanisms in neonates through transcriptome sequencing and models.<b>Methods:</b> Seven-day-old mice were exposed to 3% Sevo, and hippocampal tissue was collected for analysis of differentially expressed lncRNAs and mRNAs compared with normal mice. MiR-152-3p was selected, and the interaction between H19, USP30, and miR-152-3p was explored in BV2 microglial cells and mouse hippocampal neurons.<b>Results:</b> Sevo disrupts mitochondrial autophagy via USP30 upregulation, exacerbating neurotoxicity and activating NLRP1 inflammasome-mediated inflammation.<b>Conclusion:</b> Sevo neurotoxicity is mediated through the H19/miR-152-3p/USP30 axis, implicating microglial regulation of neuronal pyroptosis.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1231-1252"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11485883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344109","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
Exploring the role of EZH2 modulation in shaping the tumor microenvironment. 探索 EZH2 调节在塑造肿瘤微环境中的作用。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-10-10 DOI: 10.1080/17501911.2024.2410693
Irene Fischetti, Michele De Luca, Elena Jachetti
{"title":"Exploring the role of EZH2 modulation in shaping the tumor microenvironment.","authors":"Irene Fischetti, Michele De Luca, Elena Jachetti","doi":"10.1080/17501911.2024.2410693","DOIUrl":"10.1080/17501911.2024.2410693","url":null,"abstract":"","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1265-1268"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11534139/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142461104","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
Epigenetic identification of LTBP4 as a putative tumor suppressor in breast cancer. 表观遗传学鉴定 LTBP4 为乳腺癌的假定肿瘤抑制因子。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-08-28 DOI: 10.1080/17501911.2024.2388017
Wenfeng He, Jingheng Zhang, Siyuan Wen, Ying Li, Lin Shen, Tiejun Zhou, Qinglian Wen, Yu Fan
{"title":"Epigenetic identification of LTBP4 as a putative tumor suppressor in breast cancer.","authors":"Wenfeng He, Jingheng Zhang, Siyuan Wen, Ying Li, Lin Shen, Tiejun Zhou, Qinglian Wen, Yu Fan","doi":"10.1080/17501911.2024.2388017","DOIUrl":"10.1080/17501911.2024.2388017","url":null,"abstract":"<p><p><b>Aim:</b> To explore the LTBP4's expression, prognostic significance and molecular mechanism of action in breast cancer (BC).<b>Methods:</b> On the basis of omics datasets and experiments, we conducted a synthetical analysis of LTBP4 in BC.<b>Results & conclusion:</b> LTBP4 was downregulated in BC with high promoter methylation and low genetic alteration. DNA methylation was negatively associated with LTBP4 mRNA expression. Higher LTBP4 associated with better survival. LTBP4 was enrichment in extracellular matrix receptor interactions, cell adhesion molecules, cell cycle and MAPK pathway. LTBP4 expression and methylation were positively and negatively associated with tumor infiltrating immune cells, respectively. In conclusion, LTBP4 is a putative tumor suppressor in BC, which expression is regulated by DNA methylation and relates with prognosis.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"999-1012"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11404579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142079780","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
Low expression levels of miRNA-155 and miRNA-499a are associated with obesity in Type 2 diabetes. miRNA-155 和 miRNA-499a 的低表达水平与 2 型糖尿病患者的肥胖有关。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-01-15 DOI: 10.2217/epi-2023-0320
Andrea Latini, Giada De Benedittis, Cinzia Ciccacci, Giuseppe Novelli, Vincenza Spallone, Paola Borgiani
