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Long noncoding rna KCNMB2-AS1 acts as an oncogene in ovarian cancer

生物化学与生物物理学报（英文版） 2023年第11期55卷 1844-1846页

作者： Siyu Cao Min Liu Ziyi Guo Yanli Li Department of Gynecologic Oncology Fudan University Shanghai Cancer CenterShanghai 200032China Lab for Noncoding RNA and Cancer School of Life SciencesShanghai UniversityShanghai 200444China

Ovarian cancer(OC),a gynecologic cancer,has a poor prognosis and limited treatment *** than 75％of patients are initially diagnosed with advanced OC[1].The 5-year overall survival rate of OC has remained virtually unchanged,which means it is still low[2].Therefore,research on OC is unceasing,and new therapeutic targets and biomarkers are urgently needed[3].

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Interaction of Magnesium Ion and Acetate Anion in Bulk Water:Toward High-Level Machine Learning Potential

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Chinese Journal of Chemical Physics 2025年第1期38卷 95-101,I0056页

作者： Jiaying Gu Jin Xiao Xingyu Wu Xi Zhu Huimin Chen John ZHZhang Tong Zhu Ya Gao Zhixiang Yin School of Mathematics Physics and StatisticsShanghai University of Engineering ScienceShanghai 201620China Shanghai Engineering Research Center of Molecular Therapeutics&New Drug Development School of Chemistry and Molecular EngineeringEast China Normal UniversityShanghai 200062China CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062China Department of Chemistry New York UniversityNew York 10003USA Collaborative Innovation Center of Extreme Optics Shanxi UniversityTaiyuan 030006China Shanghai Frontiers Science Research Center for Druggability of Cardiovascular Noncoding RNA Shanghai 201620China

Metal ions play crucial roles in various biologi-cal functions,in-cluding maintain-ing homeostasis,regulating mus-cle contraction,and facilitating enzyme ***,accurately simulating the interaction between metal ions and amino acid side chain analogs using high-level wave function theories remains challenging due to the significant computational costs *** this study,deep potential molecular dynamics(DeePMD)simulation was employed to investigate the solvation structure of the Mg^(2+)-Ac^(−)ion pair in aqueous *** address the computational bottleneck associated with expensive quan-tum mechanics(QM)methods,the Deep Kohn-Sham(DeePKS)approach was utilized,which allows us to generate highly accurate self-consistent energy functionals while significantly re-ducing computational *** root mean square error and mean absolute error of energies and atomic forces indicate close agreement between DeePKS predictions and QM strongly constrained and appropriately normed(SCAN)***,the neural network potential(NNP)generated using the SCAN-level dataset predicted by DeePKS exhibits high-er accuracy compared to previous work,which employed a moderate BLYP *** potential of mean force for the Mg^(2+)-Ac−system was further examined,revealing a prefer-ence for monodentate coordination of Mg^(2+)with a~5.8 kcal/mol energy barrier between bidentate and monodentate ***,this work provides a comprehensive,precise,and reliable methodology for investigating metal ions’properties in aqueous solutions.

关键词： Molecular dynamics simulation Umbrella sampling Neural network potential Machine learning

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Identification and Analysis of Human Sex-biased Micrornas

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Genomics, Proteomics & Bioinformatics 2018年第3期16卷 200-211页

作者： Chunmei Cui Weili Yang Jiangcheng Shi Yong Zhou Jichun Yang Qinghua Cui Yuan Zhou Department of Biomedical Informatics Department of Physiology and Pathophysiology Center for Noncoding RNA Medicine MOE Key Laboratory of Cardiovascular Sciences School of Basic Medical Sciences Peking University Department of Physiology and Pathophysiology Center for Noncoding RNA Medicine School of Basic Medical SciencesPeking University Beijing Institute of Heart Lung and Blood Vessel Diseases Beijing Anzhen Hospital Capital Medical University

Sex differences are widely observed under various circumstances ranging from physiolog- ical processes to therapeutic responses, and a myriad of sex-biased genes have been identified. In recent years, transcriptomic datasets of micrornas （mirnas）, an important class of non-coding rnas, become increasingly accessible. However, comprehensive analysis of sex difference in mirna expression has not been performed. Here, we identified the differentially-expressed miR- NAs between males and females by examining the transcriptomic datasets available in public data- bases and conducted a systemic analysis of their biological characteristics. Consequently, we identified 73 female-biased mirnas （FmiRs） and 163 male-biased mirnas （MmiRs） across four tissues including brain, colorectal mucosa, peripheral blood, and cord blood. Our results suggest that compared to FmiRs, MmiRs tend to be clustered in the human genome and exhibit higher evolutionary rate, higher expression tissue specificity, and lower disease spectrum width. In *** enrichment analysis of mirnas show that FmiR genes are significantly associated with metabolism process and cell cycle process, whereas MmiR genes tend to be enriched for functions like histone modification and circadian rhythm. In all, the identification and analysis of sex-biased mirnas together could provide new insights into the biological differences between females and males and facilitate the exploration of sex-biased disease susceptibility and therapy.

