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DNA methylation heterogeneity attributable to a complex tumor immune microenvironment prompts prognostic risk in glioma. 复杂的肿瘤免疫微环境导致的DNA甲基化异质性提示胶质瘤的预后风险。
IF 3.7 3区 生物学
Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-03-05 DOI: 10.1080/15592294.2024.2318506
Shuangyue Ma, Xu Pan, Jing Gan, Xiaxin Guo, Jiaheng He, Haoyu Hu, Yuncong Wang, Shangwei Ning, Hui Zhi
{"title":"DNA methylation heterogeneity attributable to a complex tumor immune microenvironment prompts prognostic risk in glioma.","authors":"Shuangyue Ma, Xu Pan, Jing Gan, Xiaxin Guo, Jiaheng He, Haoyu Hu, Yuncong Wang, Shangwei Ning, Hui Zhi","doi":"10.1080/15592294.2024.2318506","DOIUrl":"10.1080/15592294.2024.2318506","url":null,"abstract":"<p><p>Gliomas are malignant tumours of the human nervous system with different World Health Organization (WHO) classifications, glioblastoma (GBM) with higher grade and are more malignant than lower-grade glioma (LGG). To dissect how the DNA methylation heterogeneity in gliomas is influenced by the complex cellular composition of the tumour immune microenvironment, we first compared the DNA methylation profiles of purified human immune cells and bulk glioma tissue, stratifying three tumour immune microenvironmental subtypes for GBM and LGG samples from The Cancer Genome Atlas (TCGA). We found that more intermediate methylation sites were enriched in glioma tumour tissues, and used the Proportion of sites with Intermediate Methylation (PIM) to compare intertumoral DNA methylation heterogeneity. A larger PIM score reflected stronger DNA methylation heterogeneity. Enhanced DNA methylation heterogeneity was associated with stronger immune cell infiltration, better survival rates, and slower tumour progression in glioma patients. We then created a Cell-type-associated DNA Methylation Heterogeneity Contribution (CMHC) score to explore the impact of different immune cell types on heterogeneous CpG site (<i>CpG</i><sup><i>ct</i></sup>) in glioma tissues. We identified eight prognosis-related <i>CpG</i><sup><i>ct</i></sup> to construct a risk score: the Cell-type-associated DNA Methylation Heterogeneity Risk (CMHR) score. CMHR was positively correlated with cytotoxic T-lymphocyte infiltration (CTL), and showed better predictive performance for IDH status (AUC = 0.96) and glioma histological phenotype (AUC = 0.81). Furthermore, DNA methylation alterations of eight <i>CpG</i><sup><i>ct</i></sup> might be related to drug treatments of gliomas. In conclusion, we indicated that DNA methylation heterogeneity is associated with a complex tumour immune microenvironment, glioma phenotype, and patient's prognosis.</p>","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10936651/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140027750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","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 N6-methyladenosine-related lncRnas in pseudoexfoliation glaucoma. N6-甲基腺苷相关 lncRnas 在假性剥脱性青光眼中的作用
IF 3.7 3区 生物学
Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-05-08 DOI: 10.1080/15592294.2024.2348840
Jieying Guan, Xiaohong Chen, Zhidong Li, Shuifeng Deng, Aizezi Wumaier, Yuncheng Ma, Lingling Xie, Shengsong Huang, Yingting Zhu, Yehong Zhuo
{"title":"Role of N6-methyladenosine-related lncRnas in pseudoexfoliation glaucoma.","authors":"Jieying Guan, Xiaohong Chen, Zhidong Li, Shuifeng Deng, Aizezi Wumaier, Yuncheng Ma, Lingling Xie, Shengsong Huang, Yingting Zhu, Yehong Zhuo","doi":"10.1080/15592294.2024.2348840","DOIUrl":"10.1080/15592294.2024.2348840","url":null,"abstract":"<p><p>To explore the role of lncRNA m<sup>6</sup>A methylation modification in aqueous humour (AH) of patients with pseudoexfoliation glaucoma (PXG). Patients with open-angle PXG under surgery from June 2021 to December 2021 were selected. Age- and gender-matched patients with age-related cataract (ARC) were chosen as control. Patients underwent detailed ophthalmic examinations. 