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MicroRNAs as potential biomarkers for gastric cancer

World Journal of Gastroenterology 2014年第34期20卷 12007-12017页

作者： han-Shao Liu Hua-Sheng Xiao national Engineering Research center for Biochip at {2. shanghai-most {2. laboratory for Disease and health genomics Chinese National Human Genome Center at Shanghai Advanced Institute of Translational Medicine Tongji University

Gastric cancer is the fourth most common cancer in the world and the second leading cause of cancer-related death. More than 80% of diagnoses occur at the middle to late stage of the disease, highlighting an urgent need for novel biomarkers detectable at earlier stages. Recently, aberrantly expressed microRNAs (miRNAs) have received a great deal of attention as potential sensitive and accurate biomarkers for cancer diagnosis and prognosis. This review summarizes the current knowledge about potential miRNA biomarkers for gastric cancer that have been reported in the publicly available literature between 2.08 and 2.13. Available evidence indicates that aberrantly expressed miRNAs in gastric cancer correlate with tumorigenesis, tumor proliferation, distant metastasis and invasion. Furthermore, tissue and cancer types can be classified using miRNA expression profiles and next-generation sequencing. As miRNAs in plasma/serum are well protected from RNases, they remain stable under harsh conditions. Thus, potential functions of these circulating miRNAs can be deduced and may implicate their diagnostic value in cancer detection. Circulating miRNAs, as well as tissue miRNAs, may allow for the detection of gastric cancer at an early stage, prediction of prognosis, and monitoring of recurrence and/or lymph node metastasis. Taken together, the data suggest that the participation of miRNAs in biomarker development will enhance the sensitivity and specificity of diagnostic and prognostic tests for gastric cancer. (C) 2.14 Baishideng Publishing Group Inc. All rights reserved.

关键词： MicroRNAs Gastric cancer Biomarker Clinical application

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基于单细胞靶向测序探究基因碱基突变的方法

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遗传 2020年第7期42卷 703-713页

作者：赵利楠王娜杨国良苏现斌韩泽广上海交通大学系统生物医学研究院系统生物医学教育部重点实验室上海200240 上海交通大学医学院附属仁济医院泌尿科上海200127

分析基因碱基突变是探究肿瘤细胞克隆演化的研究方法之一。目前,常取组织不同区域的群体细胞测序,基于群体水平的基因碱基突变频率等信息绘制出肿瘤的克隆演化过程。但是,该方法易遗失低频突变,并且组织群体细胞类型不单一,不能代表特... 详细信息

分析基因碱基突变是探究肿瘤细胞克隆演化的研究方法之一。目前,常取组织不同区域的群体细胞测序,基于群体水平的基因碱基突变频率等信息绘制出肿瘤的克隆演化过程。但是,该方法易遗失低频突变,并且组织群体细胞类型不单一,不能代表特定细胞群体的克隆演化过程。本研究以前列腺基底细胞癌(prostate basal cell carcinoma, BCC)为例,建立了一种探究肿瘤单细胞的基因碱基突变方法,实现了基于单细胞基因碱基突变分析肿瘤细胞的克隆演化过程。首先通过HepG2.胞优化了单细胞全基因组扩增方法,其次用Fluidigm公司的微流控芯片捕获BCC单细胞进行全基因组扩增,然后通过外显子组测序获得SCUBE3和MST1L基因碱基突变信息。通过单细胞靶向扩增和Sanger测序,成功在BCC单细胞中检测到SCUBE3和MST1L基因碱基突变信息。本研究建立的方法为肿瘤细胞的克隆演化研究提供了一种可靠的技术方案。

关键词：肿瘤细胞基因碱基突变克隆演化单细胞

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New approaches for archaeal genome-guided cultivation

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Science china Earth Sciences 2021年第10期64卷 1658-1673页