{"title":"Low expression levels of miRNA-155 and miRNA-499a are associated with obesity in Type 2 diabetes.","authors":"Andrea Latini, Giada De Benedittis, Cinzia Ciccacci, Giuseppe Novelli, Vincenza Spallone, Paola Borgiani","doi":"10.2217/epi-2023-0320","DOIUrl":"10.2217/epi-2023-0320","url":null,"abstract":"<p><p><b>Background & aims:</b> This study investigated a possible correlation between three circulating miRNAs, previously observed to be associated to diabetic polyneuropathy, and the obesity condition. <b>Methods & results:</b> The expression levels of miR-128a, miR-155 and miR499a were evaluated in 49 participants with Type 2 diabetes, divided into different groups based on the presence or absence of obesity and central obesity. The analyses revealed a significant decrease of miR-155 and miR-499a expression levels in obese subjects. In particular, the reduction appears to be even more significant in Type 2 diabetes subjects with central obesity. <b>Conclusion:</b> The results suggest that these miRNAs could be involved in obesity-driven pathogenetic mechanisms.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"85-91"},"PeriodicalIF":3.8,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139466495","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
Differentially methylated regions interrogated for metastable epialleles associate with offspring adiposity. 可转移外显子的不同甲基化区域与后代肥胖有关。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-09-12 DOI: 10.1080/17501911.2024.2359365
Stephanie W Waldrop, Katherine A Sauder, Sierra S Niemiec, Katerina J Kechris, Ivana V Yang, Anne P Starling, Wei Perng, Dana Dabelea, Sarah J Borengasser
{"title":"Differentially methylated regions interrogated for metastable epialleles associate with offspring adiposity.","authors":"Stephanie W Waldrop, Katherine A Sauder, Sierra S Niemiec, Katerina J Kechris, Ivana V Yang, Anne P Starling, Wei Perng, Dana Dabelea, Sarah J Borengasser","doi":"10.1080/17501911.2024.2359365","DOIUrl":"10.1080/17501911.2024.2359365","url":null,"abstract":"<p><p><b>Aim:</b> Assess if cord blood differentially methylated regions (DMRs) representing human metastable epialleles (MEs) associate with offspring adiposity in 588 maternal-infant dyads from the Colorado Health Start Study.<b>Materials & methods:</b> DNA methylation was assessed via the Illumina 450K array (~439,500 CpG sites). Offspring adiposity was obtained via air displacement plethysmography. Linear regression modeled the association of DMRs potentially representing MEs with adiposity.<b>Results & conclusion:</b> We identified two potential MEs, <i>ZFP57</i>, which associated with infant adiposity change and <i>B4GALNT4</i>, which associated with infancy and childhood adiposity change. Nine DMRs annotating to genes that annotated to MEs associated with change in offspring adiposity (false discovery rate <0.05). Methylation of approximately 80% of DMRs identified associated with decreased change in adiposity.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1215-1230"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11486027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142282448","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
Impact of prematurity on LINE-1 promoter methylation. 早产对 LINE-1 启动子甲基化的影响
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-09-19 DOI: 10.1080/17501911.2024.2397329
Paulo Victor Barbosa Eleutério Dos Santos, Aline de Araújo Brasil, Leo Travassos Vieira Milone, Georgia Chalfun, Stephanie Cristina Alves de Oliveira Saide, Margarida Dos Santos Salú, Mariana Barros Genuíno de Oliveira, Jaqueline Rodrigues Robaina, Fernanda Lima-Setta, Gustavo Rodrigues-Santos, Maria Clara de Magalhães-Barbosa, Antônio José Ledo Alves da Cunha, Arnaldo Prata-Barbosa
{"title":"Impact of prematurity on LINE-1 promoter methylation.","authors":"Paulo Victor Barbosa Eleutério Dos Santos, Aline de Araújo Brasil, Leo Travassos Vieira Milone, Georgia Chalfun, Stephanie Cristina Alves de Oliveira Saide, Margarida Dos Santos Salú, Mariana Barros Genuíno de Oliveira, Jaqueline Rodrigues Robaina, Fernanda Lima-Setta, Gustavo Rodrigues-Santos, Maria Clara de Magalhães-Barbosa, Antônio José Ledo Alves da Cunha, Arnaldo Prata-Barbosa","doi":"10.1080/17501911.2024.2397329","DOIUrl":"10.1080/17501911.2024.2397329","url":null,"abstract":"<p><p><b>Aim:</b> Promoter methylation of LINE-1 may be affected by prematurity, but there is little evidence in the literature.<b>Materials & methods:</b> Blood from premature and full-term neonates on days 0, 5, 30 and 90 was analyzed for DNA methylation percentage in a promoter region of the LINE-1, after bisulfite conversion and pyrosequencing.