Epigenetics最新文献_第6页

ZSCAN25 methylation predicts seizures and severe alcohol withdrawal syndrome. ZSCAN25 甲基化可预测癫痫发作和严重酒精戒断综合征。

IF 3.7 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-01-03 DOI: 10.1080/15592294.2023.2298057

Allan Andersen, Emily Milefchik, Emma Papworth, Brandan Penaluna, Kelsey Dawes, Joanna Moody, Gracie Weeks, Ellyse Froehlich, Kaitlyn deBlois, Jeffrey D Long, Robert Philibert

{"title":"ZSCAN25 methylation predicts seizures and severe alcohol withdrawal syndrome.","authors":"Allan Andersen, Emily Milefchik, Emma Papworth, Brandan Penaluna, Kelsey Dawes, Joanna Moody, Gracie Weeks, Ellyse Froehlich, Kaitlyn deBlois, Jeffrey D Long, Robert Philibert","doi":"10.1080/15592294.2023.2298057","DOIUrl":"10.1080/15592294.2023.2298057","url":null,"abstract":"Currently, clinicians use their judgement and indices such as the Prediction of Alcohol Withdrawal Syndrome Scale (PAWSS) to determine whether patients are admitted to hospitals for consideration of withdrawal syndrome (AWS). However, only a fraction of those admitted will experience severe AWS. Previously, we and others have shown that epigenetic indices, such as the Alcohol T-Score (ATS), can quantify recent alcohol consumption. However, whether these or other alcohol biomarkers, such as carbohydrate deficient transferrin (CDT), could identify those at risk for severe AWS is unknown. To determine this, we first conducted genome-wide DNA methylation analyses of subjects entering and exiting alcohol treatment to identify loci whose methylation quickly reverted as a function of abstinence. We then tested whether methylation at a rapidly reverting locus, cg07375256, or other existing metrics including PAWSS scores, CDT levels, or ATS, could predict outcome in 125 subjects admitted for consideration of AWS. We found that PAWSS did not significantly predict severe AWS nor seizures. However, methylation at cg07375256 (ZSCAN25) and CDT strongly predicted severe AWS with ATS (p < 0.007) and cg07375256 (p < 6 × 10-5) methylation also predicting AWS associated seizures. We conclude that epigenetic methods can predict those likely to experience severe AWS and that the use of these or similar Precision Epigenetic approaches could better guide AWS management.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2298057"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10766392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139080447","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

A promising application of kidney-specific cell-free DNA methylation markers in real-time monitoring sepsis-induced acute kidney injury. 肾脏特异性无细胞 DNA 甲基化标记在实时监测败血症诱发的急性肾损伤中的应用前景广阔。

IF 2.9 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-10-07 DOI: 10.1080/15592294.2024.2408146

Ruilian You, Xiangming Quan, Peng Xia, Chao Zhang, Anlei Liu, Hanshu Liu, Ling Yang, Huadong Zhu, Limeng Chen

{"title":"A promising application of kidney-specific cell-free DNA methylation markers in real-time monitoring sepsis-induced acute kidney injury.","authors":"Ruilian You, Xiangming Quan, Peng Xia, Chao Zhang, Anlei Liu, Hanshu Liu, Ling Yang, Huadong Zhu, Limeng Chen","doi":"10.1080/15592294.2024.2408146","DOIUrl":"10.1080/15592294.2024.2408146","url":null,"abstract":"Sepsis-induced acute kidney injury (SI-AKI) is a common clinical syndrome that is associated with high mortality and morbidity. Effective timely detection may improve the outcome of SI-AKI. Kidney-derived cell-free DNA (cfDNA) may provide new insight into understanding and identifying SI-AKI. Plasma cfDNA from 82 healthy individuals, 7 patients with sepsis non-acute kidney injury (SN-AKI), and 9 patients with SI-AKI was subjected to genomic methylation sequencing. We deconstructed the relative contribution of cfDNA from different cell types based on cell-specific methylation markers and focused on exploring the association between kidney-derived cfDNA and SI-AKI.Based on the deconvolution of the cfDNA methylome: SI-AKI patients displayed the elevated cfDNA concentrations with an increased contribution of kidney epithelial cells (kidney-Ep) DNA; kidney-Ep derived cfDNA achieved high accuracy in distinguishing SI-AKI from SN-AKI (AUC = 0.92, 95% CI 0.7801-1); the higher kidney-ep cfDNA concentrations tended to correlate with more advanced stages of SI-AKI; strikingly, SN-AKI patients with potential kidney damage unmet by SI-AKI criteria showed higher levels of kidney-Ep derived cfDNA than healthy individuals. The autonomous screening of kidney-Ep (n = 24) and kidney endothelial (kidney-Endo, n = 12) specific methylation markers indicated the unique identity of kidney-Ep/kidney-Endo compared with other cell types, and its targeted assessment reproduced the main findings of the deconvolution of the cfDNA methylome. Our study first demonstrates that kidney-Ep- and kidney-Endo-specific methylation markers can serve as a novel marker for SI-AKI emergence, supporting further exploration of the utility of kidney-specific cfDNA methylation markers in the study of SI-AKI.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2408146"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11459754/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380309","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

