Article
Multidisciplinary Sciences
Juqing Zhang, Yaqi Zhou, Wei Yue, Zhenshuo Zhu, Xiaolong Wu, Shuai Yu, Qiaoyan Shen, Qin Pan, Wenjing Xu, Rui Zhang, Xiaojie Wu, Xinmei Li, Yayu Li, Yunxiang Li, Yu Wang, Sha Peng, Shiqiang Zhang, Anmin Lei, Xinbao Ding, Fan Yang, Xingqi Chen, Na Li, Mingzhi Liao, Wei Warg, Jinlian Hua
Summary: Pluripotent stem cells in different mammals are maintained by distinct mechanisms, and super-enhancers (SEs) play a crucial role in controlling cell identity and pluripotency. BRD4 is an important activator of pluripotency-associated SEs in mammals, and three specific SEs show conservation in different placental mammals.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Le Xiong, Erik A. Tolen, Jinmi Choi, Sergiy Velychko, Livia Caizzi, Taras Velychko, Kenjiro Adachi, Caitlin M. MacCarthy, Michael Lidschreiber, Patrick Cramer, Hans R. Schoeler
Summary: The transcription factor Oct4 is essential for stem cell pluripotency, and this study investigates its functions by depleting and recovering it in embryonic stem cells. Oct4 depletion results in loss of binding to enhancers and decreased mRNA synthesis of target genes involved in maintaining pluripotency. Partial recovery of Oct4 expression increases chromatin accessibility but does not fully restore enhancer transcription. These findings suggest that Oct4 has concentration-dependent activities.
Article
Cell Biology
Pixi Yan, J. Yuyang Lu, Jing Niu, Juntao Gao, Michael Q. Zhang, Yafei Yin, Xiaohua Shen
Summary: The study reveals that long noncoding RNA (lncRNA) genes are preferentially located next to super-enhancers (SEs) and depletion of SE-associated lncRNA transcripts can dysregulate the activity of nearby SEs in mouse embryonic stem cells (mESCs). Specifically, the lncRNA gene Platr22 plays a critical regulatory role in modulating the activity of a nearby SE and the expression of pluripotency regulator ZFP281, contributing to pluripotency maintenance and proper differentiation of mESCs.
JOURNAL OF MOLECULAR CELL BIOLOGY
(2021)
Review
Cell Biology
Puja Agrawal, Sridhar Rao
Summary: Cell fate decisions rely on gene expression changes mediated by regulatory elements like enhancers and CTCF binding sites. These elements play crucial roles in early mammalian development and impact cell-type specific gene expression.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yuan Jiang, Yan-Yi Jiang, De-Chen Lin
Summary: This review summarizes the methods for identifying super-enhancers and core regulatory circuits in cancer cells, as well as the mechanisms by which master transcription factors and super-enhancers cooperatively regulate cancer-specific expression programs. It also discusses the cancer type and subtype specificity of core regulatory circuits and their significance in cancer biology.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Genetics & Heredity
Wensheng Shi, Bowen Zhong, Jiaming Dong, Xiheng Hu, Lingfang Li
Summary: Triple-negative breast cancer (TNBC) is a clinically aggressive subtype of breast cancer. In this study, the researchers systematically characterized the core transcriptional regulatory circuitry (CRC) in TNBC and found its involvement in DNA conformation change, metabolism process, and signaling response. They also discovered that CRC transcription factors (TFs) and their partners play a specific role in TNBC, especially in relation to the immune phenotype.
FRONTIERS IN GENETICS
(2023)
Article
Oncology
Mark Primeaux, Xiangdong Liu, Saiprasad Gowrikumar, Iram Fatima, Kurt W. Fisher, Dhundy Bastola, Alex J. Vecchio, Amar B. Singh, Punita Dhawan
Summary: High expression of CLDN1 in CRC is associated with cancer stemness and chemoresistance signaling pathways. CLDN1 promotes stemness and chemoresistance through a direct interaction with EPHA2 tyrosine kinase.
