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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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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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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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Synthesis of nitrogen-tethered 1,6-enynes through CuI/TFA catalysis

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Organic Chemistry Frontiers 2022年第2期9卷 394-399页

作者： Leilei Cao Liliang Huang Xianjun Xu Erik V.Van der Eycken Huangdi Feng College of Chemistry and Chemical Engineering Shanghai University of Engineering ScienceShanghai201620China Laboratory for Organic&Microwave-Assisted Chemistry(LOMAC) Department of ChemistryKU LeuvenCelestijnenlaan 200FLeuvenB-3001Belgium Shanghai Peoples’Friendship University of Russia(RUDN University) Miklukho-Maklaya Street 6Moscow117198Russia Shanghai Frontiers Science Research Center for Druggability of Cardiovascular noncoding RNA Institute for Frontier Medical TechnologyShanghai University of Engineering ScienceShanghai201620China

A novel method for the concise and effective construction of nitrogen-tethered 1,6-enynes in moderate to good yields was *** transformation involves a TFA-promoted Pictet-Spengler reaction/iminium formation,copper-catalyzed alkyne-iminium ene reaction/alkynylation of a 2-arylethan-1-amine,formaldehyde solution,and a terminal *** process features exclusive chemoselectivity,simple operation,and high atom *** experimental studies suggest that the alkyne-iminium ene reaction involving an intermolecular hydride transfer is the key step in the current methodology.

关键词： catalysis hydride promoted

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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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Microrna–disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice

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Genomics, Proteomics & Bioinformatics 2023年第5期21卷 1030-1042页

作者： Yicong Shen Yuanxu Gao Jiangcheng Shi Zhou Huang Rongbo Dai Yi Fu Yuan Zhou Wei Kong Qinghua Cui Department of Physiology and Pathophysiology School of Basic Medical SciencesState Key Laboratory of Vascular Homeostasis and RemodelingPeking UniversityBeijing 100191China State Key Laboratory of Lunar and Planetary Sciences Macao University of Science and TechnologyMacao Special Administrative Region 999078China Department of Biomedical Informatics Center for Noncoding RNA MedicineSchool of Basic Medical SciencesPeking UniversityBeijing 100191China

Abdominal aortic aneurysm(AAA)is a permanent dilatation of the abdominal aorta and is highly *** main purpose of the current study is to search for noninvasive medical therapies for AAA,for which there is currently no effective drug *** medicine represents a cuttingedge technology,as analysis and modeling of disease networks can provide critical clues regarding the etiology of specific diseases and therapeutics that may be ***,we proposed a novel algorithm to quantify disease relations based on a large accumulated microrna–disease association dataset and then built a disease network covering 15 disease classes and 304 *** revealed some patterns for these *** instance,diseases tended to be clustered and coherent in the ***,we found that AAA showed the strongest similarity with rheumatoid arthritis and systemic lupus erythematosus,both of which are autoimmune diseases,suggesting that AAA could be one type of autoimmune diseases in *** on this observation,we further hypothesized that drugs for autoimmune diseases could be repurposed for the prevention and therapy of ***,animal experiments confirmed that methotrexate,a drug for autoimmune diseases,was able to alleviate the formation and development of AAA.

关键词： Abdominal aortic aneurysm Network medicine Microrna-derived disease network Autoimmune disease Methotrexate

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Identiffcation and Analysis of Sex-Biased Copy Number Alterations

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Health Data Science 2024年第1期4卷 355-363页

作者： Chenhao Zhang Yang Yang Qinghua Cui Dongyu Zhao Chunmei Cui Department of Biomedical Informatics Center for Noncoding RNA MedicineState Key Laboratory of Vascular Homeostasis and RemodelingSchool of Basic Medical SciencesPeking University38 Xueyuan RdBeijing 100191China Department of Biochemistry and Biophysics School of Basic Medical SciencesPeking University Health Science CenterBeijing 100191China School of Sports Medicine Wuhan Institute of Physical EducationNo.461 Luoyu Rd.Wuchang DistrictWuhan 430079Hubei ProvinceChina

Background:Sex difference has long been recognized at cancer incidence,outcomes,and responses to *** the somatic mutation proffles of large-scale cancer samples between the sexes have revealed several potential drivers of cancer with sex ***,it is still a demand for indepth scrutinizing the sex-biased characteristics of genome instability to link the clinical differences for individual cancer ***:Here,we utilized a published framework devised to speciffcally compare the copy number proffles between 2 groups to identify the sex-biased copy number alterations(CNAs)across 16 cancer types from the The Cancer Genome Atlas Program database,and dissected the impact of those ***:Totally,81 male-biased CNA regions and 23 female-biased CNA regions in 16 cancer types were *** annotation analysis showed that several critical biological functions associated with sex-biased CNAs are shared in multiple cancer types,including immune-related pathways and regulation of cellular *** sex-biased CNAs have a substantial effect on transcriptional consequence,where the average of over 68%of genes have a linear relationship with CNAs across cancer types,and 14%of those genes are affected by the combination of the sex and copy ***,29 sex-biased CNA regions show latent capacity to be sex-speciffc prognostic biomarker such as CNA on 11q13.4 for head and neck cancer and lung ***:This analysis offers new insights into the role of sex in cancer etiology and prognosis through a detailed characterization of sex differences in genome instability of diverse cancers.

