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TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics

Genomics, Proteomics & Bioinformatics 2022年第5期20卷 974-988页

作者： Yiran Shan Qian Zhang Wenbo Guo Yanhong Wu Yuxin Miao Hongyi Xin qiuyu lian Jin Gu MOE Key Laboratory of Bioinformatics BNRIST Bioinformatics DivisionDepartment of AutomationTsinghua UniversityBeijing 100084China UM-SJTU Joint Institute Shanghai Jiao Tong UniversityShanghai 200240China Department of Automation Shanghai Jiao Tong UniversityShanghai 200240China

Sequencing-based spatial transcriptomics(ST)is an emerging technology to study in situ gene expression patterns at the whole-genome ***,ST data analysis is still complicated by high technical noises and low *** addition to the transcriptomic data,matched histopathological images are usually generated for the same tissue sample along the ST *** matched high-resolution histopathological images provide complementary cellular phenotypical information,providing an opportunity to mitigate the noises in ST *** present a novel ST data analysis method called transcriptome and histopathological image integrative analysis for ST(TIST),which enables the identification of spatial clusters(SCs)and the enhancement of spatial gene expression patterns by integrative analysis of matched transcriptomic data and *** devises a histopathological feature extraction method based on Markov random field(MRF)to learn the cellular features from histopathological images,and integrates them with the transcriptomic data and location information as a network,termed *** on TIST-net,SCs are identified by a random walk-based strategy,and gene expression patterns are enhanced by neighborhood *** benchmark TIST on both simulated datasets and 32 real samples against several state-of-the-art *** show that TIST is robust to technical noises on multiple analysis tasks for sequencing-based ST data and can find interesting microstructures in different biological *** is available at http://***/software/tist/and https://***/biocode/tools/BT007317.

关键词： Spatial transcriptomics Multimodal information integration Network-based analysis Spatial cluster identification Gene expression enhancement

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HCCDB: A Database of Hepatocellular Carcinoma Expression Atlas

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Genomics, Proteomics & Bioinformatics 2018年第4期16卷 269-275页

作者： qiuyu lian Shicheng Wang Guchao Zhang Dongfang Wang Guijuan Luo Jing Tang Lei Chen Jin Gu MOE Key Laboratory of Bioinformatics Beijing National Research Center for Information Science and TechnologyBioinformatics Division Department of Automation Tsinghua University International Co-operation Laboratory on Signal Transduction Eastern Hepatobiliary Surgery Institute Second Military Medical University

Hepatocellular carcinoma （HCC） is highly heterogeneous in nature and has been one of the most common cancer types worldwide. To ensure repeatability of identified gene expression patterns and comprehensively annotate the transcriptomes of HCC, we carefully curated 15 public HCC expression datasets that cover around 4000 clinical samples and developed the database HCCDB to serve as a one-stop online resource for exploring HCC gene expression with userfriendly interfaces. The global differential gene expression landscape of HCC was established by analyzing the consistently differentially expressed genes across multiple datasets. Moreover, a 4D metric was proposed to fully characterize the expression pattern of each gene by integrating data from The Cancer Genome Atlas （TCGA） and Genotype-Tissue Expression （GTEx）. To facilitate a comprehensive understanding of gene expression patterns in HCC, HCCDB also provides links to third-party databases on drug, proteomics, and literatures, and graphically displays the results from computational analyses, including differential expression analysis, tissue-specific and tumorspecific expression analysis, survival analysis, and co-expression analysis. HCCDB is freely accessible at http：//***/database/hccdb.

关键词： Hepatocellular carcinoma Database Transcriptome Integrative analysis Meta-analysis

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HCCDB v2.0:Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 131-142页

作者： Ziming Jiang Yanhong Wu Yuxin Miao Kaige Deng Fan Yang Shuhuan Xu Yupeng Wang Renke You Lei Zhang Yuhan Fan Wenbo Guo qiuyu lian Lei Chen Xuegong Zhang Yongchang Zheng Jin Gu Eight-Year Program of Clinical Medicine Peking Union Medical College HospitalChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100006China MOE Key Laboratory of Bioinformatics BNRIST Bioinformatics DivisionInstitute for Precision Medicine&Department of AutomationTsinghua UniversityBeijing 100084China Department of Liver Surgery Peking Union Medical College HospitalChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100730China Fuzhou Institute for Data Technology Fuzhou 350207China University of Michigan-Shanghai Jiao Tong University Joint Institute Shanghai Jiao Tong UniversityShanghai 200240China Department of Automation Shanghai Jiao Tong UniversityShanghai 200240China International Cooperation Laboratory on Signal Transduction Eastern Hepatobiliary Surgery InstituteSecond Military Medical UniversityShanghai 200438China National Center for Liver Cancer Shanghai 201805China