作者： Yinzhao WANG Yoichi KAMAGATA Meng LI Feifei han Fengping WANG Xiang XIAO State key laboratory of Microbial Metabolism School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Bioproduction Research Institute National Institute of Advanced Industrial Science and Technology(AIST)Tsukuba 310-8555Japan Shenzhen key laboratory of Marine Microbiome Engineering Institute for Advanced StudyShenzhen 518052China Department of Surgery Massachusetts General Hospital and Harvard Medical SchoolBoston MA 02114USA School of Oceanography Shanghai Jiao Tong UniversityShanghai 200240China State key laboratory of Ocean Engineering Ocean and Civil EngineeringShanghai Jiao Tong UniversityShanghai 200240China

Archaea,one of the three domains of life along with Bacteria and Eukarya,contains ancient life forms such as methanogen that are observed today on Earth,and one lineage Asgard archaea is also considered the closest ancestor of ***,with the development of interdisciplinary studies from Earth and Life sciences,archaeal organisms are considered to play pivotal roles in geochemical cycling in ***,our understanding of the attributes,origin and evolution,geochemical and ecological functions of Archaea is hampered by the scarcity of archaeal isolates,which has represented a challenge to researchers for the last 40 ***-independent sequencing and phylogenomic analyses have demonstrated a considerable diversity of Archaea with more than 2. novel ***,only four archaeal phyla have cultured representatives,leaving large gaps in our knowledge of the metabolic capabilities and ecological functions of the majority of archaeal strains identified exclusively by DNA *** this review,we summarize the discovery and development of archaeal research,highlight the knowledge gap between uncultured and cultured archaeal microbes,and call on the importance of devoting greater research efforts to archaeal ***,we outlined new ideas and strategic approaches,namely,(1){2.-based methods,(2.microbial network information-based methods,(3){2.-scale model-guided methods,and(4)machine learning methods,to enable the cultivation of uncultivated archaeal microbes using accumulated high-throughput sequencing data.

关键词： Archaea Cultivation Next-generation sequencing Uncultured archaea genome Metabolic network

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High-throughput genome editing in rice with a virus-based surrogate system

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Journal of Integrative Plant Biology 2023年第3期65卷 646-655页

作者： Yifu Tian Dating Zhong Xinbo Li Rundong Shen han han Yuqin Dai Qi Yao Xuening Zhang Qi Deng Xuesong Cao Jian-Kang Zhu Yuming Lu shanghai center for Plant Stress Biology Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 201602China center for Advanced Bioindustry Technologies Institute of Crop SciencesChinese Academy of Agricultural SciencesBeiing 100081China Hainan Yazhou Bay Seed Lab Sanya 572024China shanghai Collaborative Innovation center of Agri Seeds Joint Center for Single Cell BiologySchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Institute of Advanced Biotechnology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China

With the widespread use of clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated nuclease(Cas) technologies in plants, large-scale genome editing is increasingly needed. Here, we developed a geminivirus-mediated surrogate system, called Wheat Dwarf Virus-Gate(WDV-surrogate), to facilitate high-throughput genome ***-Gate has two parts: one is the recipient callus from a transgenic rice line expressing Cas9 and a mutated hygromycin-resistant gene(HygM) for surrogate selection;the other is a WDV-based construct expressing two single guide RNAs(sgRNAs) targeting HygM and a gene of interest, respectively. We evaluated WDV-Gate on six rice loci by producing a total of 874 T_0 plants. Compared with the conventional method, the WDV-Gate system, which was characterized by a transient and high level of sgRNA expression, significantly increased editing frequency(66.8% vs. 90.1%), plantlet regeneration efficiency(2.31-fold increase), and numbers of homozygous-edited plants(36.3%vs. 70.7%). Large-scale editing using pooled sg RNAs targeting the SLR1 gene resulted in a high editing frequency of 94.4%, further demonstrating its feasibility. We also tested WDVGate on sequence knock-in for protein *** co-delivering a chemically modified donor DNA with the WDV-Gate plasmid, 3xFLAG peptides were successfully fused to three loci with an efficiency of up to 13%. Thus, by combining transiently expressed sgRNAs and a surrogate selection system, WDV-Gate could be useful for high-throughput gene knock-out and sequence knock-in.

