Review
Neurosciences
Jean Lud Cadet, Subramaniam Jayanthi
Summary: This review discusses the evidence of methamphetamine exposure causing changes in epigenetic modifications and the correlations between these changes and behavioral alterations. Studies on rats have shown associations between prolonged methamphetamine self-administration with compulsive drug-taking and abstinent phenotypes, as well as increased DNA hydroxymethylation and mRNA expression in genes encoding potassium channels in the nucleus accumbens. Further research is needed to understand how pharmacological or genetic manipulations of epigenetic alterations and potassium channel expression can affect methamphetamine-taking behaviors and relapse after long periods of abstinence.
CURRENT NEUROPHARMACOLOGY
(2021)
Review
Cell Biology
Feng-Ming Tien, Hsuan-Hsuan Lu, Shu-Yung Lin, Hsing-Chen Tsai
Summary: The tumor immune microenvironment is a complex system where immune cell subtypes interact with cancer cells and stromal cells. The composition and characteristics of the immune landscape during cancer development greatly impact the effectiveness of systemic antitumor therapy in patients. Epigenetic mechanisms play a key role in antitumor immunity and immune state transitions. Targeting epigenetic modifiers to reshape the immune microenvironment has the potential to improve cancer immunotherapy and overcome therapeutic challenges.
JOURNAL OF BIOMEDICAL SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Chuizheng Kong, Guangyao Zhao, Lifeng Gao, Xiuying Kong, Daowen Wang, Xu Liu, Jizeng Jia
Summary: In this study, the association between transposons (TEs), chromatin states, and chromatin accessibility in Aegilops tauschii was analyzed. It was found that TEs contributed to the diverse distribution of chromatin states and affected the chromatin state and openness of potential regulatory elements. Some TE superfamilies carried active/open chromatin regions. Furthermore, the accessibility shaped by TEs was associated with the histone mark H3K9ac. These findings highlight the role of TEs in shaping the epigenetic landscape and regulating gene expression in Aegilops tauschii.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Zhenhui Zhong, Suhua Feng, Sascha H. Duttke, Magdalena E. Potok, Yiwei Zhang, Javier Gallego-Bartolom, Wanlu Liu, Steven E. Jacobsen
Summary: DNA methylation influences chromatin accessibility, particularly in heterochromatin, in plants. Different sequence contexts of DNA methylation interact with each other, and methylation can impact chromatin structure through mechanisms other than transcription. Increased chromatin accessibility is associated with enhanced long-range chromatin interactions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Virology
Fang Lu, Urvi Zankharia, Olga Vladimirova, Yanjie Yi, Ronald G. Collman, Paul M. Lieberman
Summary: HIV-infected macrophages have a unique epigenetic control pattern, with viral genomes maintained in a noncanonical bivalent state. These findings may contribute to the discovery of new mechanisms for controlling chronic HIV expression in infected macrophages.
JOURNAL OF VIROLOGY
(2022)
Article
Neurosciences
Anna Welle, Carmen Kasakow, Annemarie M. Jungmann, Davide Gobbo, Laura Stopper, Karl Nordstroem, Abdulrahman Salhab, Gilles Gasparoni, Anja Scheller, Frank Kirchhoff, Joern Walter
Summary: This study reveals significant differences in gene expression and DNA methylation between astrocytes from the cerebral cortex and cerebellum, linked to region-specific transcription factor networks. The epigenetic variations suggest complex combinatorial regulation of regional astrocyte transcriptomes.
Review
Endocrinology & Metabolism
Xiaoqiang Sun, Liu Wang, S. M. Bukola Obayomi, Zong Wei
Summary: Epigenetic signatures play a crucial role in defining beta cell identity during development and maintaining function in homeostatic states, but they are disrupted during the progression of T2DM.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Immunology
Suhas Sureshchandra, Norma Mendoza, Allen Jankeel, Randall M. Wilson, Nicole E. Marshall, Ilhem Messaoudi
Summary: Maternal obesity has been shown to disrupt fetal immune system development and increase susceptibility to infection in offspring. Offspring of obese mothers show higher frequencies of memory CD4 T cells, potential signs of in vivo activation, and possible functional defects. These abnormalities are associated with genomic changes and may explain the link between the obesogenic maternal environment and fetal immune reprogramming.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Cell Biology
Jose Ramon Hernandez Mora, Claudia Buhigas, Stephen Clark, Raquel Del Gallego Bonilla, Dagne Daskeviciute, Ana Monteagudo-Sanchez, Maria Eugenia Poo-Llanillo, Jose Vicente Medrano, Carlos Simon, Marcos Meseguer, Gavin Kelsey, David Monk
Summary: During pre-implantation stages, stored material in mammalian development promotes epigenetic profile erasure and genome activation. Through single-cell methylome and transcriptome sequencing, we analyzed the expression and methylation in oocytes and human embryos, identifying key events in epigenetic reprogramming and genome activation. Failure to achieve these milestones negatively impacts the developmental potential of embryos and may affect the success of assisted reproductive cycles.