Article
Medicine, Research & Experimental
Chenchen Feng, Chao Song, Yong Jiang, Jun Zhao, Jian Zhang, Yuezhu Wang, Mingxue Yin, Jiang Zhu, Bo Ai, Qiuyu Wang, Fengcui Qian, Yuexin Zhang, Desi Shang, Jiaqi Liu, Chunquan Li
Summary: This study identifies core transcription factors and their regulatory circuits in large cell/tissue samples. The local module analysis highlights the essential functions and prognostic performance of the core circuitry. Tissue-specific core circuits are related to cell identity and exhibit potential for disease markers and cancer immunotherapy.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Oncology
Jingxuan Li, Jiying Wang, Yanping Wang, Xueyan Zhao, Tao Su
Summary: This study identified and characterized LINC01004 as a crucial oncogene in hepatocellular carcinoma (HCC) and a potential therapeutic target. LINC01004 was upregulated in liver cancer tissues and associated with poor patient prognosis. It promoted cell proliferation and metastasis in HCC, and its transcription was regulated by the binding of E2F1 to the super-enhancer.
CLINICAL EPIGENETICS
(2023)
Article
Biochemistry & Molecular Biology
Feifeng Song, Qi Zhang, Xixuan Lu, Tong Xu, Qing Hu, Xiaoping Hu, Weijiao Fan, Yiwen Zhang, Ping Huang
Summary: Recent studies have found that Rab11-family interacting proteins (Rab11-FIPs) are crucial in tumorigenesis and progression. Specifically, Rab11-FIP4 is significantly upregulated in hepatocellular carcinoma (HCC), and its elevated expression promotes stemness and cancer cell formation. Conversely, silencing Rab11-FIP4 suppresses cancer stem-like features and increases sensitivity to sorafenib. Mechanistically, Rab11-FIP4 interacts with ADP-ribosylation factor 5 (ARF5) to influence cell cycle-related proteins, suggesting Rab11-FIP4 as a potential target for HCC therapy.
JOURNAL OF PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Oncology
Yingxi Xu, Junli Mou, Ying Wang, Wei Zhou, Qing Rao, Haiyan Xing, Zheng Tian, Kejing Tang, Min Wang, Jianxiang Wang
Summary: Tregs can promote the stemness of AML cells through IL10 activation of the PI3K/AKT pathway, and blocking the IL10/IL10R/PI3K/AKT signal can reduce the stemness of AML cells. The interaction between Tregs and AML cells may be a new approach to target LSCs in AML treatment.
Article
Oncology
Youran Chen, Yi Pan, Hanyu Gao, Yunmeng Yi, Shijie Qin, Fei Ma, Xue Zhou, Miao Guan
Summary: This study developed an 11-gene risk score prognostic model that can effectively predict the survival rate of GBM patients. The model is correlated with immune cell infiltration and chemotherapeutic sensitivity, providing potential implications for prognosis determination and treatment choice in GBM patients.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2023)
Article
Genetics & Heredity
Hang Li, Caiping Zhao, Zeli Li, Kainan Yao, Jingjing Zhang, Wenwen Si, Xiaohong Liu, Yong Jiang, Meiling Zhu
Summary: Abnormal fibroblast differentiation into myofibroblast is a crucial mechanism of pulmonary fibrosis. Super-enhancers are believed to regulate cell identity and their abnormal activation may be involved in the pathogenesis of PF. This study aimed to identify potential pathogenic super-enhancer-driven genes in PF, and identified overlap genes that are predicted to play a role in the disease's pathology. LTBP2, a predicted super-enhancer-driven pathogenic gene, was validated to be upregulated in PF mouse models and TGF-beta stimulated fibroblasts. It was found that interference with super-enhancers could decrease the expression of LTBP2, suggesting a potential new therapeutic avenue for PF.