0.05-0.1 ml AH were extracted during surgery for MeRIP-Seq and RNA-Seq. Joint analysis was used to screen lncRNAs with differential m<sup>6</sup>A methylation modification and expression. Online software tools were used to draw lncRNA-miRNA-mRNA network (ceRNA). Expression of lncRNAs and mRNAs was confirmed using quantitative real-time PCR. A total of 4151 lncRNAs and 4386 associated m<sup>6</sup>A methylation modified peaks were identified in the PXG group. Similarly, 2490 lncRNAs and 2595 associated m<sup>6</sup>A methylation modified peaks were detected in the control. Compared to the ARC group, the PXG group had 234 hypermethylated and 402 hypomethylated m<sup>6</sup>A peaks, with statistically significant differences (| Fold Change (FC) |≥2, <i>p</i> < 0.05). Bioinformatic analysis revealed that these differentially methylated lncRNA enriched in extracellular matrix formation, tight adhesion, TGF- β signalling pathway, AMPK signalling pathway, and MAPK signalling pathway. Joint analysis identified 10 lncRNAs with differential m<sup>6</sup>A methylation and expression simultaneously. Among them, the expression of ENST000000485383 and ROCK1 were confirmed downregulated in the PXG group by RT-qPCR. m<sup>6</sup>A methylation modification may affect the expression of lncRNA and participate in the pathogenesis of PXG through the ceRNA network. ENST000000485383-hsa miR592-ROCK1 May be a potential target pathway for further investigation in PXG m<sup>6</sup>A methylation.</p>","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11086004/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140876161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Retracted article: MYCN contributes to the sensitization of acute myelogenous leukemia cells to cisplatin by targeting SRY-box transcription factor 4. 被撤回的文章:MYCN通过靶向SRY-box转录因子4促使急性髓性白血病细胞对顺铂敏感
IF 4.9 4区 生物学
Bioengineered Pub Date : 2024-12-01 Epub Date: 2021-10-28 DOI: 10.1080/21655979.2021.1997697
Xianbao Huang, Ling Qi, Wei Lu, Ziye Li, Wuping Li, Fei Li
{"title":"Retracted article: MYCN contributes to the sensitization of acute myelogenous leukemia cells to cisplatin by targeting SRY-box transcription factor 4.","authors":"Xianbao Huang, Ling Qi, Wei Lu, Ziye Li, Wuping Li, Fei Li","doi":"10.1080/21655979.2021.1997697","DOIUrl":"10.1080/21655979.2021.1997697","url":null,"abstract":"<p><p>Xianbao Huang, Ling Qi, Wei Lu, Ziye Li, Wuping Li and Fei Li. MYCN contributes to the sensitization of acute myelogenous leukemia cells to cisplatin by targeting SRY-box transcription factor 4. Bioengineered. 2021 Oct. doi: 10.1080/21655979.2021.1997697.Since publication, significant concerns have been raised about the compliance with ethical policies for human research and the integrity of the data reported in the article.When approached for an explanation, the authors provided some original data but were not able to provide all the necessary supporting information. As verifying the validity of published work is core to the scholarly record's integrity, we are retracting the article. All authors listed in this publication have been informed.We have been informed in our decision-making by our editorial policies and the COPE guidelines.The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as 'Retracted.'</p>","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10841026/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39565966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Statement of Retraction: Knockdown of long non-coding RNA AGAP2-AS1 suppresses the proliferation and metastasis of glioma by targeting microRNA-497-5p. 撤回声明:敲除长非编码RNA AGAP2-AS1通过靶向microRNA-497-5p抑制胶质瘤的增殖和转移
IF 4.9 4区 生物学
Bioengineered Pub Date : 2024-12-01 Epub Date: 2024-01-18 DOI: 10.1080/21655979.2024.2302648
{"title":"Statement of Retraction: Knockdown of long non-coding RNA AGAP2-AS1 suppresses the proliferation and metastasis of glioma by targeting microRNA-497-5p.","authors":"","doi":"10.1080/21655979.2024.2302648","DOIUrl":"10.1080/21655979.2024.2302648","url":null,"abstract":"","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802191/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139490490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Statement of Retraction: MYCN contributes to the sensitization of acute myelogenous leukemia cells to cisplatin by targeting SRY-box transcription factor 4. 撤回声明:MYCN 通过靶向 SRY-box 转录因子 4 使急性髓性白血病细胞对顺铂敏感。
IF 4.9 4区 生物学
Bioengineered Pub Date : 2024-12-01 Epub Date: 2024-02-01 DOI: 10.1080/21655979.2024.2302650
{"title":"Statement of Retraction: MYCN contributes to the sensitization of acute myelogenous leukemia cells to cisplatin by targeting SRY-box transcription factor 4.","authors":"","doi":"10.1080/21655979.2024.2302650","DOIUrl":"10.1080/21655979.2024.2302650","url":null,"abstract":"","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10841030/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139650263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Calling the question: what is mammalian transgenerational epigenetic inheritance? 提出问题:什么是哺乳动物的跨代表观遗传?