关键词： Sex bias Micrornas Conservation Disease association Personalized medicine

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Distinctive hydrogen binding interactions enable fluorescent sensor to Discriminate HSA from BSA in fluorescent sensing

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Microchemical Journal 2025年

作者： Yiyi Qiao Jian Cao Yanan Li Chuanxiao Wang Jiayu Gao Linlin Wang Wenwen Sun Le Wang Yuanhao Li Zhicheng Zuo School of Chemistry and Chemical Engineering Shanghai University of Engineering Science 333 Longteng Road Shanghai 201600 PR China Shanghai Frontiers Science Research Center for Druggability of Cardiovascular noncoding RNA Institute for Frontier Medical Technology Shanghai University of Engineering Science Shanghai 201600 PR China

Human serum albumin (HSA), the most abundant protein in plasma, plays essential roles in various physiological processes. In this study, a novel hydrogen bond-driven fluorescent sensor (Rho-A) was developed for the selective and sensitive detection of HSA. Rho-A was constructed by integrating rhodanine as the fluorophore with N,N-dimethylaniline as an electron-donating group through a π-conjugated double bond. The binding mechanism between the sensor and HSA was elucidated through a series of analytical techniques, including UV–Vis absorption spectroscopy, 1 H NMR, DLS, zeta potential measurements, fluorescence lifetime analysis, Raman spectroscopy, and CD spectrum, before and after the addition of HSA. The results reveal that Rho-A enters the cavity of HSA and specifically interacts with HSA via N-H···X hydrogen bonding (X = acceptor sites on HSA), triggering the disassembly of Rho-A aggregates and leading to significant fluorescent activation through a disaggregation-induced emission (DIE) mechanism. Isothermal titration calorimetry (ITC) was employed to quantify the thermodynamic parameters (K D , ΔG, ΔH, and ΔS) of Rho-A binding to HSA and BSA. The sensor specifically distinguishes HSA from BSA with high sensitivity (LOD: 0.452 mg/L, 10 s rapid response), good selectivity, anti-interference capability, ion tolerance, and stability under physiological pH and elevated temperatures. Rho-A was successfully applied for the detection of HSA in real urine samples and for fluorescent imaging in HepG-2 cancer cells, demonstrating its promising potential in clinical diagnostics and bioimaging applications.

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The role of noncoding rnas in the tumor microenvironment of hepatocellular carcinoma

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生物化学与生物物理学报（英文版） 2023年第11期55卷 1697-1706页

作者： Qianqian Yang Hui Tian Ziyi Guo Zhongliang Ma Guangzhi Wang Laboratory for Noncoding RNA and Cancer School of Life SciencesShanghai UniversityShanghai 200444China Department of Geriatrics Zhongshan HospitalFudan UniversityShanghai 200032China School of Medical Imaging Weifang Medical UniversityWeifang 261053China Department of Medical Imaging Center Affiliated Hospital of Weifang Medical UniversityWeifang 261053China

Hepatocellular carcinoma(HCC)is the leading fatal malignancy *** tumor microenvironment(TME)can affect the survival,proliferation,migration,and even dormancy of cancer *** is an important component of the TME,and hypoxia-inducible factor-1α(HIF-1α)is the most important transcriptional *** rnas(ncrnas),including micrornas(mirnas),long noncoding rnas(lncrnas),and circular rnas(circrnas),comprise a large part of the human transcriptome and play an important role in regulating the tumorigenesis of *** review discusses the role of ncrnas in hepatocarcinogenesis,epithelial-mesenchymal transition(EMT),and angiogenesis in a hypoxic microenvironment,as well as the interactions between ncrnas and key components of the *** further discusses their use as biomarkers and the potential clinical value of drugs,as well as the challenges faced in the future.