FRONTIERS IN GENETICS
(2021)
Article
Oncology
Qi Shen, Rui Wang, Xinling Liu, Ping Song, Mingzhu Zheng, Xiaomin Ren, Jingang Ma, Zhong Lu, Jiaqiu Li
Summary: Based on recent research, this study explores the regulatory mechanism of glutamine metabolism in cancer cells, focusing on the activation of super-enhancers and their relationship to the transcription factor HSF1. The study identifies an HSF1-mediated super enhancer, lncRNA-LINC00857, which promotes the expression of SLC1A5/ASCT2 and facilitates glutamine transport. Targeting the HSF1/LINC00857/ANXA11 axis may provide a valuable therapeutic strategy against colorectal cancer.
Article
Medicine, General & Internal
Shang-Xin Liu, Chong Wang, Ruo-Bin Lin, Wei-Yue Ding, Gaurab Roy, Hong-Bo Wang, Ting Yang, Qian Liu, Yi-Ling Luo, Shui-Lin Jin, Mu-Sheng Zeng, Bo Zhao, Qian Zhong
Summary: This study revealed the critical role of super-enhancers associated with SOX2 in the tumorigenesis of nasopharyngeal carcinoma (NPC). High expression of SOX2 was correlated with poor prognosis. Inhibition of SOX2 suppressed tumor growth, highlighting the potential of SOX2 as a therapeutic target for NPC patients.
Article
Materials Science, Multidisciplinary
Meng-Shiue Lee, Yueh Chien, Pai-Chi Teng, Xuan-Yang Huang, Yi-Ying Lin, Ting-Yi Lin, Shih-Jie Chou, Chian-Shiu Chien, Yu-Jer Hsiao, Yi-Ping Yang, Wensyang Hsu, Shih-Hwa Chiou
Summary: This study demonstrates that the doubly reentrant topology (DRT) surfaces have a significant antibiofouling effect that can effectively prevent viral contamination. This effect still exists even if the DRT surface is made of a hydrophilic material. By minimizing the contact area between pathogens and surfaces, fomite transmission of viruses can be effectively prevented. The unique geometric features of DRT surfaces also contribute to their excellent antibiofouling ability, which may shed light on pathogen elimination in alleviating the COVID-19 pandemic.
ADVANCED MATERIALS TECHNOLOGIES
(2023)
Article
Cell Biology
Chih-Jung Chen, Ya-Chuan Hu, Yueh Chien, Wei-Chieh Huang, Chi-Sheng Wu, Chung-Ying Tsai, Yang-Hsiang Lin, Meng-Shiue Lee, Chian-Shiu Chien, Yi-Ping Yang, Meng-Chou Lee, Chung-Chih Tseng, Hsiang-Cheng Chi
Summary: This study reveals the correlation between the malignancy of neuroblastoma (NB) cells and the expression of Calreticulin (CALR), as well as their radioresistant and stem cell properties. Manipulating CALR expression can alter the stem cell characteristics and radioresistance of NB cells. CALR overexpression increases ROS production and secretion of proinflammatory cytokines, significantly inhibiting the growth of NB tumors, especially when combined with radiotherapy.
OXIDATIVE MEDICINE AND CELLULAR LONGEVITY
(2023)
Article
Genetics & Heredity
Joannie St-Germain, Muhammad Riaz Khan, Viktoriia Bavykina, Rebecka Desmarais, Micah Scott, Guylain Boissonneault, Marie A. Brunet, Benoit Laurent
Summary: Most pseudogenes are formed through the reverse transcription and integration of RNA transcripts into the genome. Pseudogenes are often imperfect copies of functional genes, accumulating mutations in their sequence. In this study, a retrotransposed pseudogene, Pfh8-ps, was identified in the mouse genome. Unlike typical pseudogenes, Pfh8-ps has an intact coding sequence and can produce a functional protein, PHF8-PS. However, PHF8-PS lacks the demethylase activity of its parental protein and exhibits different subcellular localization.