Article
Multidisciplinary Sciences
M. Ali Al-Radhawi, Shubham Tripathi, Yun Zhang, Eduardo D. Sontag, Herbert Levine
Summary: In this paper, the authors investigate the complex interactions between epigenetic marks, external signals, and gene-regulatory elements that lead to the emergence and transitions between distinct phenotypes in isogenic cells. They propose a mathematical modeling framework that considers both local and global competition effects between antagonistic epigenetic regulators, as well as the influence of local transcription factors. Applying this approach to experimental findings on the epithelial-mesenchymal transition, they are able to explain the observed data and provide verifiable predictions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Genetics & Heredity
Ranjan Kumar Maji, Beate Czepukojc, Michael Scherer, Sascha Tierling, Cristina Cadenas, Kathrin Gianmoena, Nina Gasparoni, Karl Nordstroem, Gilles Gasparoni, Stephan Laggai, Xinyi Yang, Anupam Sinha, Peter Ebert, Maren Falk-Paulsen, Sarah Kinkley, Jessica Hoppstaedter, Ho-Ryun Chung, Philip Rosenstiel, Jan G. Hengstler, Joern Walter, Marcel H. Schulz, Sonja M. Kessler, Alexandra K. Kiemer
Summary: In this study, the effects of a high-fat and alcohol-containing diet on epigenetic aging in mouse hepatocytes were investigated using a multi-omics approach. Four gene network clusters associated with steatosis were identified, and specific transcription factors that may modulate these clusters were predicted. Additionally, four CpG loci linked to aging-related differential methylation were discovered, which showed minimal overlap with altered methylation in steatosis.
EPIGENETICS & CHROMATIN
(2023)
Article
Oncology
Adria-Jaume Roura, Paulina Szadkowska, Katarzyna Poleszak, Michal J. Dabrowski, Aleksandra Ellert-Miklaszewska, Kamil Wojnicki, Iwona A. Ciechomska, Karolina Stepniak, Bozena Kaminska, Bartosz Wojtas
Summary: In this study, TFs-gene regulatory networks related to glioblastomas (GBMs) were predicted and intersected with putative TF binding sites identified in human glioma cells and GBM patient samples. The expression of c-Jun was found to be higher in GBMs than in normal brain, and c-Jun binding sites were identified in multiple genes overexpressed in GBMs. The binding of c-Jun to the VIM gene promoter was stronger in GBM-derived cells than in cells derived from benign glioma, implying the modulatory role of DNA methylation in c-Jun-dependent gene expression.
CLINICAL EPIGENETICS
(2023)
Review
Reproductive Biology
Jianyu Gan, Xin Zhang, Yongchang Lu, Zhenfang Wu, Gengyuan Cai, Linjun Hong
Summary: This article describes four epigenetic modifications involved in porcine embryonic development and explores the possible crosstalk between them. Researching porcine embryonic development is crucial for understanding human reproductive diseases and improving litter size in commercial pigs.
BIOLOGY OF REPRODUCTION
(2022)
Review
Plant Sciences
Jie Liu, Meng Ke, Yuhan Sun, Shihui Niu, Wenli Zhang, Yun Li
Summary: Plant rejuvenation involves resetting gene expression patterns, chromatin remodeling, and histone modifications, resulting in the restoration of juvenile characteristics. The epigenetic mechanisms underlying this process are still in the early stages of study.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biotechnology & Applied Microbiology
Annett Erkes, Stefanie Mucke, Maik Reschke, Jens Boch, Jan Grau
Summary: The study suggests a strategy to improve prediction accuracy by considering the epigenetic state of the host plant genome in the region of the target box. By incorporating chromatin accessibility and DNA methylation of the target boxes, an improvement in prediction accuracy was observed, especially when using both epigenetic features in combination. The results also indicate the potential of collecting condition-specific chromatin accessibility data and methylation information when studying putative virulence targets of Xanthomonas TALEs.