关键词： genome editing high-throughput protein tagging rice

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基于合成致死策略寻找ARID1A突变肝细胞癌的治疗靶点

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基因组学与应用生物学 2019年第7期38卷 3297-3304页

作者：王光兴石毅王小晟张跃韩泽广何昆燕上海交通大学系统生物医学研究院系统生物医学教育部重点实验室上海200240 中国药科大学基础医学与临床药学学院基础医学系南京211198 哈尔滨医科大学第一临床医学院风湿免疫科哈尔滨150001

ARID1A编码的BAF2.0a蛋白是SWI/SNF(SWItch/Sucrose Non-Fermentable)染色质重组复合物BAF(BRG1-associated factors)的亚基之一,参与改变染色体的结构和可接近性。ARID1A在肝细胞癌(hepatocellular carcinoma,HCC)中的突变率高达13%,但目前尚无有效的治疗药物。本研究旨在利用合成致死策略寻找携带ARID1A突变HCC的治疗新靶标。首先,本研究通过分析ARID1A突变与肿瘤恶性程度的相关性发现ARID1A突变的肿瘤恶性度增加;进而分析Achilles和NCI-60癌症细胞系中ARID1A突变和野生型细胞系的基因表型值(gene phenotype value,GPV)和高表达基因,获得ARID1A突变细胞低GPV和高表达的重叠基因,再扩大样本使用CCLE(Cancer Cell Line Encyclopedia)细胞系的高表达基因进行重叠基因分析;最后并在TCGA(the Cancer genome Atlas)肝癌数据库中进行筛选,获得116个潜在的ARID1A合成致死基因。本研究运用生物信息学方法计算获得多个ARID1A的潜在合成性致死基因,为ARID1A突变HCC患者提供新的治疗靶点,也为靶向药物研发提供了新靶标和新策略。

关键词： ARID1A 合成致死 HCC

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Rice Protein Tagging Project:A Call for International Collaborations on genome-wide In-Locus Tagging of Rice Proteins

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Molecular Plant 2020年第12期13卷 1663-1665页

作者： Yuming Lu Pamela C.Ronald Bin han Jiayang Li Jian-Kang Zhu shanghai center for Plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina Department of Plant Pathology and the genome center University of CaliforniaDavisCAUSA national center for Gene Research CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina State key laboratory of Plant {2. and National Center for Plant Gene Research(Beijing)Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijingChina Department of Horticulture and Landscape Architecture Purdue UniversityWest LafayetteINUSA

In September 1997,the International Rice genome Sequencing Project was *** initiative pooled the resources of ten nations to obtain the first complete rice genome sequence,and promoted rice research and breeding into the post-genomics era(Li et al.,2.18).In 2.08,an internationally coordinated project named "RICE2.2." was proposed to systematically and fully characterize all rice genes,transcripts,and proteins(Zhang et al.,2.08).While genes and their transcripts can be readily characterized by sequencing-and PCR-based methods,the characterization of protein dynamics including protein levels,subcellular localizations,post-transla-tional modifications,and interactions with macromolecules(e.g.,proteins,DNA,RNA,carbohydrates,and lipids)and small molecules(e.g.,metabolites and ligands)is much more challenging and usually requires antibodies that specifically recognize the protein of *** it is very difficult to systematically produce reliable antibodies for the specific recognition of individual plant proteins,a common practice is to transform a tag-fused open reading frame(ORF)of a gene to the corresponding loss-of-function mutant ***,such an ectopically expressed tagged protein may not fully reca-pitulate the properties of the endogenous protein due to the random insertion of the transgene,even when the transgene is expressed under the endogenous gene promoter.A preferred so-lution is to genetically label the coding sequence of the gene of interest,at its in vivo locus,with a sequence encoding a fluores-cent protein tag or an affinity tag such as FLAG or *** "in-locus" protein tagging,as we are naming it here,has been carried out genome-wide in yeast,Caenorhabditis elegans,fly,and mammalian cultured cells,greatly facilitating the characterization of proteins in these organisms(Jiang et al.,2.18).In 2.17,a genome Tagging Project was launched in mice,aiming to label every protein using a CRISPR/Cas9-based "artificial spermatids"method(