关键词： noncoding rnas HIF-1α hepatocellular carcinoma tumor microenvironment

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Degradable nanocatalyst enables antitumor/antibacterial therapy and promotion of wound healing for diabetes via self-enhanced cascading reaction

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Chinese Chemical Letters 2023年第7期34卷 155-161页

作者： Xiang Wang Cheng Ding Ziwen Zhang Chunlin Li Dongmiao Cao Linjing Zhao Guoying Deng Yu Luo Chunping Yuan Jie Lu Xijian Liu School of Chemistry and Chemical Engineering Shanghai Engineering Technology Research Center for Pharmaceutical Intelligent EquipmentShanghai Frontiers Science Research Center for Druggability of Cardiovascular Noncoding RNAInstitute for Frontier Medical TechnologyShanghai University of Engineering ScienceShanghai201620China Affiliated Sixth People's Hospital Shanghai JiaoTong UniversityShanghai 200233China Trauma Center Shanghai General HospitalShanghai Jiaotong University School of MedicineShanghai 201620China

Diabetic patients often have problems such as residual tumor and wound infection after tumor resection,causing severe clinical *** is urgent to develop effective therapies to reach oncotherapy/antiinfection/promotion of wound healing combined ***,we propose CS/MnO_(2)-GO_x (CMGO_x)nanocatalysts for the specific catalytic generation of ~·OH to inhibit tumors and bacteria in a hyperglycemic *** good biocompatible chitosan (CS),as a carrier for the catalyst,exhibits excellent antibacterial effect as well as promotes wound *** oxidase (GO_x) is loaded on the surface of CS nanoparticles to generate H_(2)O_(2) and gluconic acid by consuming glucose (starvation therapy,ST) and O_(2).The MnO_(2) depletes glutathione (GSH) to produce Mn^(2+),amplifying oxidative stress and further promoting the activity of Mn^(2+)-mediated Fenton-like reaction to produce~·OH (chemodynamic therapy,CDT)in weak acidic ***,the produced gluconic acid lowers the p H of the environment,enhancing chemodynamic therapy (ECDT).The tumor cells and bacteria are efficiently eliminated by the synergistic effect of ST and *** MnO_(2) nanoparticles at neutral environment decomposes H_(2)O_(2) into O_(2),which cooperate with CS to promote *** self-enhanced cascade reaction of CMGO_x in situ exhibits excellent effects of antitumor/antibacterial therapy and promotion of wound healing,offering a promising integrated treatment for diabetic patients after tumor surgical resection.

关键词： Self-cascade reaction Starvation therapy Chemodynamic therapy Antitumor Antibacterial Wound healing

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Visualized and cascade-enhanced gene silencing by smart DNAzyme-graphene nanocomplex

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Nano Research 2020年第8期13卷 2165-2174页

作者： Lingjie Ren Xiaoxia Chen Chang Feng Lei Ding Xiaomin Liu Tianshu Chen Fan Zhang Yanli Li Zhongliang Ma Bo Tian Xiaoli Zhu Center for Molecular Recognition and Biosensing School of Life SciencesShanghai UniversityShanghai200444China School of Medical Shanghai UniversityShanghai200444China Lab for Noncoding RNA and Cancer School of Life SciencesShanghai UniversityShanghai200444China State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200032China

BCL-2 gene as well as its products is recognized as a promising target for the molecular targeted therapy of ***,due to certain defense measures of tumor cells,the therapeutic effect based on the gene silencing of BCL-2 is greatly *** we fabricate a smart response nucleic acid therapeutic that could silence the gene effectively through a dual-targeted and cascade-enhanced *** brief,nano-graphene oxide(GO),working as a nano-carrier,is loaded with a well-designed DNAzyme,which can target and silence the BCL-2 ***,upon binding with the BCL-2 mrna,the enzymatic activity of the DNAzyme can be initiated,cutting a substrate oligonucleotide to produce an anti-nucleolin aptamer ***,a nucleolar phosphoprotein,is known as a stabilizer of BCL-2 *** binding and inactivating the nucleolin,AS1411 can destabilize BCL-2 *** this means of simultaneously targeting mrna and its stabilizer in an integrated system,effective silencing of the BCL-2 gene of tumor cells is achieved at both the cellular and in vivo *** being dosed with this nucleic acid therapeutic and without any chemotherapeutics,apoptosis of tumor cells at the cellular level and apparent shrinkage of tumors in vivo are *** labeling a molecular beacon on the substrate of DNAzyme,visualization of the enzymatic activity as well as the tumor in vivo can be also *** work presents a pure bio-therapeutic strategy that has positive implications for enhancing tumor treatment and avoiding side effects of chemotherapeutics.