Observational methods for human studies of transgenerational effects. 人类跨代效应研究的观察方法。

IF 3.7 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-06-13 DOI: 10.1080/15592294.2024.2366065

Rebecca Richards-Steed, Neng Wan, Amanda Bakian, Richard M Medina, Simon C Brewer, Ken R Smith, James A VanDerslice

{"title":"Observational methods for human studies of transgenerational effects.","authors":"Rebecca Richards-Steed, Neng Wan, Amanda Bakian, Richard M Medina, Simon C Brewer, Ken R Smith, James A VanDerslice","doi":"10.1080/15592294.2024.2366065","DOIUrl":"10.1080/15592294.2024.2366065","url":null,"abstract":"There are substantial challenges in studying human transgenerational epigenetic outcomes resulting from environmental conditions. The task requires specialized methods and tools that incorporate specific knowledge of multigenerational relationship combinations of probands and their ancestors, phenotype data for individuals, environmental information of ancestors and their descendants, which can span historical to present datasets, and informative environmental data that chronologically aligns with ancestors and descendants over space and time. As a result, there are few epidemiologic studies of potential transgenerational effects in human populations, thus limiting the knowledge of ancestral environmental conditions and the potential impacts we face with modern human health outcomes. In an effort to overcome some of the challenges in studying human transgenerational effects, we present two transgenerational study designs: transgenerational space-time cluster detection and transgenerational case-control study design. Like other epidemiological methods, these methods determine whether there are statistical associations between phenotypic outcomes (e.g., adverse health outcomes) among probands and the shared environments and environmental factors facing their ancestors. When the ancestor is a paternal grandparent, a statistically significant association provides some evidence that a transgenerational inheritable factor may be involved. Such results may generate useful hypotheses that can be explored using epigenomic data to establish conclusive evidence of transgenerational heritable effects. Both methods are proband-centric: They are designed around the phenotype of interest in the proband generation for case selection and family pedigree creation. In the examples provided, we incorporate at least three generations of paternal lineage in both methods to observe a potential transgenerational effect.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2366065"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11178273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141317181","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

IL21R hypomethylation as a biomarker for distinguishing benign and malignant breast tumours. IL21R 低甲基化是区分良性和恶性乳腺肿瘤的生物标记物。

IF 3.7 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-05-09 DOI: 10.1080/15592294.2024.2352683

Zishan Zang, Yifei Yin, Chunlan Liu, Qiang Zhu, Xuandong Huang, Hong Li, Rongxi Yang

{"title":"IL21R hypomethylation as a biomarker for distinguishing benign and malignant breast tumours.","authors":"Zishan Zang, Yifei Yin, Chunlan Liu, Qiang Zhu, Xuandong Huang, Hong Li, Rongxi Yang","doi":"10.1080/15592294.2024.2352683","DOIUrl":"10.1080/15592294.2024.2352683","url":null,"abstract":"Some benign and malignant breast tumours are similar in pathological morphology, which are difficult to be distinguished in clinical diagnosis. In this study, we intended to explore novel biomarkers for differential diagnosis of benign and malignant breast tumours. Methylation EPIC 850K beadchip and RNA-sequencing were used to analyse 29 tissue samples from patients with early-stage breast cancer (BC) and benign breast tumours for differently methylated and expressed genes. The altered methylation of IL21R was semi-quantitatively validated in an independent study with 566 tissue samples (279 BC vs. 287 benign breast tumours) using mass spectrometry. Binary logistic regression analysis was performed to evaluate the association between IL21R methylation and BC. BC-associated IL21R hypomethylation and overexpression were identified in the discovery round. In the validation round, BC patients presented significant IL21R hypomethylation compared to women with benign breast tumours (ORs ≥1.29 per-10% methylation, p-values ≤ 5.69E-14), and this hypomethylation was even enhanced in BC patients with ER-negative and PR-negative tumours as well as with triple-negative tumours. The methylation of IL21R showed efficient discriminatory power to distinguish benign breast tumours from BC (area under curve (AUC) = 0.88), and especially from ER-negative BC (AUC = 0.95), PR-negative BC (AUC = 0.93) and triple-negative BC (AUC = 0.96). We disclosed significant IL21R hypomethylation in patients with BC compared to women with benign breast tumours, and revealed the somatic change of DNA methylation could be a potential biomarker for molecular pathology of BC.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2352683"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11086039/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897502","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