IF 3.7 3区 生物学
Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-03-25 DOI: 10.1080/15592294.2024.2333586
Hasan Khatib, Jessica Townsend, Melissa A Konkel, Gabi Conidi, Julia A Hasselkus
{"title":"Calling the question: what is mammalian transgenerational epigenetic inheritance?","authors":"Hasan Khatib, Jessica Townsend, Melissa A Konkel, Gabi Conidi, Julia A Hasselkus","doi":"10.1080/15592294.2024.2333586","DOIUrl":"10.1080/15592294.2024.2333586","url":null,"abstract":"<p><p>While transgenerational epigenetic inheritance has been extensively documented in plants, nematodes, and fruit flies, its existence in mammals remains controversial. Several factors have contributed to this debate, including the lack of a clear distinction between intergenerational and transgenerational epigenetic inheritance (TEI), the inconsistency of some studies, the potential confounding effects of in-utero vs. epigenetic factors, and, most importantly, the biological challenge of epigenetic reprogramming. Two waves of epigenetic reprogramming occur: in the primordial germ cells and the developing embryo after fertilization, characterized by global erasure of DNA methylation and remodelling of histone modifications. Consequently, TEI can only occur if specific genetic regions evade this reprogramming and persist through embryonic development. These challenges have revived the long-standing debate about the possibility of inheriting acquired traits, which has been strongly contested since the Lamarckian and Darwinian eras. As a result, coupled with the absence of universally accepted criteria for transgenerational epigenetic studies, a vast body of literature has emerged claiming evidence of TEI. Therefore, the goal of this study is to advocate for establishing fundamental criteria that must be met for a study to qualify as evidence of TEI. We identified five criteria based on the consensus of studies that critically evaluated TEI. To assess whether published original research papers adhere to these criteria, we examined 80 studies that either claimed or were cited as supporting TEI. The findings of this analysis underscore the widespread confusion in this field and highlight the urgent need for a unified scientific consensus on TEI requirements.</p>","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10965103/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140206498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Non-coding 886 (nc886/vtRNA2-1), the epigenetic odd duck - implications for future studies. 非编码 886(nc886/vtRNA2-1),表观遗传学的怪鸭--对未来研究的启示。
IF 3.7 3区 生物学
Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-03-25 DOI: 10.1080/15592294.2024.2332819
Emma Raitoharju, Sonja Rajić, Saara Marttila
{"title":"Non-coding 886 (<i>nc886</i>/<i>vtRNA2-1</i>), the epigenetic odd duck - implications for future studies.","authors":"Emma Raitoharju, Sonja Rajić, Saara Marttila","doi":"10.1080/15592294.2024.2332819","DOIUrl":"10.1080/15592294.2024.2332819","url":null,"abstract":"<p><p>Non-coding 886 (<i>nc886</i>, <i>vtRNA2-1</i>) is the only human polymorphically imprinted gene, in which the methylation status is not determined by genetics. Existing literature regarding the establishment, stability and consequences of the methylation pattern, as well as the nature and function of the <i>nc886</i> RNAs transcribed from the locus, are contradictory. For example, the methylation status of the locus has been reported to be stable through life and across somatic tissues, but also susceptible to environmental effects. The nature of the produced <i>nc886</i> RNA(s) has been redefined multiple times, and in carcinogenesis, these RNAs have been reported to have conflicting