Article
Oncology
Sheng-Fan Wang, Yuh-Lih Chang, Wen-Liang Fang, Anna Fen-Yau Li, Chian-Feng Chen, Tien-Shun Yeh, Giun-Yi Hung, Kuo-Hung Huang, Hsin-Chen Lee
Summary: This study investigates the role of growth differentiation factor 15 (GDF15) in chemoresistance of gastric cancer. The results demonstrate that GDF15 serum levels can serve as a valuable biomarker for predicting prognosis in gastric cancer. Additionally, GDF15 upregulation is associated with cisplatin resistance in gastric cancer cells by increasing intracellular glutathione (GSH) content and antioxidant activities.
Article
Environmental Sciences
Jinfeng Liu, Jiebo Lin, Jiafeng Chen, Yasen Maimaitiyiming, Kunhui Su, Siqi Sun, Guankai Zhan, Chih-Hung Hsu
Summary: Bisphenol C (BPC), a common substitute for Bisphenol A (BPA), was found to cause liver and intestinal developmental defects in zebrafish by disrupting the GPER-AKT-mTOR-RPS6 pathway. These results not only revealed the toxicity of BPC during organ development, but also provided insights into the underlying mechanism.
Review
Endocrinology & Metabolism
Sheng-Fan Wang, Yi-Sheng Lin, Wan-Yu Yeh, Yuh-Lih Chang, Chern-En Chiang, Chen-Huan Chen, Ling-Ming Tseng, Hsin-Chen Lee, Chun-Yu Liu, Hao-Min Cheng
Summary: This study summarizes the clinical effects of antiresorptive agents in patients with early breast cancer receiving endocrine therapy. The results show that antiresorptive agents have significant clinical benefits on disease recurrence and locoregional recurrence in these patients. However, there is a potential risk of osteonecrosis of the jaw with the use of these agents.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2023)
Article
Multidisciplinary Sciences
Zhengyi Li, Haiyan Xu, Jiaqun Li, Xiao Xu, Junjiao Wang, Danya Wu, Jiateng Zhang, Juan Liu, Ziwei Xue, Guankai Zhan, Bobby Cheng Peow Tan, Di Chen, Yun-Shen Chan, Huck Hui Ng, Wanlu Liu, Chih-Hung Hsu, Dan Zhang, Yang Shen, Hongqing Liang
Summary: This study reveals the role of ZFP352 in facilitating the dissolution of the totipotency network during early embryonic development. By binding to different retrotransposon families, ZFP352 triggers the activation of later developmental programs, leading to timely embryonic development.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Sheng-Fan Wang, Kuan-Wei Huang, Yueh-Ching Chou, Hsin-Chen Lee, Po-Kuei Wu, Wei-Ming Chen, Giun-Yi Hung, Yuh-Lih Chang
Summary: Taiwanese patients receiving high-dose methotrexate (HD-MTX) treatment often experience severe hepatotoxicity, which affects subsequent treatment. Co-administration of proton pump inhibitors (PPIs), trimethoprim-sulfamethoxazole (TMP-SMX), or non-steroidal anti-inflammatory drugs (NSAIDs) with MTX can lead to drug-drug interactions. However, limited real-world analyses have been conducted on the effects of these co-medications and other potential risk factors on HD-MTX-mediated acute hepatotoxicity in patients with osteogenic sarcoma (OGS) in East Asia.
Review
Medicine, Research & Experimental
Muhammad Riaz Khan, Mariano Avino, Raymund J. Wellinger, Benoit Laurent
Summary: Alternative splicing of RNA molecules significantly contributes to transcriptome diversity, with 90%-95% of multi-exon genes in humans producing alternatively spliced RNA transcripts. This includes long non-coding RNA (lncRNA) genes, which undergo conventional and alternative splicing. Emerging evidence suggests that lncRNA splice variants play important roles in cell biology and are associated with various diseases, including cancer. This review provides insights into the landscape of lncRNA alternative splicing and discusses its functional relevance at the molecular level, including RNA-based differential functions, production of micropeptides, and generation of circular RNAs. It also highlights exciting perspectives for this emerging field and outlines future research directions.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Review
Genetics & Heredity
Jeru Manoj Manuel, Noe Guilloy, Ines Khatir, Xavier Roucou, Benoit Laurent
Summary: Alternative splicing (AS) is a mechanism that generates multiple mature transcripts from protein-coding genes and long non-coding RNA (lncRNA) genes, increasing transcriptome complexity and producing different protein isoforms. Despite the identification of numerous alternatively spliced transcripts, the low detection rate of protein isoforms has raised questions about the contribution of AS to proteomic diversity and the functional relevance of AS events.