关键词： alterations utilized latent

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YBX1 inhibits mitochondrial-mediated apoptosis in ischemic heart through the PI3K/AKT signaling pathway

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Frigid Zone Medicine 2024年第1期4卷 51-64页

作者： Fangfang Bi Miao Cao Yuquan Wang Qingming Pan Zehong Jing Danyang Bing Lifang Lyu Tong Yu Tianyu Li Xuelian Li Haihai Liang Hongli Shan Yuhong Zhou Department of Pharmacology(State-Province Key Laboratories of Biomedicine-Pharmaceutics of China Key Laboratory of Cardiovascular ResearchMinistry of Education)College of PharmacyHarbin Medical UniversityHarbin 150081China Shanghai Frontiers Science Research Center for Druggability of Cardiovascular noncoding RNA Institute for Frontier Medical TechnologyShanghai University of Engineering ScienceShanghai 201620China Department of Basic Medicine Xiamen Medical CollegeXiamen 361023China

Background:Myocardial infarction(MI)is associated with higher morbidity and mortality in the world,especially in cold ***1 is an rna-binding protein that is required for pathological growth of cardiomyocyte by regulating cell growth and protein *** YBX1,as an individual rna-binding protein,regulates cardiomyocytes through signaling cascades during myocardial infarction remain largely ***:In vivo,the mouse MI model was induced by ligating the left anterior descending coronary artery(LAD),and randomly divided into sham operation group,MI group,MI+YBX1 knockdown/overexpression group and MI+negative control(NC)*** protective effect of YBX1 was verified by echocardiography and triphenyltetrazolium chloride *** vitro,mitochondrial-dependent apoptosis was investigated by using CCK8,TUNEL staining,reactive oxygen species(ROS)staining and JC-1 staining in hypoxic neonatal mouse cardiomyocytes(NMCMs).Results:YBX1 expression of cardiomyocytes was downregulated in a mouse model and a cellular model on the ischemic *** to mice induced by MI,YBX1 overexpression mediated by adeno-associated virus serotype 9(AAV9)vector reduced the infarcted size and improved cardiac *** of endogenous YBX1 by shrna partially aggravated ischemia-induced cardiac *** hypoxic cardiomyocytes,YBX1 overexpression decreased lactic dehydrogenase(LDH)release,increased cell viability,and inhibited apoptosis by affecting the expression of apoptosis related proteins,while knockdown of endogenous YBX1 by sirna had the opposite *** of YBX1 restored mitochondrial dysfunction in hypoxic NMCMs by increasing mitochondrial membrane potential and ATP content and decreasing *** hypoxic NMCMs,YBX1 overexpression increased the expression of phosphorylated phosphatidylinositol 3 kinase(PI3K)/AKT,and the anti-apoptosis effect of YBX1 was eliminated t by LY294002,PI3K/AKT ***:YBX1 protected the heart

关键词： YBX1 PI3K/AKT apoptosis mitochondrial function myocardial infarction

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Pictet-Spengler-Based Multicomponent Domino Reactions to Construct Polyheterocycles

Pharmaceutical Fronts

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Pharmaceutical Fronts 2023年第4期5卷 E227-E242页

作者： Hu, Jun-Duo Huang, Li-Liang Feng, Huang-Di Department of Pharmaceutical Engineering College of Chemistry and Chemical Engineering Shanghai University of Engineering Science Shanghai China Shanghai Frontiers Science Research Center for Druggability of Cardiovascular Noncoding RNA Institute for Frontier Medical Technology Shanghai University of Engineering Science Shanghai China

The Pictet-Spengler reaction is one of the important methodological arsenals in synthetic and medicinal chemistry, acting as an amenable tool for preparing tetrahydroisoquinoline, tetrahydro-β-carbolines, polycyclic skeletons, and value-Added products. More than 100 years after its initial discovery, the Pictet-Spengler reaction's response has not withdrawn from the stage, but it has once again become the focus of attention with new features. The review summarizes recent advances in Pictet- Spengler-based multicomponent reactions from 2007 to 2022, including three-component and four-component Pictet-Spengler cyclization reactions in the presence of metal catalysts, organocatalysts, biological enzyme catalysts, and so on. These Pictet- Spengler-based multicomponent protocols provide an atom-/step economic approach for the synthesis of a library of new chemical entities. © 2023 Wolters Kluwer Medknow Publications. All rights reserved.

关键词： cyclization domino reactions heterocycles multicomponent reactions Pictet-Spengler reaction

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