Article
Oncology
Seong Hwi Hong, Keun Hong Son, Sang Yun Ha, Tae In Wee, Sung Kyung Choi, Ji Eun Won, Hee Dong Han, Youngtae Ro, Yeong-Min Park, Jung Woo Eun, Suk Woo Nam, Jeung-Whan Han, Keunsoo Kang, Jueng Soo You
Summary: This study uncovers a novel protumorigenic role for SMARCB1 in liver cancer and reveals significant links between nucleoporins and chromatin remodelers in cancer through identifying NUP210 as a critical coregulator of SMARCB1 chromatin remodeling activity.
Article
Oncology
Gil Ho Lee, Hyo Jung Cho, Garam Lee, Han Gyeol Kim, Hee Jung Wang, Bong-Wan Kim, Mi Young Lee, So Young Yoon, Choong-Kyun Noh, Chul Won Seo, Jung Woo Eun, Jae Youn Cheong, Sung Won Cho, Soon Sun Kim
Summary: The study demonstrated that the preoperative edema index using bioelectrical impedance analysis can predict post-hepatectomy complications, especially in patients with liver cirrhosis. Tumor size was identified as the only significant predictive factor for short-term survival after hepatectomy.
ANNALS OF TRANSLATIONAL MEDICINE
(2021)
Article
Oncology
Soon Sun Kim, Geum Ok Baek, Ju A. Son, Hye Ri Ahn, Moon Kyung Yoon, Hyo Jung Cho, Jung Hwan Yoon, Suk Woo Nam, Jae Youn Cheong, Jung Woo Eun
Summary: This study explores the diagnostic potential of serum small extracellular vesicle-derived long noncoding RNAs (EV-lncRNAs) for hepatocellular carcinoma (HCC). Promising driver onco-lncRNA candidates show high discriminant ability in the diagnosis of very early HCC. Serum small EV-MALAT1, EV-DLEU2, EV-HOTTIP, and EV-SNHG1 represent potential diagnostic markers for early-stage HCC.
MOLECULAR ONCOLOGY
(2021)
Article
Oncology
Hye Ri Ahn, Geum Ok Baek, Moon Gyeong Yoon, Ju A. Son, Donglim You, Jung Hwan Yoon, Hyo Jung Cho, Soon Sun Kim, Jae Yeon Cheong, Jung Woo Eun
Summary: This study identified the most stable reference gene HMBS for normalization of relative gene expression in HCC tissues and blood samples using systematic literature search and RT-qPCR techniques.
Article
Medicine, General & Internal
Hyo Jung Cho, Geum Ok Baek, Moon Gyeong Yoon, Hye Ri Ahn, Ju A. Son, Soon Sun Kim, Jae Youn Cheong, Jung Woo Eun
Summary: Novel protein contents of hepatocellular carcinoma (HCC)-derived exosomes (HEX) were identified, with CCT8 and CFL1 showing potential as biomarkers for HCC diagnosis and prognosis, correlated with disease progression and survival rates in patients.
Article
Gastroenterology & Hepatology
Hyo Jung Cho, Young Hwan Ahn, Min Suh Sim, Jung Woo Eun, Soon Sun Kim, Bong Wan Kim, Jimi Huh, Jei Hee Lee, Jai Keun Kim, Buil Lee, Jae Youn Cheong, Bohyun Kim
Summary: The study identified high MRE-LS, low serum albumin, major hepatic resection, higher albumin-bilirubin score, and higher serum alpha-fetoprotein as independent risk factors for PHLF. A risk prediction model based on MRE-LS showed excellent performance in predicting PHLF, especially grade B and C PHLF.
Article
Oncology
Ju A. Son, Hye Ri Ahn, Donglim You, Geum Ok Baek, Moon Gyong Yoon, Jung Hwan Yoon, Hyo Jung Cho, Soon Sun Kim, Suk Woo Nam, Jung Woo Eun, Jae Youn Cheong
Summary: Investigating molecular markers for predicting HCC recurrence revealed novel gene signatures, potentially serving as prognostic indicators for patients.
