EpigenomicsPub Date : 2024-03-01Epub Date: 2024-02-07DOI: 10.2217/epi-2023-0428
Balapal S Basavarajappa, Shivakumar Subbanna
{"title":"Unlocking the epigenetic symphony: histone acetylation's impact on neurobehavioral change in neurodegenerative disorders.","authors":"Balapal S Basavarajappa, Shivakumar Subbanna","doi":"10.2217/epi-2023-0428","DOIUrl":"10.2217/epi-2023-0428","url":null,"abstract":"<p><p>Recent genomics and epigenetic advances have empowered the exploration of DNA/RNA methylation and histone modifications crucial for gene expression in response to stress, aging and disease. Interest in understanding neuronal plasticity's epigenetic mechanisms, influencing brain rewiring amid development, aging and neurodegenerative disorders, continues to grow. Histone acetylation dysregulation, a commonality in diverse brain disorders, has become a therapeutic focus. Histone acetyltransferases and histone deacetylases have emerged as promising targets for neurodegenerative disorder treatment. This review delves into histone acetylation regulation, potential therapies and future perspectives for disorders like Alzheimer's, Parkinson's and Huntington's. Exploring genetic-environmental interplay through models and studies reveals molecular changes, behavioral insights and early intervention possibilities targeting the epigenome in at-risk individuals.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"331-358"},"PeriodicalIF":3.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10910622/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139697212","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}
EpigenomicsPub Date : 2024-03-01Epub Date: 2024-02-27DOI: 10.2217/epi-2023-0382
Monu Pandey, Jayanta Bhattacharyya
{"title":"Gut microbiota and epigenetics in colorectal cancer: implications for carcinogenesis and therapeutic intervention.","authors":"Monu Pandey, Jayanta Bhattacharyya","doi":"10.2217/epi-2023-0382","DOIUrl":"10.2217/epi-2023-0382","url":null,"abstract":"<p><p>Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. The occurrence of CRC is associated with various genetic and epigenetic mutations in intestinal epithelial cells that transform them into adenocarcinomas. There is increasing evidence indicating the gut microbiota plays a crucial role in the regulation of host physiological processes. Alterations in gut microbiota composition are responsible for initiating carcinogenesis through diverse epigenetic modifications, including histone modifications, ncRNAs and DNA methylation. This work was designed to comprehensively review recent findings to provide insight into the associations between the gut microbiota and CRC at an epigenetic level. These scientific insights can be used in the future to develop effective strategies for early detection and treatment of CRC.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"403-418"},"PeriodicalIF":3.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139971499","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}
EpigenomicsPub Date : 2024-03-01Epub Date: 2024-03-05DOI: 10.2217/epi-2023-0381
Annunziata G Cicatiello, Annarita Nappi, Fabiana Franchini, Immacolata C Nettore, Maddalena Raia, Carmine Rocca, Tommaso Angelone, Monica Dentice, Paola Ungaro, Paolo E Macchia
{"title":"The histone methyltransferase SMYD1 is induced by thermogenic stimuli in adipose tissue.","authors":"Annunziata G Cicatiello, Annarita Nappi, Fabiana Franchini, Immacolata C Nettore, Maddalena Raia, Carmine Rocca, Tommaso Angelone, Monica Dentice, Paola Ungaro, Paolo E Macchia","doi":"10.2217/epi-2023-0381","DOIUrl":"10.2217/epi-2023-0381","url":null,"abstract":"<p><p><b>Aim:</b> To study the expression of histone methyltransferase SMYD1 in white adipose tissue (WAT) and brown adipose tissue and during differentiation of preadipocytes to white and beige phenotypes. <b>Methods:</b> C57BL/6J mice