Large-scale transcriptomic data are crucial for understanding the molecular features of hepatocellular carcinoma(HCC).Integrated 15 transcriptomic datasets of HCC clinical samples,the first version of HCC database(HCCDB v1.0)was released in *** the meta-analysis of differentially expressed genes and prognosis-related genes across multiple datasets,it provides a systematic view of the altered biological processes and the inter-patient heterogeneities of HCC with high reproducibility and *** four years having passed,the database now needs integration of recently published ***,the latest single-cell and spatial transcriptomics have provided a great opportunity to decipher complex gene expression variations at the cellular level with spatial ***,we present HCCDB v2.0,an updated version that combines bulk,single-cell,and spatial transcriptomic data of HCC clinical *** dramatically expands the bulk sample size by adding 1656 new samples from 11 datasets to the existing 3917 samples,thereby enhancing the reliability of transcriptomic meta-analysis.A total of 182,832 cells and 69,352 spatial spots are added to the single-cell and spatial transcriptomics sections,respectively.A novel single-cell level and 2-dimension(sc-2D)metric is proposed as well to summarize cell type-specific and dysregulated gene expression *** are all graphically visualized in our online portal,allowing users to easily retrieve data through a user-friendly interface and navigate between different *** extensive clinical phenotypes and transcriptomic data in the database,we show two applications for identifying prognosis-associated cells and tumor *** v2.0 is available at http://***/database/hccdb2.

关键词： Hepatocellular carcinoma Database Integrative analysis Single-cell RNA sequencing Spatial transcriptomics

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Integrative molecular analysis of hepatocellular carcinoma by HCCDB

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Cancer Biology & Medicine 2018年第S1期15卷 7-7页

作者： qiuyu lian Shicheng Wang Dongfang Wang Jin Gu BNRIST Bioinformatics Division Department of AutomationTsinghua UniversityBeijingChina

Objective:Hepatocellular carcinoma(HCC)is one of the most common and lethal cancer *** the past decades,transcriptomic data have been accumulated vastly and applied widely in molecular classification and biomarker ***... 详细信息

关键词： Integrative molecular HCCDB

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HER-2/EGFR, the major targets for anti-metastasis effect of tetraarsenic oxide on SKBR3 breast cancer cells

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Journal of Chinese Pharmaceutical Sciences 2017年第2期26卷 87-94页

作者： qiuyu Liu Illju Bae Linlin Qian Zenglin lian School of Pharmaceutical Sciences Beij＇ing University of Chinese Medicine Beijing 100102 China Chonjisan Biological Medicine Technology Development （Beijing） Co. Ltd. Beijing 100080 China Institute of Biological Chinese Medicine Beijing 101111 China

Breast cancer is one of the most common female malignant tumors in the world. Although many therapeutic methods for HER-2 positive breast cancer have been developed, the drug resistance and distant metastasis still remain. Tetraarsenic oxide（As_4O_6） has been demonstrated with an anticancer effect on squamous cell carcinoma and cervical cancer. However, there is no report about the relationship between As_4O_6 and HER-2 positive breast cancer. In the present study, we detected the inhibitory efficacy and mechanism of As_4O_6 on the migration and invasion of SKBR3 breast cancer cells using molecular biological methods. The wound-healing assay, matrigel migration assay, transwell invasion assay and cell adhesion assay were used to assess the migration, invasion and adhesion of SKBR3 cells intervened by As_4O_6. Meanwhile, the reverse transcription-PCR and western blotting were performed to investigate the mechanism of As_4O_6 on the migration and invasion of SKBR3 breast cancer cells. The results demonstrated that As_4O_6 could efficiently inhibit the migration and invasion of SKBR3 cells, the HER-2 positive breast cancer cells, and the adhesion of SKBR3 cells was decreased after As_4O_6 treatment. The mechanism revealed that As_4O_6 anticancer efficacy was related to HER-2/EGFR pathways. As_4O_6 exerted its inhibitory effects on migration and invasion in HER-2 positive breast cancer cells by regulating the factors（EGFR, HER-2, Akt, MMP-9） in HER2/ EGFR signaling pathway and other key molecules. In conclusion, the present study indicated that As_4O_6 inhibited the invasion and migration process of HER-2 positive breast cancer SKBR3 cells by negatively regulating the HER-2/EGFR-mediated signaling pathway. These data provided evidence that As_4O_6 might serve as potential anti-metastasis drug for clinical treatment of breast cancer.

