Article
Medicine, Research & Experimental
Michelle M. Gonzalez, Adebowale O. Bamidele, Phyllis A. Svingen, Mary R. Sagstetter, Thomas C. Smyrk, Joseph M. Gaballa, Feda H. Hamdan, Robyn Laura Kosinsky, Hunter R. Gibbons, Zhifu Sun, Zhenqing Ye, Asha Nair, Guilherme P. Ramos, Manuel B. Braga Neto, Alexander Q. Wixom, Angela J. Mathison, Steven A. Johnsen, Raul Urrutia, William A. Faubion
Summary: Research has shown that BMI1 regulates the inflammatory enhancer network in Treg cells, and its loss leads to systemic inflammation and phenotypic conversion of Treg cells, which is relevant to CD4(+) T cells associated with Crohn's disease.
JOURNAL OF CLINICAL INVESTIGATION
(2021)
Article
Multidisciplinary Sciences
Xiao Chen, Yinglu Li, Fang Zhu, Xinjing Xu, Brian Estrella, Manuel A. Pazos II, John T. McGuire, Dimitris Karagiannis, Varun Sahu, Mustafo Mustafokulov, Claudio Scuoppo, Francisco J. Sanchez-Rivera, Yadira M. Soto-Feliciano, Laura Pasqualucci, Alberto Ciccia, Jennifer E. Amengual, Chao Lu
Summary: Co-dependency mapping assays have identified genetic dependencies in cancer and can provide insights into chromatin crosstalk mechanisms. The authors developed a pipeline to integrate co-dependency mapping with molecular information in pan-cancer cell lines to uncover chromatin complexes and potential drug targets. This study sheds light on trans-regulatory interactions as mechanisms of chromatin regulation and potential synthetic lethality targets.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Amira Fitieh, Andrew J. Locke, Mobina Motamedi, Ismail Hassan Ismail
Summary: Polycomb group proteins play roles in stem cell maintenance, gene silencing, and DNA damage repair. BMI1, a member of PRC1, is involved in DNA repair and genome integrity, making it a potential pharmacological target.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Yamato Fukui, Yasushi Hirota, Shizu Aikawa, Akihiko Sakashita, Ryoko Shimizu-Hirota, Norihiko Takeda, Chihiro Ishizawa, Rei Iida, Tetsuaki Kaku, Tomoyuki Hirata, Takehiro Hiraoka, Shun Akaeda, Mitsunori Matsuo, Yutaka Osuga
Summary: Infertility affects 15% of couples worldwide, with recurrent implantation failure (RIF) being a major issue in IVF-ET programs. This study revealed that a uterine gene network regulated by the polycomb repressive complex 2 (PRC2) controls embryo implantation. Dysregulation of PRC2 components and target genes was observed in patients with RIF. Knockout mice studies showed that stromal Ezh2 plays a crucial role in female fertility. This research highlighted the importance of the EZH2-PRC2-H3K27me3 axis in preparing the endometrium for successful embryo invasion.
CELL DEATH & DISEASE
(2023)
Article
Multidisciplinary Sciences
Ahmed H. Ghobashi, Truc T. Vuong, Jane W. Kimani, Christopher A. Ladaika, Peter C. Hollenhorst, Heather M. O'Hagan
Summary: In colorectal cancer (CRC), active AKT phosphorylates EZH2 on serine 21, leading to the modulation of gene expression through the AKT/EZH2/beta-catenin axis. EZH2 interacts with and methylates beta-catenin, increasing its binding to chromatin and promoting transcription. Furthermore, EZH2-mediated beta-catenin trimethylation enhances its interaction with TCF1 and RNA polymerase II, resulting in significant gains in genomic regions with beta-catenin occupancy.
Article
Oncology
Petter Holland, Mari Wildhagen, Mette Istre, Olaug Marie Reiakvam, John Arne Dahl, Arne Soraas
Summary: This study provides a deep analysis of the epigenetics of Cri du chat syndrome, revealing distinct DNA methylation patterns in patients compared to controls. The study identifies DNA methylation changes in the gene promoters associated with symptoms of the syndrome, indicating potential epigenetic involvement in embryonic development.
CLINICAL EPIGENETICS
(2022)
Article
Oncology
Liya Ma, Bin Liang, Huixian Hu, Wenli Yang, Shengyun Lin, Lihong Cao, Kongfei Li, Yuemin Kuang, Lihong Shou, Weimei Jin, Jianping Lan, Xingnong Ye, Jing Le, Huyi Lei, Jiaping Fu, Ying Lin, Wenhua Jiang, Zhiying Zheng, Songfu Jiang, Lijuan Fu, Chuanyong Su, XiuFeng Yin, Lixia Liu, Jiayue Qin, Jie Jin, Shenxian Qian, Guifang Ouyang, Hongyan Tong
Summary: By reviewing 140 MDS patients with SF3B1 mutation, researchers have developed a personalized prediction model that can better predict the survival of these patients.