fed a high-fat diet (and exposed to cold) and 3T3-L1 cells stimulated to differentiate into white and beige adipocytes were used. <b>Results:</b> SMYD1 expression increased in WAT of high-fat diet fed mice and in WAT and brown adipose tissue of cold-exposed mice, suggesting its role in thermogenesis. SMYD1 expression was higher in beige adipocytes than in white adipocytes, and its silencing leads to a decrease in mitochondrial content and in <i>Pgc-1α</i> expression. <b>Conclusion:</b> These data suggest a novel role for SMYD1 as a positive regulator of energy control in adipose tissue.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"359-374"},"PeriodicalIF":3.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140027809","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}
EpigenomicsPub Date : 2024-03-01Epub Date: 2024-02-05DOI: 10.2217/epi-2023-0321
Shota Nishitani, Alicia K Smith, Akemi Tomoda, Takashi X Fujisawa
{"title":"Data science using the human epigenome for predicting multifactorial diseases and symptoms.","authors":"Shota Nishitani, Alicia K Smith, Akemi Tomoda, Takashi X Fujisawa","doi":"10.2217/epi-2023-0321","DOIUrl":"10.2217/epi-2023-0321","url":null,"abstract":"<p><p>Tweetable abstract This article reviews machine learning models that leverages epigenomic data for predicting multifactorial diseases and symptoms as well as how such models can be utilized to explore new research questions.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"273-276"},"PeriodicalIF":3.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139680903","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}
EpigenomicsPub Date : 2024-02-01Epub Date: 2024-01-29DOI: 10.2217/epi-2023-0213
Basireh Bahrami, Markus Wolfien, Parvaneh Nikpour
{"title":"Integrated analysis of transcriptome and epigenome reveals <i>ENSR00000272060</i> as a potential biomarker in gastric cancer.","authors":"Basireh Bahrami, Markus Wolfien, Parvaneh Nikpour","doi":"10.2217/epi-2023-0213","DOIUrl":"10.2217/epi-2023-0213","url":null,"abstract":"<p><p><b>Background:</b> Enhancer RNAs (eRNAs) are involved in gene expression regulation. Although functional roles of eRNAs in the pathophysiology of neoplasms have been reported, their involvement in gastric cancer (GC) is less known. <b>Materials & methods:</b> A network-based integrative approach was utilized for analyzing transcriptome and epigenome alterations in GC, and an eRNA was selected for experimental validation. Survival analysis and clinicopathological associations were also performed. <b>Results:</b> A hub eRNA, <i>ENSR00000272060</i>, showed significantly increased expression in tumor versus nontumor tissues, as well as an association with clinicopathological features. A seven-gene prognostic model was also constructed. <b>Conclusion:</b> The constructed network provides a comprehensive understanding of the underlying processes implicated in the progression of GC, along with a starting point from which to derive potential diagnostic/prognostic biomarkers.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"159-173"},"PeriodicalIF":3.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139570148","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}
EpigenomicsPub Date : 2024-02-01Epub Date: 2024-02-05DOI: 10.2217/epi-2023-0265
Andrea Stoccoro, Adam R Smith, Lorena Mosca, Alessandro Marocchi, Francesca Gerardi, Christian Lunetta, Katie Lunnon, Lucia Migliore, Fabio Coppedè