FRONTIERS IN GENETICS
(2023)
Article
Cell Biology
Ines Khatir, Marie A. Brunet, Anna Meller, Florent Amiot, Tushar Patel, Xavier Lapointe, Jessica Avila Lopez, Noe Guilloy, Anne Castonguay, Mohammed Amir Husain, Joannie St Germain, Francois-Michel Boisvert, Melanie Plourde, Xavier Roucou, Benoit Laurent
Summary: By comparing the transcriptome and proteome of the mouse cortex during aging, this study explores the relationship between changes in gene expression and the decline in physical and cognitive abilities. The findings show that aging mainly activates gene expression in the cortex, and an increase in mRNA expression correlates with protein expression, particularly in the anterior cingulate cortex. Genes involved in sensory perception and immune functions show increased mRNA and protein levels during aging, while specific proteins involved in translation, ribosome assembly, and protein degradation exhibit stable mRNA levels.
Article
Computer Science, Information Systems
Yuan-Yu Chang, Sheng-Tang Wong, Emmanuel O. Salawu, Ming-Hsuan Liao, Jui-Hung Hung, Lee-Wei Yang
Summary: Since the 90s, keyword-based search engines have been the primary option for people to find relevant web content. However, users had to expose their queries to the service providers. This article presents a new method for searching the internet using a full article as a query, while protecting user privacy. The method utilizes encoding and indexing techniques and can be performed on the user's device. By submitting the encoded queries to a cloud service for plagiarism checks, identical content can be detected in a database. The method offers high accuracy, fast speed, and user privacy protection.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
(2023)
Review
Cell Biology
Sheng-Fan Wang, Ling-Ming Tseng, Hsin-Chen Lee
Summary: Dysregulating cellular metabolism is an emerging cancer hallmark, and mitochondria play a crucial role in cancer progression. This review discusses the alterations in mitochondrial DNA and dynamics in cancer, as well as the regulatory mechanisms of mitochondrial dysfunction-mediated retrograde signaling pathways. It also explores the impact of mitochondria on immune regulation and the potential of targeting mitochondria and metabolism for cancer immunotherapy.
JOURNAL OF BIOMEDICAL SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Sheng-Fan Wang, Yuh-Lih Chang, Ting-Yu Liu, Kuo-Hung Huang, Wen-Liang Fang, Anna Fen-Yau Li, Tien-Shun Yeh, Giun-Yi Hung, Hsin-Chen Lee
Summary: This study found that high expression of GDF15 protein may increase disease recurrence in adjuvant chemotherapy-treated gastric cancer patients. Additionally, treatment with mitochondrial inhibitors can upregulate GDF15 and enhance cisplatin insensitivity in human gastric cancer cells. Mechanistically, the activating transcription factor 4-C/EBP homologous protein pathway plays a crucial role in the heightened manifestation of GDF15. This research reveals that mitochondrial dysfunction enhances cisplatin insensitivity through GDF15 upregulation.
Article
Allergy
Vincent Yi-Fong Su, Szu-Wen Ko, Yuh-Lih Chang, Yueh-Ching Chou, Hsin-Chen Lee, Kuang-Yao Yang, Kun-Ta Chou, Chia-Chen Hsu
Summary: This study found that cardioselective beta-blockers, ARBs, and DHP CCB therapies may lower the risk of acute exacerbation in patients with ACO.
ALLERGY ASTHMA & IMMUNOLOGY RESEARCH
(2022)