roles. In addition, due to the bimodal methylation pattern of the <i>nc886</i> locus, traditional genome-wide methylation analyses can lead to false-positive results, especially in smaller datasets. Herein, we aim to summarize the existing literature regarding <i>nc886</i>, discuss how the characteristics of <i>nc886</i> give rise to contradictory results, as well as to reinterpret, reanalyse and, where possible, replicate the results presented in the current literature. We also introduce novel findings on how the distribution of the <i>nc886</i> methylation pattern is associated with the geographical origins of the population and describe the methylation changes in a large variety of human tumours. Through the example of this one peculiar genetic locus and RNA, we aim to highlight issues in the analysis of DNA methylation and non-coding RNAs in general and offer our suggestions for what should be taken into consideration in future analyses.</p>","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10965113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140206526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Statement of Retraction: Dehydroevodiamine suppresses inflammatory responses in adjuvant-induced arthritis rats and human fibroblast-like synoviocytes. 撤回声明:脱氢乙二胺可抑制佐剂诱导的关节炎大鼠和人类成纤维细胞样滑膜细胞的炎症反应。
IF 4.9 4区 生物学
Bioengineered Pub Date : 2024-12-01 Epub Date: 2024-02-20 DOI: 10.1080/21655979.2024.2299578
{"title":"Statement of Retraction: Dehydroevodiamine suppresses inflammatory responses in adjuvant-induced arthritis rats and human fibroblast-like synoviocytes.","authors":"","doi":"10.1080/21655979.2024.2299578","DOIUrl":"https://doi.org/10.1080/21655979.2024.2299578","url":null,"abstract":"","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139904899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Statement of Retraction: Forkhead-box C1 attenuates high glucose-induced trophoblast cell injury during gestational diabetes mellitus via activating adenosine monophosphate-activated protein kinase through regulating fibroblast growth factor 19. 撤回声明:叉头盒C1通过调节成纤维细胞生长因子19激活单磷酸腺苷激活的蛋白激酶,从而减轻妊娠糖尿病期间高糖诱导的滋养层细胞损伤。
IF 4.9 4区 生物学
Bioengineered Pub Date : 2024-12-01 Epub Date: 2024-02-20 DOI: 10.1080/21655979.2024.2299608
{"title":"Statement of Retraction: Forkhead-box C1 attenuates high glucose-induced trophoblast cell injury during gestational diabetes mellitus via activating adenosine monophosphate-activated protein kinase through regulating fibroblast growth factor 19.","authors":"","doi":"10.1080/21655979.2024.2299608","DOIUrl":"10.1080/21655979.2024.2299608","url":null,"abstract":"","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139904903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Statement of Retraction: Knockdown of small nucleolar RNA host gene 10 (SNHG10) alleviates the injury of human neuroblastoma cells via the miR-1277-5p/insulin substrate receptor 2 axis. 撤回声明:敲除小核仁RNA宿主基因10(SNHG10)可通过miR-1277-5p/胰岛素底物受体2轴减轻人神经母细胞瘤细胞的损伤。
IF 4.9 4区 生物学
Bioengineered Pub Date : 2024-12-01 Epub Date: 2024-02-20 DOI: 10.1080/21655979.2024.2299623
{"title":"Statement of Retraction: Knockdown of small nucleolar RNA host gene 10 (SNHG10) alleviates the injury of human neuroblastoma cells via the miR-1277-5p/insulin substrate receptor 2 axis.","authors":"","doi":"10.1080/21655979.2024.2299623","DOIUrl":"10.1080/21655979.2024.2299623","url":null,"abstract":"","PeriodicalId":8919,"journal":{"name":"Bioengineered","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139904951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","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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