关键词： BCL-2 gene gene silencing DNAzyme graphene oxide AS1411

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A CRISPR evolutionary arms race: structural insights into viral anti-CRISPR/Cas responses

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细胞研究（英文版） 2016年第10期26卷 1165-1168页

作者： Jiuyu Wang Jun Ma Zhi Cheng Xu Meng Lilan You Min Wang Xinzheng Zhang Key Laboratory of RNA Biology Beijing 100101 China Beijing Key Laboratory of Noncoding RNA Beijing 100101 China National Laboratory of Biomacromolecules Beijing 100101 China Center for Biological Imaging CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China Key Laboratory of RNA Biology Beijing 100101 China Institute of Life Sciences Jiangsu University Zhenjiang Jiangsu 212013 China Key Laboratory of RNA Biology Beijing 100101 China Beijing Key Laboratory of Noncoding RNA Beijing 100101 China University of Chinese Academy of Sciences Beijing 100049 China

Dear Editor,CRISPR/Cas systems are widespread rna-mediated prokaryotic adaptive immune systems providing protection against invading nucleic acids [1].However,throughout evolution,this host defense system has not resulted in the eradication of phages,suggesting that phages have evolved counter strategies to thrive within bacteria despite these mechanisms [2].Thus,both bacterial CRISPR system and phage anti-CRISPR system are part of a continuing evolutionary battle between bacterial host and their bacteriophage invaders.

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Author Correction: Catestatin attenuates endoplasmic reticulum induced cell apoptosis by activation type 2 muscarinic acetylcholine receptor in cardiac ischemia/reperfusion

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Scientific reports 2020年第1期10卷 19543页

作者： Feng Liao Yang Zheng Junyan Cai Jinghui Fan Jing Wang Jichun Yang Qinghua Cui Guoheng Xu Chaoshu Tang Bin Geng Department of Physiology and Pathophysiology School of Basic Medical Science Peking University Beijing P.R. China. Center for Noncoding RNA Medicine Peking University Health Science Center Beijing 100191 China. Department of Physiology and Pathophysiology School of Basic Medical Science Peking University Beijing P.R. China. bingeng@***. Center for Noncoding RNA Medicine Peking University Health Science Center Beijing 100191 China. bingeng@***.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Genomic characterization of peritoneal lavage cytology-positive gastric cancer

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Chinese Journal of Cancer Research 2024年第1期36卷 66-77页

作者： Zhouqiao Wu Tingfei Gu Changxian Xiong Jinyao Shi Jingpu Wang Ting Guo Xiaofang Xing Fei Pang Ning He Rulin Miao Fei Shan Yuan Zhou Ziyu Li Jiafu Ji Key Laboratory of Carcinogenesis and Translational Research(Ministry of Education/Beijing) Gastrointestinal Cancer CenterPeking University Cancer Hospital&InstituteBeijing 100142China Department of Biomedical Informatics Department of Physiology and PathophysiologyCenter for Noncoding RNA MedicineMOE Key Lab of Cardiovascular SciencesSchool of Basic Medical SciencesPeking UniversityBeijing 100191China State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers Beijing Key Laboratory of Carcinogenesis and Translational ResearchGastrointestinal Cancer CenterPeking University Cancer Hospital&InstituteBeijing 100142China

Objective: Positive peritoneal lavege cytology(CY1) gastric cancer is featured by dismal prognosis, with high risks of peritoneal metastasis. However, there is a lack of evidence on pathogenic mechanism and signature of CY1and there is a continuous debate on CY1 therapy. Therefore, exploring the mechanism of CY1 is crucial for treatment strategies and targets for CY1 gastric ***: In order to figure out specific driver genes and marker genes of CY1 gastric cancer, and ultimately offer clues for potential marker and risk assessment of CY1, 17 cytology-positive gastric cancer patients and 31matched cytology-negative gastric cancer patients were enrolled in this study. The enrollment criteria were based on the results of diagnostic laparoscopy staging and cytology inspection of exfoliated cells. Whole exome sequencing was then performed on tumor samples to evaluate genomic characterization of cytology-positive gastric ***: Least absolute shrinkage and selection operator(LASSO) algorithm identified 43 cytology-positive marker genes, while Mut Sig CV identified 42 cytology-positive specific driver genes. CD3G and CDKL2 were both driver and marker genes of CY1. Regarding mutational signatures, driver gene mutation and tumor subclone architecture, no significant differences were observed between CY1 and negative peritoneal lavege cytology(CY0).Conclusions: There might not be distinct differences between CY1 and CY0, and CY1 might represent the progression of CY0 gastric cancer rather than constituting an independent subtype. This genomic analysis will thus provide key molecular insights into CY1, which may have a direct effect on treatment recommendations for CY1and CY0 patients, and provides opportunities for genome-guided clinical trials and drug development.

关键词： Cytology gastric carcinoma peritoneal metastasis whole exome sequencing

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