Integration of miRNA expression analysis of purified leukocytes and whole blood reveals blood-borne candidate biomarkers for lung cancer. 整合纯化白细胞和全血的 miRNA 表达分析揭示了肺癌的血源性候选生物标志物。

IF 2.9 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-08-20 DOI: 10.1080/15592294.2024.2393948

Guini Hong, Yue Huo, Yaru Gao, Liyuan Ma, Shuang Li, Tian Tian, Haijian Zhong, Hongdong Li

{"title":"Integration of miRNA expression analysis of purified leukocytes and whole blood reveals blood-borne candidate biomarkers for lung cancer.","authors":"Guini Hong, Yue Huo, Yaru Gao, Liyuan Ma, Shuang Li, Tian Tian, Haijian Zhong, Hongdong Li","doi":"10.1080/15592294.2024.2393948","DOIUrl":"10.1080/15592294.2024.2393948","url":null,"abstract":"Changes in leukocyte populations may confound the disease-associated miRNA signals in the blood of cancer patients. We aimed to develop a method to detect differentially expressed miRNAs from lung cancer whole blood samples that are not influenced by variations in leukocyte proportions. The Ref-miREO method identifies differential miRNAs unaffected by changes in leukocyte populations by comparing the within-sample relative expression orderings (REOs) of miRNAs from healthy leukocyte subtypes and those from lung cancer blood samples. Over 77% of the differential miRNAs observed between lung cancer and healthy blood samples overlapped with those between myeloid-derived and lymphoid-derived leukocytes, suggesting the potential impact of changes in leukocyte populations on miRNA profile. Ref-miREO identified 16 differential miRNAs that target 19 lung adenocarcinoma-related genes previously linked to leukocytes. These miRNAs showed enrichment in cancer-related pathways and demonstrated high potential as diagnostic biomarkers, with the LASSO regression models effectively distinguishing between healthy and lung cancer blood or serum samples (all AUC > 0.85). Additionally, 12 of these miRNAs exhibited significant prognostic correlations. The Ref-miREO method offers valuable candidates for circulating biomarker detection in cancer that are not affected by changes in leukocyte populations.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2393948"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11340745/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142008522","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

Epigenetic aging of semen is associated with inflammation. 精液的表观遗传老化与炎症有关。

IF 2.9 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-12-05 DOI: 10.1080/15592294.2024.2436304

Junxi Feng, Liudmilla Rubbi, Reza Kianian, Jesse Nelson Mills, Vadim Osadchiy, John Tucker Sigalos, Sriram Venkata Eleswarapu, Matteo Pellegrini

{"title":"Epigenetic aging of semen is associated with inflammation.","authors":"Junxi Feng, Liudmilla Rubbi, Reza Kianian, Jesse Nelson Mills, Vadim Osadchiy, John Tucker Sigalos, Sriram Venkata Eleswarapu, Matteo Pellegrini","doi":"10.1080/15592294.2024.2436304","DOIUrl":"10.1080/15592294.2024.2436304","url":null,"abstract":"Male infertility has been a primary cause of global infertility, affecting 8-12% of couples worldwide. Previous studies have shown that semen quality decreases with advanced aging with an increased presence of inflammatory cells. In this study, we examined changes in the epigenome across a diverse cohort that includes both fertile and infertile men. We also compare the age-associated changes in semen to those observed in buccal swabs in order to characterize differences in epigenetic aging across diverse tissues. We found that variations in the semen methylome associated with aging are linked to inflammatory genes. Many age-associated sites are demethylated with advanced aging and are associated with the activation of inflammatory pathways. By contrast, we do not observe age-associated changes in inflammatory genes in buccal swab methylomes, which instead are characterized by changes to bivalent promoters. Our findings highlight the potential of epigenetic markers as indicators of male reproductive health.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2436304"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11622584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784751","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

ANRIL upregulates TGFBR1 to promote idiopathic pulmonary fibrosis in TGF-β1-treated lung fibroblasts via sequestering let-7d-5p. ANRIL上调TGFBR1，通过隔离et-7d-5p促进TGF-β1处理的肺成纤维细胞特发性肺纤维化。

IF 2.9 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-11-29 DOI: 10.1080/15592294.2024.2435682