{"title":"Mitochondrial D-loop methylation levels inversely correlate with disease duration in amyotrophic lateral sclerosis.","authors":"Andrea Stoccoro, Adam R Smith, Lorena Mosca, Alessandro Marocchi, Francesca Gerardi, Christian Lunetta, Katie Lunnon, Lucia Migliore, Fabio Coppedè","doi":"10.2217/epi-2023-0265","DOIUrl":"10.2217/epi-2023-0265","url":null,"abstract":"<p><p><b>Aim:</b> To correlate mitochondrial D-loop region methylation levels and mtDNA copy number with disease duration in familial amyotrophic lateral sclerosis (ALS) patients. <b>Patients & methods:</b> The study population included 12 ALS patients with a mutation in <i>SOD1</i> and 13 ALS patients with the <i>C9orf72</i> hexanucleotide repeat expansion. Methylation levels of the D-loop region and mtDNA copy number were quantified using pyrosequencing and quantitative PCR, respectively. <b>Results:</b> We observed that D-loop methylation levels inversely correlated while mtDNA copy number positively correlated with disease duration. <b>Conclusion:</b> Considering the central role played by mitochondria in ALS, this preliminary study provides new knowledge for future studies aimed at identifying biomarkers of disease progression and new targets for therapeutic interventions.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"203-214"},"PeriodicalIF":3.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139680925","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}
EpigenomicsPub Date : 2024-02-01Epub Date: 2023-12-22DOI: 10.2217/epi-2023-0298
Anna K Knight, Jessica B Spencer, Alicia K Smith
{"title":"DNA methylation as a window into female reproductive aging.","authors":"Anna K Knight, Jessica B Spencer, Alicia K Smith","doi":"10.2217/epi-2023-0298","DOIUrl":"10.2217/epi-2023-0298","url":null,"abstract":"<p><p>People with ovaries experience reproductive aging as their reproductive function and system declines. This has significant implications for both fertility and long-term health, with people experiencing an increased risk of cardiometabolic disorders after menopause. Reproductive aging can be assessed through markers of ovarian reserve, response to fertility treatment or molecular biomarkers, including DNA methylation. Changes in DNA methylation with age associate with poorer reproductive outcomes, and epigenome-wide studies can provide insight into genes and pathways involved. DNA methylation-based epigenetic clocks can quantify biological age in reproductive tissues and systemically. This review provides an overview of hallmarks and theories of aging in the context of the reproductive system, and then focuses on studies of DNA methylation in reproductive tissues.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"175-188"},"PeriodicalIF":3.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10841041/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138828915","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}
EpigenomicsPub Date : 2024-02-01Epub Date: 2023-12-19DOI: 10.2217/epi-2023-0279
Madia Lozupone, Vincenzo Solfrizzi, Rodolfo Sardone, Vittorio Dibello, Fabio Castellana, Roberta Zupo, Luisa Lampignano, Ilaria Bortone, Antonio Daniele, Francesco Panza
{"title":"The epigenetics of frailty.","authors":"Madia Lozupone, Vincenzo Solfrizzi, Rodolfo Sardone, Vittorio Dibello, Fabio Castellana, Roberta Zupo, Luisa Lampignano, Ilaria Bortone, Antonio Daniele, Francesco Panza","doi":"10.2217/epi-2023-0279","DOIUrl":"10.2217/epi-2023-0279","url":null,"abstract":"<p><p>The conceptual change of frailty, from a physical to a biopsychosocial phenotype, expanded the field of frailty, including social and behavioral domains with critical interaction between different frailty models. Environmental exposures - including physical exercise, psychosocial factors and diet - may play a role in the frailty pathophysiology. Complex underlying mechanisms involve the progressive interactions of genetics with epigenetics and of multimorbidity with environmental factors. Here we review the literature on possible mechanisms explaining the association between epigenetic hallmarks (i.e., global DNA methylation, DNA methylation age acceleration and microRNAs) and frailty, considered as biomarkers of aging. Frailty could be considered the result of environmental epigenetic factors on biological aging, caused by conflicting DNA methylation age and chronological age.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"189-202"},"PeriodicalIF":3.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138799266","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}