<b>Results:</b> Premature infants, as a whole, showed significantly lower methylation percentage at birth, but this difference diminished over time. However, the subgroup of extremely premature (<28 weeks gestational age) had higher methylation percentages, similar to full-term newborns.<b>Conclusion:</b> This research underscores the critical role of prematurity on the methylation pattern of LINE-1. These findings underline the complexity of epigenetic regulation in prematurity and emphasize the need for further studies.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"1253-1264"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11486321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142282451","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
Role of transcription in imprint establishment in the male and female germ lines. 转录在雄性和雌性种系的印记建立中的作用。
IF 3 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2023-12-21 DOI: 10.2217/epi-2023-0344
Ji Liao, Piroska E Szabó
{"title":"Role of transcription in imprint establishment in the male and female germ lines.","authors":"Ji Liao, Piroska E Szabó","doi":"10.2217/epi-2023-0344","DOIUrl":"10.2217/epi-2023-0344","url":null,"abstract":"<p><p>The authors highlight an area of research that focuses on the establishment of genomic imprints: how the female and male germlines set up opposite instructions for imprinted genes in the maternally and paternally inherited chromosomes. Mouse genetics studies have solidified the role of transcription across the germline differentially methylated regions in the establishment of maternal genomic imprinting. One work now reveals that such transcription is also important in paternal imprinting establishment. This allows the authors to propose a unifying mechanism, in the form of transcription across germline differentially methylated regions, that specifies DNA methylation imprint establishment. Differences in the timing, genomic location and nature of such transcription events in the male versus female germlines in turn explain the difference between paternal and maternal imprints.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"127-136"},"PeriodicalIF":3.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10825728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138828924","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
Evaluating the clinical performance of SDC2/NDRG4 methylation for colorectal cancer detection. 评估 SDC2/NDRG4 甲基化在结直肠癌检测中的临床表现。
IF 3.8 4区 医学
Epigenomics Pub Date : 2024-01-01 Epub Date: 2024-01-16 DOI: 10.2217/epi-2023-0290
Ke Zhang, Qing He, Qin Cao, Jun Chuan, Ang Qin, Lin Tang, Xinyue Zhang, Changhe Xiao, Biyin Zhu, Meiling Hu, Lei Chang, Zhong Xin Bu, Lanqi Fu, Ting Yang, Yu Wang, Weidong Liu
{"title":"Evaluating the clinical performance of <i>SDC2/NDRG4</i> methylation for colorectal cancer detection.","authors":"Ke Zhang, Qing He, Qin Cao, Jun Chuan, Ang Qin, Lin Tang, Xinyue Zhang, Changhe Xiao, Biyin Zhu, Meiling Hu, Lei Chang, Zhong Xin Bu, Lanqi Fu, Ting Yang, Yu Wang, Weidong Liu","doi":"10.2217/epi-2023-0290","DOIUrl":"10.2217/epi-2023-0290","url":null,"abstract":"<p><p><b>Purpose:</b> The performance and clinical accuracy of combined <i>SDC2/NDRG4</i> methylation were evaluated in diagnosing colorectal cancer (CRC) and advanced adenoma. <b>Methods:</b> A total of 2333 participants were enrolled to assess the sensitivity and specificity of biomarkers in diagnosing CRC in a multicenter clinical trial through feces DNA methylation tests. <b>Results:</b> <i>SDC2/NDRG4</i> methylation showed excellent performance for CRC detection in biomarker research and the real world. Its sensitivity for detecting CRC, early CRC and advanced adenoma were 92.06%, 91.45% and 62.61%, respectively. Its specificity was 94.29%, with a total coincidence rate of 88.28%. When interference samples were included, the specificity was still good (82.61%). Therefore, the <i>SDC2/NDRG4</i> methylation test showed excellent performance in detecting CRC and advanced adenoma under clinical application.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"93-108"},"PeriodicalIF":3.8,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139472390","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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