Weidong Wu, Nanding Yu, Weiming Chen, Yong Zhu

{"title":"ANRIL upregulates TGFBR1 to promote idiopathic pulmonary fibrosis in TGF-β1-treated lung fibroblasts via sequestering let-7d-5p.","authors":"Weidong Wu, Nanding Yu, Weiming Chen, Yong Zhu","doi":"10.1080/15592294.2024.2435682","DOIUrl":"10.1080/15592294.2024.2435682","url":null,"abstract":"Idiopathic pulmonary fibrosis (IPF) is a progressive and life-threatening respiratory disease characterized by worsening lung function due to excessive scarring. The objective of this study was to investigate the role of the long non-coding RNA ANRIL (antisense non-coding RNA in the INK4 locus) in the development of IPF. Our research revealed a significant increase in ANRIL expression in pulmonary fibrosis, consistent with prior studies indicating elevated ANRIL levels in fibrotic tissues. In vitro experiments demonstrated that elevated ANRIL expression promoted fibroblast activation, as evidenced by the upregulation of fibrosis-related markers. Mechanistically, we found that ANRIL interacts with let-7d-5p, a microRNA involved in gene regulation, acting as a sponge for let-7d-5p. Functional experiments confirmed a potential influence of let-7d-5p on fibroblast activation through direct interaction with ANRIL. Furthermore, our investigation identified TGFBR1 as a potential mediator of ANRIL's fibrogenic effects. Silence of TGFBR1 mitigated the fibrotic phenotype induced by ANRIL overexpression. Collectively, these results suggest that ANRIL promotes fibroblast activation and fibrosis development, possibly through the let-7d-5p/TGFBR1 axis, indicating that ANRIL could be a potential therapeutic target for pulmonary fibrosis.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2435682"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11610569/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142754895","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

Chemotherapy-induced acceleration of DNA methylation-based biological age in breast cancer. 化疗诱导的乳腺癌 DNA 甲基化生物年龄加速。

IF 3.7 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-05-31 DOI: 10.1080/15592294.2024.2360160

Drew R Nannini, Rene Cortese, Christopher VonTungeln, Gerhard C Hildebrandt

{"title":"Chemotherapy-induced acceleration of DNA methylation-based biological age in breast cancer.","authors":"Drew R Nannini, Rene Cortese, Christopher VonTungeln, Gerhard C Hildebrandt","doi":"10.1080/15592294.2024.2360160","DOIUrl":"10.1080/15592294.2024.2360160","url":null,"abstract":"Breast cancer is the most common cancer diagnosed in women and is often treated with chemotherapy. Although previous studies have demonstrated increasing biological age in patients who receive chemotherapy, evaluation of this association with DNA methylation-based markers of biological ageing may provide novel insight into the role of chemotherapy on the ageing process. We therefore sought to investigate the association between chemotherapy and markers of biological ageing as estimated from DNA methylation in women with breast cancer. DNA methylation profiling was performed on peripheral blood collected from 18 patients before and after the first cycle of chemotherapy using the Infinium HumanMethylation450 BeadChip. Six markers of biological age acceleration were estimated from DNA methylation levels. Multiple linear regression analyses were performed to evaluate the association between each metric of biological age acceleration and chemotherapy. After adjusting for chronological age and race, intrinsic epigenetic age acceleration (p = 0.041), extrinsic epigenetic age acceleration (p = 0.050), PhenoAge acceleration (p = 0.001), GrimAge acceleration (p < 0.001), and DunedinPACE (p = 0.006) were significantly higher and telomere length (p = 0.027) was significantly lower following the first cycle of chemotherapy compared to before treatment initiation. These results demonstrate greater biological ageing as estimated from DNA methylation following chemotherapy in women with breast cancer. Our findings illustrate that cytotoxic therapies may modulate the ageing process among breast cancer patients and may also have implications for age-related health conditions in cancer survivors.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2360160"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11146438/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141183295","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

Clinical significance of peripheral blood DDR1 and CtBP gene methylation detection in patients with acute pancreatitis. 急性胰腺炎患者外周血 DDR1 和 CtBP 基因甲基化检测的临床意义。

IF 2.9 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-11-01 DOI: 10.1080/15592294.2024.2421631