关键词： breeding genome endogenous

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Characterization of prognosis and immune infiltration by a novel glutamine metabolism-related model in cutaneous melanoma

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生物细胞(英文) 2023年第9期47卷 1931-1945页

作者： MENGQIN ZHU TIANYI XU han ZhanG XIN FAN YULAN WANG JIAJIA ZhanG FEI YU shanghai Clinical College Anhui Medical UniversityShanghai200040China The Fifth Clinical Medical College Anhui Medical UniversityHefei230032China Department of Nuclear Medicine Shanghai Tenth People’s HospitalTongji University School of MedicineShanghai200040China Institute of Nuclear Medicine Tongji University School of MedicineShanghai200040China national genomics Data {2. and CAS key laboratory of genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China Department of Biomedical Engineering Nanjing University of Aeronautics and AstronauticsNanjing210000China

Glutamine metabolism(GM)plays an important role in tumor growth and *** cutaneous melanoma(SKCM)is a glutamine-dependent ***,the molecular characteristics and action mechanism of GM on SKCM remain ***,we aimed to explore the effects of GM-related genes on survival,clinicopathological characteristics,and the tumor microenvironment in *** this study,682.SKCM samples were obtained from the Cancer genome Atlas(TCGA)and Gene Expression Omnibus(GEO)*** clustering was used to classify SKCM samples into distinct subtypes based on 41 GM-related *** in survival,immune infiltration,clinical characteristics,and Kyoto Encyclopedia of Genes and genomes(KEGG)pathways as well as differentially expressed genes(DEGs)between subgroups were evaluated.A prognostic model was constructed according to prognostic *** analyses in survival,immune infiltration,tumor microenvironment(TME),tumor mutation burden(TMB),stemness,and drug sensitivity between risk groups were *** identified two distinct GM-related subtypes on SKCM and found that GM-related gene alterations were associated with survival probability,clinical features,biological function,and immune *** a risk model based on six DEGs(IL18,SEMA6A,PAEP,TNFRSF17,AIM2.and CXCL10)was constructed and validated for predicting overall survival in SKCM *** results showed that the risk score was negatively correlated with CD8+T cells,activated CD4+memory T cells,M1 macrophages,andγδT *** group with a low-risk score was accompanied by a better survival rate with higher TME scores and lower stemness ***,the group with high-and low-risk score had a significant difference with the sensitivity of 75 drugs(p<0.001).Overall,distinct subtypes in SKCM patients based on GM-related genes were identified and the risk model was constructed,which might contribute to prognosis prediction,guide clinical therapy,and develop novel

关键词： Glutamine metabolism Cutaneous melanoma Immune infiltration Overall survival

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Transportation,germs,culture:a dynamic graph model of COVID-19 outbreak

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Quantitative Biology 2020年第3期8卷 238-244页

作者： Xiaofei Yang Tun Xu Peng Jia han Xia Li Guo Lei Zhang Kai Ye School of Computer Science and Technology Faculty of Electronic and Information EngineeringXi'an Jiaotong UniversityXi'an 710049China MOE key Lab for Intelligent Networks&Networks Security Faculty of Electronic and Information EngineeringXi'an Jiaotong UniversityXi'an 710049China School of Automation Science and Engineering Faculty of Electronic and Information EngineeringXi'an Jiaotong UniversityXi'an 710049China Hugobiotech Co. Ltd.Beijing 102600China The School of Life Science and Technology Xi'an Jiaotong UniversityXi'an 710049China china-Australia Joint Research center for Infectious Diseases School of Public HealthXi'an Jiaotong University Health Science CenterXi'an 710061China Melbourne Sexual health Centre Alfred HealthMelbourneVIC 3004Australia Central Clinical School Faculty of MedicineNursing and Health SciencesMonash UniversityMelbourneVIC 3004Australia Department of Epidemiology and Biostatistics College of Public HealthZhengzhou UniversityZhengzhou 450001China genome Institute the First Affiliated Hospital of Xi'an Jiaotong UniversityXi'an 710061China