EpigenomicsPub Date : 2024-02-01Epub Date: 2024-02-06DOI: 10.2217/epi-2023-0100
Jun Li, Pei-Ting Li, Wei Wu, Bo-Ni Ding, Yan-Guang Wen, Hai-Lin Cai, Shuang-Xi Liu, Tao Hong, Jian-Fei Zhang, Jian-Da Zhou, Li-Yuan Qian, Juan Du
{"title":"POU2F2-mediated upregulation of lncRNA <i>PTPRG-AS1</i> inhibits ferroptosis in breast cancer via miR-376c-3p/SLC7A11 axis.","authors":"Jun Li, Pei-Ting Li, Wei Wu, Bo-Ni Ding, Yan-Guang Wen, Hai-Lin Cai, Shuang-Xi Liu, Tao Hong, Jian-Fei Zhang, Jian-Da Zhou, Li-Yuan Qian, Juan Du","doi":"10.2217/epi-2023-0100","DOIUrl":"10.2217/epi-2023-0100","url":null,"abstract":"<p><p><b>Background:</b> Triple-negative breast cancer (TNBC) is a subtype of BC with high rates of mortality. The mechanism of <i>PTPRG-AS1</i> in ferroptosis of TNBC was investigated. <b>Methods:</b> Chromatin immunoprecipitation and dual-luciferase reporter assays were used to measure intermolecular relationships. MTT and colony formation assays detected cell viability and proliferation. Kits detected Fe<sup>2+</sup> and reactive oxygen species levels. The role of PTPRG-AS1 in tumor growth was analyzed <i>in vivo</i>. <b>Results:</b> <i>PTPRG-AS1</i> was increased in TNBC tissues and cells. <i>PTPRG-AS1</i> silencing increased the reduction of glutathione and GPX4, increased Fe<sup>2+</sup> and reactive oxygen species in erastin-treated cells and inhibited proliferation. POU2F2 transcriptionally upregulated <i>PTPRG-AS1</i>. <i>PTPRG-AS1</i> targeted miR-376c-3p to upregulate <i>SLC7A11</i>. <i>PTPRG-AS1</i> knockdown suppressed tumor growth <i>in vivo</i>. <b>Conclusion:</b> POU2F2 transcriptionally activates <i>PTPRG-AS1</i> to modulate ferroptosis and proliferation by miR-376c-3p/SLC7A11, promoting TNBC.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"215-231"},"PeriodicalIF":3.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691541","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}
EpigenomicsPub Date : 2024-02-01Epub Date: 2024-02-12DOI: 10.2217/epi-2023-0406
Jing Hua, Miaomiao Chu, Chaohui Wang, Hangfan Zhang, Jing Luan, Yifei Zhang, Qiang Li, Taiwu Xiao, Chuansheng Zhu, Xuan Li, Bo Fu
{"title":"Digital PCR-based <i>GRHL2</i> methylation testing in acute myeloid leukemia: diagnosis, prognosis and monitoring.","authors":"Jing Hua, Miaomiao Chu, Chaohui Wang, Hangfan Zhang, Jing Luan, Yifei Zhang, Qiang Li, Taiwu Xiao, Chuansheng Zhu, Xuan Li, Bo Fu","doi":"10.2217/epi-2023-0406","DOIUrl":"10.2217/epi-2023-0406","url":null,"abstract":"<p><p><b>Background:</b> Acute myeloid leukemia (AML) is a challenging disease with high rates of recurrence. The role of the cancer-related gene <i>GRHL2</i> in AML has not been widely studied. <b>Methods:</b> Peripheral blood samples were collected from 73 AML patients and 68 healthy controls. Droplet digital PCR was used to detect <i>GRHL2</i> methylation levels to explore the value of <i>GRHL2</i> methylation in the diagnosis, treatment response and prognosis of AML. <b>Result:</b> <i>GRHL2</i> methylation was significantly increased in AML patients (p < 0.01), with high diagnostic accuracy (area under the curve: 0.848; p < 0.001). <i>GRHL2</i> methylation was correlated with chemotherapy response (p < 0.05) and is an independent prognostic factor for AML (p < 0.05). <b>Conclusion:</b> <i>GRHL2</i> methylation is expected to serve as a biomarker for diagnosing AML patients and predicting prognosis.</p>","PeriodicalId":11959,"journal":{"name":"Epigenomics","volume":" ","pages":"233-247"},"PeriodicalIF":3.8,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139722175","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}