FRONTIERS IN ONCOLOGY
(2022)
Article
Cell Biology
Rebecca J. Burgess, Zhiyu Zhao, Daisuke Nakada, Sean J. Morrison
Summary: The study showed that deficiency of Bmi1 leads to increased division of HSCs without inducing senescence. Bmi1 promotes HSC quiescence by negatively regulating ARX expression and promoting proteostasis by suppressing protein synthesis.
GENES & DEVELOPMENT
(2022)
Article
Biochemistry & Molecular Biology
Jun Wang, Kwang-Su Park, Xufen Yu, Weida Gong, H. Shelton Earp, Gang Greg Wang, Jian Jin, Ling Cai
Summary: This study reveals the non-canonical (co-)activator recruitment and gene activation functions of EZH2 in prostate cancer and suggests that EZH2-targeting PROTACs could be a potential therapeutic approach for aggressive prostate cancer.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Liping Chu, Yuxiu Qu, Yang An, Linjun Hou, Juewan Li, Weijia Li, Gaofeng Fan, Bao-Liang Song, En Li, Liye Zhang, Wei Qi
Summary: This study investigates the pharmacological mechanism of the PRC2 inhibitor MAK683 and identifies a group of senescence-associated genes that are derepressed upon PRC2 inhibition, leading to tumor regression and improved therapeutic efficacy. Furthermore, the combination of PRC2 inhibitors and CDK4/6 inhibitors shows even better effects, providing a novel strategy for clinical treatment.
CELL DEATH & DISEASE
(2022)
Article
Cell Biology
Ruiqi Liu, Yonglin Peng, Wenfei Du, Yunqiang Wu, Wen Zhang, Congxia Hu, Min Liu, Xinhua Liu, Ji Wu, Jielin Sun, Xiaodong Zhao
Summary: BMI1 is a critical marker of spermatogonial stem cells and plays multifunctional roles in maintaining the fate of undifferentiated spermatogonia. It preserves the PI3K-Akt signaling pathway and interacts with the transcription factor SALL4 to regulate gene expression programs of undifferentiated spermatogonia.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Bo Zhang, Chen Zhao, Wenchen Shen, Wei Li, Yue Zheng, Xiangfei Kong, Junbao Wang, Xudong Wu, Tao Zeng, Ying Liu, Yan Zhou
Summary: The hippocampus plays a crucial role in learning and memory, and its development requires precise coordination of cell patterning, proliferation, differentiation, and migration. In this study, it was found that KDM2B mediates a gene repressive program that controls fate specification and cell migration in the hippocampus, affecting its morphology and related behaviors.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Lihu Gong, Xiuli Liu, Lianying Jiao, Xin Yang, Andrew Lemoff, Xin Liu
Summary: The authors identify SUZ12 as a cellular substate of casein kinase 2 (CK2) and highlight its role in promoting PRC2 function in cell identity maintenance during stem cell differentiation. This phosphorylation-dependent mechanism stimulates PRC2 enzymatic activity, enhancing its binding to substrates and promoting gene repression. Loss of this phosphorylation impairs PRC2 recruitment and compromises its ability to maintain differentiated cell identity.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Ka-Wing Fong, Jonathan C. Zhao, Xiaodong Lu, Jung Kim, Andrea Piunti, Ali Shilatifard, Jindan Yu
Summary: PALI1 is a newly identified accessory protein that plays a role in advanced prostate cancer. It competes with JARID2 for binding to the PRC2 core subunit SUZ12 and interacts with the H3K9 methyltransferase G9A, forming a unique super-complex involved in dual H3K9/K27 methylation and gene repression. PALI1 and G9A promote prostate cancer cell proliferation and invasion, and drive tumor growth in xenograft models.
Article
Biochemistry & Molecular Biology
Ngai Ting Chan, Junfeng Huang, Gui Ma, Hao Zeng, Kristine Donahue, Yidan Wang, Lingjun Li, Wei Xu
Summary: CTR9 is a scaffold subunit in PAFc complex and plays a crucial role in controlling H3K27me3 levels and genomic distribution mediated by PRC2. Loss of CTR9 leads to increased H3K27me3 levels, expanded recruitment of PRC2 on chromatin, and a shift from less active PRC2.2 to more active PRC2.1, resulting in hypersensitivity of breast cancer cells to PRC2 inhibitors.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Pathology
Lingyun Wu, Mohammad Awaji, Sugandha Saxena, Michelle L. Varney, Bhawna Sharma, Rakesh K. Singh
AMERICAN JOURNAL OF PATHOLOGY
(2020)
Article
Multidisciplinary Sciences
Xu Wang, Guohua Gan, Ling-Yun Wu
Article
Multidisciplinary Sciences
Xiao Li, Feng Xu, Ling-Yun Wu, You-Shan Zhao, Juan Guo, Qi He, Zheng Zhang, Chun-Kang Chang, Dong Wu
SCIENTIFIC REPORTS
(2020)
Letter
Hematology
Lingyun Wu, Xiao Li, Feng Xu, Dong Wu, Qi He, Luxi Song, Chao Xiao, Youshan Zhao, Zheng Zhang, Juan Guo, Liyu Zhou, Jiying Su, Chunkang Chang
BRITISH JOURNAL OF HAEMATOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Mohammad Awaji, Sugandha Saxena, Lingyun Wu, Dipakkumar R. Prajapati, Abhilasha Purohit, Michelle L. Varney, Sushil Kumar, Satyanarayana Rachagani, Quan P. Ly, Maneesh Jain, Surinder K. Batra, Rakesh K. Singh
Article
Cell Biology
Yuqian Zhu, Dandan Song, Juan Guo, Jiacheng Jin, Ying Tao, Zheng Zhang, Feng Xu, Qi He, Xiao Li, Chunkang Chang, Lingyun Wu
Summary: The study found that U2AF1 mutations are associated with poor prognosis in MDS and AML patients, significantly inhibiting cell proliferation and inducing cellular apoptosis in cell models. The results showed that U2AF1 mutations promoted FOXO3a-dependent apoptosis and NLRP3 inflammasome activation, leading to pyroptotic cell death. FOXO3a was identified as the key molecule on which these pathways converge.