Zeng-Hui Ma, Xue-Ni Ma, Hong-Wen Zhu, Long Cheng, Ling-Zhu Gou, De-Kui Zhang

{"title":"Clinical significance of peripheral blood DDR1 and CtBP gene methylation detection in patients with acute pancreatitis.","authors":"Zeng-Hui Ma, Xue-Ni Ma, Hong-Wen Zhu, Long Cheng, Ling-Zhu Gou, De-Kui Zhang","doi":"10.1080/15592294.2024.2421631","DOIUrl":"10.1080/15592294.2024.2421631","url":null,"abstract":"To investigate the clinical value of methylation levels of peripheral blood DDR1 and CtBP genes in evaluating the severity of acute pancreatitis (AP). Collect 90 blood samples from AP patients and healthy volunteers, and test methylation levels of SPINK1, STAT3, KIT, CFTR, DDR1, CtBP1, CtBP2 genes by bisulfite amplicon sequencing (BSAS). The gene methylation and clinical predictors of SAP early prediction were determined by univariate and multifactorial analysis, respectively. (1) The methylation level of CtBP1 gene and MCTSI score were independent predictors of SAP, with AUC values of 0.723 and 0.8895, respectively. (2) The methylation levels of DDR1, CtBP2, CFTR and SPINK1 genes were statistically significant in HC group vs AP group, HC group vs MAP group, and HC group vs SAP group. (3) The combined detection of CtBP1 gene methylation level and MCTSI score predicted the sensitivity, specificity, AUC, and 95%CI of SAP were 0.750, 0.957, 0.902, and 0.816-0.989, respectively. (1) The methylation level of CtBP1 gene in peripheral blood is an independent risk factor for predicting SAP and is a potentially good predictor of SAP, and the combined testing with the MCTSI score does not further significantly improve the early predictive value for SAP. (2) The methylation levels of DDR1, SPINK1, CtBP2, and CFTR genes were potential indicators for recognizing AP.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2421631"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142562560","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

N6-methyladenosine methylation analysis of long noncoding RNAs and mRNAs in 5-FU-resistant colon cancer cells. 5-FU耐药结肠癌细胞中长非编码RNA和mRNA的N6-甲基腺苷甲基化分析

IF 3.7 3区生物学

Epigenetics Pub Date : 2024-12-01 Epub Date: 2023-12-25 DOI: 10.1080/15592294.2023.2298058

Jie Lai, Zhiyong Zhou, Kan Hu, HongLong Yu, Xingyao Su, Xiaoqiang Niu, Huizi Li, Shengxun Mao

{"title":"N6-methyladenosine methylation analysis of long noncoding RNAs and mRNAs in 5-FU-resistant colon cancer cells.","authors":"Jie Lai, Zhiyong Zhou, Kan Hu, HongLong Yu, Xingyao Su, Xiaoqiang Niu, Huizi Li, Shengxun Mao","doi":"10.1080/15592294.2023.2298058","DOIUrl":"10.1080/15592294.2023.2298058","url":null,"abstract":"N6 methyladenosine (m6A), methylation at the sixth N atom of adenosine, is the most common and abundant modification in mammalian mRNAs and non-coding RNAs. Increasing evidence shows that the alteration of m6A modification level could regulate tumour proliferation, metastasis, self-renewal, and immune infiltration by regulating the related expression of tumour genes. However, the role of m6A modification in colorectal cancer (CRC) drug resistance is unclear. Here, MeRIP-seq and RNA-seq techniques were utilized to obtain mRNA, lncRNA expression, and their methylation profiles in 5-Fluorouracil (5-FU)-resistant colon cancer HCT-15 cells and control cells. In addition, we performed detailed bioinformatics analysis as well as in vitro experiments of lncRNA to explore the function of lncRNA with differential m6A in CRC progression and drug resistance. In this study, we obtained the m6A methylomic landscape of CRC cells and resistance group cells by MeRIP-seq and RNA-seq. We identified 3698 differential m6A peaks, of which 2224 were hypermethylated, and 1474 were hypomethylated. Among the lncRNAs, 60 were hypermethylated, and 38 were hypomethylated. GO and KEGG analysis annotations showed significant enrichment of endocytosis and MAPK signalling pathways. Moreover, knockdown of lncRNA ADIRF-AS1 and AL139035.1 promoted CRC proliferation and invasive metastasis in vitro. lncRNA- mRNA network showed that ADIRF-AS1 and AL139035.1 May play a key role in regulating drug resistance formation. We provide the first m6A methylation profile in 5-FU resistance CRC cells and analyse the functions of differential m6A-modified mRNAs and lncRNAs. Our results indicated that differential m6A RNAs were significantly associated with MAPK signalling and endocytosis after induction of 5-FU resistance. Knockdown of LncRNA ADIRF-AS1 and AL139035.1 promotes CRC progression and might be critical in regulating drug resistance formation.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"19 1","pages":"2298058"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10761136/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139037538","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