Article
Oncology
Hye Ri Ahn, Geum Ok Baek, Moon Gyeong Yoon, Ju A. Son, Jung Hwan Yoon, Jae Youn Cheong, Hyo Jung Cho, Ho Chul Kang, Jung Woo Eun, Soon Sun Kim
Summary: The study reveals the overexpression of WASF2 in hepatocellular carcinoma (HCC) and its correlation with patient prognosis. Inactivation of WASF2 has anti-tumorigenic effects on HCC cells, suggesting that it could be a potential therapeutic target for HCC.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2022)
Article
Medicine, General & Internal
Jung Woo Eun, Jeong Won Jang, Hee Doo Yang, Jooyoung Kim, Sang Yean Kim, Min Jeong Na, Eunbi Shin, Jin Woong Ha, Soyoung Jeon, Young Min Ahn, Won Sang Park, Suk Woo Nam
Summary: The high morbidity rate of hepatocellular carcinoma (HCC) is mainly linked to late diagnosis. Early diagnosis of this leading cause of mortality is therefore extremely important. In this study, a gene selection strategy was used to identify potential secretory proteins for the early detection of HCC. From computational approaches, 10 gene elements were suggested as potent candidate secretory markers, and four of them (HMMR, NXPH4, PITX1, THBS4) were confirmed as early-stage HCC diagnostic markers with superior predictive capability in a large cohort of patients. Serum proteins HMMR, NXPH4, PITX1 and THBS4 can complement measurement of AFP in diagnosing HCC and improve identification of patients with AFP-negative HCC as well as discriminate HCC from non-malignant chronic liver disease.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Jung Woo Eun, Hye Ri Ahn, Geum Ok Baek, Moon Gyeong Yoon, Ju A. Son, Ji Hyang Weon, Jung Hwan Yoon, Hyung Seok Kim, Ji Eun Han, Soon Sun Kim, Jae Youn Cheong, Bong-wan Kim, Hyo Jung Cho
Summary: Cancer-associated fibroblasts (CAFs) in hepatocellular carcinoma (HCC) have downregulated expression of hsa-miR-101-3p and hsa-miR-490-3p, which target TGFBR1. The downregulation of these miRs and high TGFBR1 expression are associated with poor prognosis in HCC patients. TGFBR1 expression is also correlated with infiltration of immunosuppressive immune cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Hyung Seok Kim, Su In Lee, Yu Rim Choi, Jiyun Kim, Jung Woo Eun, Kyoung Seob Song, Jee-Yeong Jeong
Summary: Epithelial-to-mesenchymal transition (EMT) plays a critical role in lung cancer development by promoting invasiveness and metastasis. The expression levels of tight junction proteins, ZO-1 and ZO-2, were found to be lower in lung cancer tissues compared to normal lung tissues. Knockdown of ZO-1 and ZO-2 regulated cell migration and invasion and affected macrophage polarization. The GNAQ-ZO-1/2 axis may have a tumor-suppressive role in lung cancer development and progression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Jung Woo Eun, Jung Hwan Yoon, Hye Ri Ahn, Seokhwi Kim, Young Bae Kim, Su Bin Lim, Won Park, Tae Wook Kang, Geum Ok Baek, Moon Gyeong Yoon, Ju A. Son, Ji Hyang Weon, Soon Sun Kim, Hyo Jung Cho, Jae Youn Cheong
Summary: This study discovered that cancer-associated fibroblasts (CAFs) play a crucial role in inducing resistance to tyrosine kinase inhibitors (TKIs) in hepatocellular carcinoma (HCC). The CAF-derived SPP1 was identified as a candidate molecule driving TKI resistance, and inhibitors of SPP1 can reverse this resistance. Additionally, the plasma level of SPP1 before TKI treatment can serve as a potential biomarker for predicting treatment response in advanced HCC patients.
CANCER COMMUNICATIONS
(2023)
Article
Oncology
Hyung Seok Kim, Jung Hwan Yoon, Geum Ok Baek, Moon Gyeong Yoon, Ji Eun Han, Hyo Jung Cho, Soon Sun Kim, Jee-Yeong Jeong, Jae Youn Cheong, Jung Woo Eun
Summary: This study introduces a comprehensive approach to identify the potential blood marker ITGA6 for early HCC detection. The upregulation of ITGA6 in HCC is confirmed, and it is associated with prognosis. Further analysis reveals that ITGA6 is predominantly expressed in TECs and enriched in angiogenesis-related pathways. This study sheds light on the potential of ITGA6 as a blood-based marker for HCC early detection and its interaction with the tumor microenvironment.
Meeting Abstract
Oncology
H. R. Ahn, J. A. Son, J. H. Weon, G. O. Baek, M. G. Yoon, J. E. Han, S. S. Kim, J. Y. Cheong, M. Kwon, J. W. Eun, H. J. Cho
EUROPEAN JOURNAL OF CANCER
(2022)
Meeting Abstract
Oncology
H. R. Ahn, J. W. Eun, J. H. Yoon, J. A. Son, J. H. Weon, G. O. Baek, M. G. Yoon, J. E. Han, M. Kwon, S. S. Kim, J. Y. Cheong, H. J. Cho
EUROPEAN JOURNAL OF CANCER
(2022)