Epigenomics最新文献_第4页

Combined replacement of lnc-MEG3 and miR-155 elicit tumor suppression in multiple myeloma. lnc-MEG3和miR-155联合替代可抑制多发性骨髓瘤的肿瘤。

IF 3 4区医学

Epigenomics Pub Date : 2025-02-01 Epub Date: 2025-01-16 DOI: 10.1080/17501911.2025.2453413

Nashwa El-Khazragy, Sara Elsayed Abdelrahman, Amal Darwish, Eman H A Hemida

引用次数: 0

PX-12 modulates vorinostat-induced acetylation and methylation marks in CAL 27 cells. PX-12调节vorinostat诱导的CAL 27细胞乙酰化和甲基化标记。

IF 3 4区医学

Epigenomics Pub Date : 2025-02-01 Epub Date: 2024-12-23 DOI: 10.1080/17501911.2024.2441652

Rafia Akhlaq, Tehmina Ahmed, Tajwali Khan, Syed Usama Yaseen Jeelani, Jazmine-Saskya N Joseph-Chowdhury, Simone Sidoli, Syed Ghulam Musharraf, Arslan Ali

{"title":"PX-12 modulates vorinostat-induced acetylation and methylation marks in CAL 27 cells.","authors":"Rafia Akhlaq, Tehmina Ahmed, Tajwali Khan, Syed Usama Yaseen Jeelani, Jazmine-Saskya N Joseph-Chowdhury, Simone Sidoli, Syed Ghulam Musharraf, Arslan Ali","doi":"10.1080/17501911.2024.2441652","DOIUrl":"10.1080/17501911.2024.2441652","url":null,"abstract":"Aim: The hypoxic tumor microenvironment (TME) in oral squamous cell carcinoma (OSCC) is primarily regulated by hypoxia-inducible factor-1 alpha (HIF-1α), impacting histone acetylation and methylation, which contribute to drug resistance. Vorinostat, a histone deacetylase inhibitor (HDACi), de-stabilizes HIF-1α, while PX-12, a thioredoxin-1 (Trx-1) inhibitor, prevents HIF-1α accumulation. Combining HDACi with a Trx-1 inhibitor may enhance efficacy and reduce resistance by increasing reactive oxygen species (ROS) in cancer cells. This study examines how PX-12 influences vorinostat-induced histone modifications under hypoxia in the OSCC cell line CAL 27 using mass spectrometry.Materials and methods: The OSCC cell line CAL 27 was used to assess histone post-translational modifications induced by PX-12 and Vorinostat under hypoxic conditions through mass spectrometry.Results: The proteomic analysis (ProteomeXchange identifier PXD053244) revealed several crucial histone marks, such as H3K4me1, H3K9ac, H3K9me, H3K14ac, H3K27me, H3K36me, H4K12Ac, and H4K16ac. Along with site-specific histone modifications, exposure of cells to vorinostat and PX-12 alone or in combination affects the global acetylation and methylation levels under hypoxia.Conclusion: Mass spectrometry-based proteomics highlighted the impact of vorinostat and PX-12 on histone acetylation and methylation, offering valuable insights into the epigenetic mechanisms in OSCC and paving a way for epigenetic-based oral cancer therapeutics.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"79-87"},"PeriodicalIF":3.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11792842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881625","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 role of lncRNAs in the interplay of signaling pathways and epigenetic mechanisms in glioma. lncrna在胶质瘤中信号通路相互作用和表观遗传机制中的作用。

IF 3 4区医学

Epigenomics Pub Date : 2025-02-01 Epub Date: 2025-01-19 DOI: 10.1080/17501911.2024.2442297

Can Bora Yildiz, Jian Du, K Naga Mohan, Geraldine Zimmer-Bensch, Sara Abdolahi

引用次数: 0

Blocking RPA-based methods for the determination of CpG methylation status and detection of gene mutations.