CELL DEATH & DISEASE
(2021)
Article
Oncology
Xiao Li, Feng Xu, Zheng Zhang, Juan Guo, Qi He, Lu-Xi Song, Dong Wu, Li-Yu Zhou, Ji-Ying Su, Chao Xiao, Chun-Kang Chang, Ling-Yun Wu
Summary: BCOR mutations are more common in CN MDS patients, predicting a higher risk of leukemia transformation. BCORMUT patients showed a better response to decitabine and achieved longer post-CR survival.
CLINICAL EPIGENETICS
(2021)
Article
Multidisciplinary Sciences
Bo Gao, Yue Zhao, Yonghang Gao, Guojun Li, Ling-Yun Wu
Summary: High-throughput biological data has provided an opportunity to illuminate the mechanisms of tumor emergence and evolution, with the tool ComCovEx being developed to explore common cancer driver gene modules between two cancers and reveal their associations. The research results offer new insights into the pathological basis of different cancer types and provide new clues for the diagnosis and treatment of associated cancers.
Review
Operations Research & Management Science
Xu Wang, Ling-Yun Wu
Summary: Blockchain technology has rapidly developed and been applied in various scenarios beyond cryptocurrencies, with a focus on security, efficiency, and resource allocation. This paper aims to analyze blockchain technology from the perspective of operations research and address relevant issues to promote its wider application in the future.
JOURNAL OF THE OPERATIONS RESEARCH SOCIETY OF CHINA
(2022)
Article
Biochemical Research Methods
Jiacheng Leng, Ling-Yun Wu
Summary: This study introduces a novel Importance-Penalized Joint Graphical Lasso method (IPJGL) for differential network inference, where the importance of genes is taken into consideration. The method is validated through simulation experiments and real datasets. Additionally, a new metric named APC2 is proposed to assess the differential levels of gene pairs.
Article
Biotechnology & Applied Microbiology
Duanchen Sun, Xiangnan Guan, Amy E. Moran, Ling-Yun Wu, David Z. Qian, Pepper Schedin, Mu-Shui Dai, Alexey Danilov, Joshi J. Alumkal, Andrew C. Adey, Paul T. Spellman, Zheng Xia
Summary: Scissor is a method that identifies cell subpopulations associated with a given phenotype from single-cell data, by quantifying the similarity between single cells and bulk samples, and optimizing a regression model with sample phenotype. Applied in lung cancer, melanoma, facioscapulohumeral muscular dystrophy, and Alzheimer's disease datasets, Scissor effectively identifies biologically and clinically relevant cell subpopulations.
NATURE BIOTECHNOLOGY
(2022)
Article
Physics, Multidisciplinary
Jiating Yu, Ling-Yun Wu
Summary: Link prediction is a classical problem in the field of complex networks, which is of great significance for understanding the evolution and dynamic development mechanisms of networks. This study proposes a novel method called MOLI, which utilizes local information from neighbors at different distances and defines a local network diffusion process via random walks on the graph, achieving better utilization of network information. The results show that MOLI outperforms other widely used link prediction methods on different types of networks.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2022)
Article
Biochemical Research Methods
Jiacheng Leng, Ling-Yun Wu
Summary: Gene-based transcriptome analysis can identify key factors causing disease production and cell differentiation, but basic life activities are mainly driven by gene interactions, requiring interaction-based transcriptome analysis to investigate insights into differential gene interactions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Physics, Multidisciplinary
Jiating Yu, Jiacheng Leng, Duanchen Sun, Ling-Yun Wu
Summary: Network models are widely used in various fields for their ability to represent relationships between variables. Network structure can be unclear due to factors like experimental noise and missing data, hindering downstream analyses such as community detection. Therefore, network denoising is necessary before analysis. However, the importance of network pre-processing for community detection has been neglected. In this study, a novel network denoising method, called Network Refinement (NR), was proposed to enhance the self-organization properties of complex networks through a global diffusion process. NR significantly improved the clarity of the network's mesoscale structure and boosted the performance of various community detection algorithms.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2023)
Article
Hematology
Yuqian Zhu, Lingyun Wu