Backgrounds Various models have been applied to predict the trend of the epidemic since the outbreak of ***:In this study,we designed a dynamic graph model,not for precisely predicting the number of infected cases,but for a glance of the dynamics under a public epidemic emergency situation and of different contributing factors・Results^We demonstrated the impact of asymptomatic transmission in this outbreak and showed the effectiveness of city lockdown to halt virus spread within a *** further illustrated that sudden emergence of a large number of cases could overwhelm the city medical system,and external medical aids are critical to not only containing the further spread of the virus but also reducing *** Our model simulation showed that highly populated modern cities are particularly vulnerable and lessons learned in china could facilitate other countries to plan the proactive and decisive actions・We shall pay close attention to the asymptomatic transmission being suggested by rapidly accumulating evidence as dramatic changes in quarantine protocol are required to contain SARS・CoV・2.from spreading globally.

关键词： dynamic graph model transportation COVID-19 SARS-CoV-2

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Prediction of potential antimalarial targets of artemisinin based on protein information from whole genome of Plasmodium falciparum

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chinese Science Bulletin 2009年第18期54卷 4234-4240页

作者： han LiPing HUANG Qiang NAN Peng ZHONG Yang School of Life Sciences and State key laboratory of Genetic Engineering Fudan University Shanghai 200433 China shanghai center for Bioinformation Technology Shanghai 201203 China

On the basis of the genomic data and protein pathway information about Plasmodium falciparum clone 3D7 from the NCBI taxonomy database and the KEGG database, eight key protein enzymes in the signal pathways were selected to perform molecular docking with artemisinin. The binding modes obtained from the molecular docking suggested that purine nucleoside phosphorylase (pfPNP), peptide deformylase (pfPDF), and ribose 5-phosphate isomerase (pfRpiA) may be involved in the antimalarial mode of action of artemisinin. Artemisinin exhibited its antimalarial activity probably by interfering with the metabolic pathways of purine, pyrimidine, methionine, glyoxylate and dicarboxylate, or pentose phosphate.

关键词：基因组信息青蒿素蛋白质抗疟药疟原虫嘌呤核苷磷酸化酶目标预测基础

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Biological data processing based on bio-processor unit(BPU), a new concept for next generation computational biology

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Science china(Life Sciences) 2018年第5期61卷 597-598页

作者： Di Liu Dongbo Bu Tieliu Shi Jianxiao Quan Depeng Wang Yongyong Shi Xiao-Chen Bo Wenbao han Computational Virology Group Wuhan Institute of Virology Chinese Academy of Sciences Wuhan 430071 China key laboratory of InteUigent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing 100190 China center for Bioinformatics and Computational Biology and the Institute of Biomedical Sciences School of Life Sciences East China Normal University Shanghai 200214 China State key laboratory of Mathematical Engineering and Advanced Computation Wuxi 214122 China Jiangsu Variable Supercomputer Tech Co Ltd. Wuxi 214125 China NextOmics Blosctences Wuhan 430074 China Bio-X Institutes Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) Shanghai Jiao Tong University Shanghai 200030 China Beijing Institute of Radiation Medicine Beifing 100850 China

The revolution of biotechnology has pushed forward life sciences into the Big Data ***,high-throughput bio-techniques have greatly accelerated the integration of biology,computing and informatics,and hence substantially pushed forward the development of bioinformatics and computational *** to the latest report of data deposition within national Centre for Biotechnology Information（NCBI）,the genome sequencing projects have increased 49.94%.

关键词：计算生物学简历处理器数据基信息科学生物信息学生命科学 NCBI

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