IF 3 4区医学

Epigenomics Pub Date : 2025-02-01 Epub Date: 2024-12-29 DOI: 10.1080/17501911.2024.2447810

Mina Ishidoya, Toshitsugu Fujita, Hodaka Fujii

引用次数: 0

Insights to aging prediction with AI based epigenetic clocks. 利用基于人工智能的表观遗传时钟洞察衰老预测。

IF 3 4区医学

Epigenomics Pub Date : 2025-01-01 Epub Date: 2024-11-25 DOI: 10.1080/17501911.2024.2432854

Joshua J Levy, Alos B Diallo, Marietta K Saldias Montivero, Sameer Gabbita, Lucas A Salas, Brock C Christensen

{"title":"Insights to aging prediction with AI based epigenetic clocks.","authors":"Joshua J Levy, Alos B Diallo, Marietta K Saldias Montivero, Sameer Gabbita, Lucas A Salas, Brock C Christensen","doi":"10.1080/17501911.2024.2432854","DOIUrl":"10.1080/17501911.2024.2432854","url":null,"abstract":"Over the past century, human lifespan has increased remarkably, yet the inevitability of aging persists. The disparity between biological age, which reflects pathological deterioration and disease, and chronological age, indicative of normal aging, has driven prior research focused on identifying mechanisms that could inform interventions to reverse excessive age-related deterioration and reduce morbidity and mortality. DNA methylation has emerged as an important predictor of age, leading to the development of epigenetic clocks that quantify the extent of pathological deterioration beyond what is typically expected for a given age. Machine learning technologies offer promising avenues to enhance our understanding of the biological mechanisms governing aging by further elucidating the gap between biological and chronological ages. This perspective article examines current algorithmic approaches to epigenetic clocks, explores the use of machine learning for age estimation from DNA methylation, and discusses how refining the interpretation of ML methods and tailoring their inferences for specific patient populations and cell types can amplify the utility of these technologies in age prediction. By harnessing insights from machine learning, we are well-positioned to effectively adapt, customize and personalize interventions aimed at aging.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"49-57"},"PeriodicalIF":3.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142709440","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

Placental expression and methylation of angiogenic factors in assisted reproductive technology pregnancies from India. 印度辅助生殖技术妊娠中胎盘血管生成因子的表达和甲基化。

IF 3 4区医学

Epigenomics Pub Date : 2025-01-01 Epub Date: 2024-12-10 DOI: 10.1080/17501911.2024.2438593

Deepali Sundrani, Aishwarya Kapare, Himanshi Yadav, Karuna Randhir, Sanjay Gupte, Sadhana Joshi

{"title":"Placental expression and methylation of angiogenic factors in assisted reproductive technology pregnancies from India.","authors":"Deepali Sundrani, Aishwarya Kapare, Himanshi Yadav, Karuna Randhir, Sanjay Gupte, Sadhana Joshi","doi":"10.1080/17501911.2024.2438593","DOIUrl":"10.1080/17501911.2024.2438593","url":null,"abstract":"Aim: This study aims to examine the gene expression and DNA methylation patterns of angiogenic factors in the placentae of Indian women who underwent assisted reproductive technology (ART) procedures and their association with maternal one-carbon metabolites and birth outcome.Methods: Placental gene expression and DNA methylation of angiogenic factors (VEGF, PlGF, FLT-1, KDR) in Indian women who underwent ART procedures (n = 64) and women who conceived naturally (Non-ART) (n = 93) was investigated using RT-qPCR and Epitect Methyl-II PCR assay kits. Maternal plasma one-carbon metabolites were assessed by CMIA technology.Result: Gene expression of FLT-1 and KDR was higher (p < 0.05) in the ART placentae. Placental global DNA methylation levels were higher (p < 0.01) and DNA methylation levels of VEGF promoter were lower (p < 0.05) in ART compared to non-ART women. Maternal plasma folate and vitamin B12 levels were higher (p < 0.01) in the ART group. Gene expression of PlGF was negatively associated with maternal plasma folate (p < 0.05) whereas KDR was positively associated with maternal plasma homocysteine (p < 0.05). Gene expression of KDR was positively associated with chest circumference of the baby (p < 0.05).Conclusion: Hypomethylation of VEGF and increased expression of FLT-1 and KDR was observed in the placentae of women who underwent ART procedure.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"21-31"},"PeriodicalIF":3.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142799603","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 rejuvenation: a journey backwards towards an epigenomic ground state. 表观遗传学返老还童：向表观遗传学基态倒退的旅程。

IF 3 4区医学

Epigenomics Pub Date : 2025-01-01 Epub Date: 2024-11-25 DOI: 10.1080/17501911.2024.2432851

Nelly N Olova

引用次数: 0

Multi-omics insights into the pathogenesis of diabetic cardiomyopathy: epigenetic and metabolic profiles. 糖尿病性心肌病发病机制的多组学研究：表观遗传和代谢谱。

IF 3 4区医学

Epigenomics Pub Date : 2025-01-01 Epub Date: 2024-12-02 DOI: 10.1080/17501911.2024.2435257

Li Zhou, Shuai Mei, Xiaozhu Ma, Qidamugai Wuyun, Ziyang Cai, Chen Chen, Hu Ding, Jiangtao Yan

{"title":"Multi-omics insights into the pathogenesis of diabetic cardiomyopathy: epigenetic and metabolic profiles.","authors":"Li Zhou, Shuai Mei, Xiaozhu Ma, Qidamugai Wuyun, Ziyang Cai, Chen Chen, Hu Ding, Jiangtao Yan","doi":"10.1080/17501911.2024.2435257","DOIUrl":"10.1080/17501911.2024.2435257","url":null,"abstract":"Aim: Diabetic cardiomyopathy (DbCM), a complex metabolic disease, greatly threatens human health due to therapeutic limitations. Multi-omics approaches facilitate the elucidation of its intrinsic pathological changes.Methods: Metabolomics, RNA-seq, proteomics, and assay of transposase-accessible chromatin (ATAC-seq) were utilized to elucidate multidimensional molecular alterations in DbCM.Results: In the heart and plasma of mice with DbCM, metabolomic analysis demonstrated significant differences in branched-chain amino acids (BCAAs) and lipids. Subsequent RNA-seq and proteomics showed that the key genes, including BCKDHB, PPM1K, Cpt1b, Fabp4, Acadm, Acadl, Acadvl, HADH, HADHA, HADHB, Eci1, Eci2, PDK4, and HMGCS2, were aberrantly regulated, contributing to the disorder of BCAAs and fatty acids. ATAC-seq analysis underscored the pivotal role of epigenetic regulation by revealing dynamic shifts in chromatin accessibility and a robust positive correlation with gene expression patterns in diabetic cardiomyopathy mice. Furthermore, motif analysis identified that KLF15 as a critical transcription factor in DbCM, regulating the core genes implicated with BCAAs metabolism.Conclusion: Our research delved into the metabolic alterations and epigenetic landscape and revealed that KLF15 may be a promising candidate for therapeutic intervention in DbCM.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"33-48"},"PeriodicalIF":3.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11727868/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766149","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

Cancer epigenetic therapy: recent advances, challenges, and emerging opportunities. 癌症表观遗传疗法：最新进展、挑战和新兴机遇。

IF 3 4区医学

Epigenomics Pub Date : 2025-01-01 Epub Date: 2024-11-27 DOI: 10.1080/17501911.2024.2430169

Rajita Vatapalli, Alex P Rossi, Ho Man Chan, Jingwen Zhang

引用次数: 0

Emergent properties of the lysine methylome reveal regulatory roles via protein interactions and histone mimicry. 赖氨酸甲基组的涌现特性揭示了通过蛋白质相互作用和组蛋白模仿的调节作用。

IF 3 4区医学

Epigenomics Pub Date : 2025-01-01 Epub Date: 2024-12-05 DOI: 10.1080/17501911.2024.2435244

Gareth Pollin, Young-In Chi, Angela J Mathison, Michael T Zimmermann, Gwen Lomberk, Raul Urrutia

{"title":"Emergent properties of the lysine methylome reveal regulatory roles via protein interactions and histone mimicry.","authors":"Gareth Pollin, Young-In Chi, Angela J Mathison, Michael T Zimmermann, Gwen Lomberk, Raul Urrutia","doi":"10.1080/17501911.2024.2435244","DOIUrl":"10.1080/17501911.2024.2435244","url":null,"abstract":"Aims: Epigenomics has significantly advanced through the incorporation of Systems Biology approaches. This study aims to investigate the human lysine methylome as a system, using a data-science approach to reveal its emergent properties, particularly focusing on histone mimicry and the broader implications of lysine methylation across the proteome.Methods: We employed a data-science-driven OMICS approach, leveraging high-dimensional proteomic data to study the lysine methylome. The analysis focused on identifying sequence-based recognition motifs of lysine methyltransferases and evaluating the prevalence and distribution of lysine methylation across the human proteome.Results: Our analysis revealed that lysine methylation impacts 15% of the known proteome, with a notable bias toward mono-methylation. We identified sequence-based recognition motifs of 13 lysine methyltransferases, highlighting candidates for histone mimicry. These findings suggest that the selective inhibition of individual lysine methyltransferases could have systemic effects rather than merely targeting histone methylation.Conclusions: The lysine methylome has significant mechanistic value and should be considered in the design and testing of therapeutic strategies, particularly in precision oncology. The study underscores the importance of considering non-histone proteins involved in DNA damage and repair, cell signaling, metabolism, and cell cycle pathways when targeting lysine methyltransferases.","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"5-20"},"PeriodicalIF":3.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142779712","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