关键词： HER-2 positive breast cancer Tetraarsenic oxide Migration Invasion Adhesion Signaling pathway

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集成先验的低复杂度Nyström-MUSIC方法

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航空学报 2023年第22期44卷 57-67页

作者：刘秋雨蒋彦雯范红旗连红飞国防科技大学自动目标识别全国重点实验室长沙410073 国防科技大学电子科学学院长沙410073

传统多重信号分类(MUSIC)方法具有较高的角度分辨率和估计精度,但其子空间分解和谱峰搜索的计算复杂度较高、实时性较差,在阵列雷达系统的实际应用中受到了极大限制。为解决算力有限时阵列雷达角度估计性能受限的难题,提出了集成先验的N... 详细信息

传统多重信号分类(MUSIC)方法具有较高的角度分辨率和估计精度,但其子空间分解和谱峰搜索的计算复杂度较高、实时性较差,在阵列雷达系统的实际应用中受到了极大限制。为解决算力有限时阵列雷达角度估计性能受限的难题,提出了集成先验的Nyström-MUSIC方法,先后通过Nyström近似降低协方差矩阵维度和先验角度信息缩小谱峰搜索范围,分别减小了子空间分解的矩阵规模和谱峰搜索次数,有效降低了MUSIC方法的计算复杂度。仿真表明:集成先验的Nyström-MUSIC方法在具备与传统MUSIC方法相当的分辨性能和估计精度的条件下,将算法复杂度降低了8倍,运行时长减少80%以上,实现了对目标方位的快速高精度估计。

关键词：角度估计低复杂度先验信息 Nyström近似多重信号分类(MUSIC)

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高性能热固性聚酰亚胺树脂研究进展

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高分子材料科学与工程 2021年第5期37卷 149-162页

作者：薛书宇雷星锋连如贺陈妍慧张秋禹西北工业大学化学与化工学院特种功能与智能高分子材料工信部重点实验室陕西西安710072

热固性聚酰亚胺树脂基复合材料具有优异的耐热性和力学性能,广泛应用于武器装备、航空航天等领域。文中系统综述了热固性聚酰亚胺树脂及其复合材料的研究进展,介绍了国内外高性能热固性聚酰亚胺树脂的代表性成果,并对其未来的发展方向... 详细信息

热固性聚酰亚胺树脂基复合材料具有优异的耐热性和力学性能,广泛应用于武器装备、航空航天等领域。文中系统综述了热固性聚酰亚胺树脂及其复合材料的研究进展,介绍了国内外高性能热固性聚酰亚胺树脂的代表性成果,并对其未来的发展方向进行了展望。

关键词：热固性聚酰亚胺基体树脂复合材料熔体黏度耐热性

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核-壳结构的脂质-聚合物杂化纳米粒的研究进展

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药学实践杂志 2018年第1期36卷 13-17页

作者：刘丹张军东廉云飞房秋雨李娟中国药科大学药学院江苏南京211198 上海昊海生物科技股份有限公司上海201600

核-壳结构的脂质-聚合物杂化纳米粒(CSLPHNs)是以具有生物可降解性的聚合物纳米粒为核,外层包覆单层或多层具有生物膜仿生性的脂质壳而形成,结合了纳米粒和脂质体的双重优点,具有粒径小、载药量高、生物相容性好及缓控释给药等优势,在... 详细信息

核-壳结构的脂质-聚合物杂化纳米粒(CSLPHNs)是以具有生物可降解性的聚合物纳米粒为核,外层包覆单层或多层具有生物膜仿生性的脂质壳而形成,结合了纳米粒和脂质体的双重优点,具有粒径小、载药量高、生物相容性好及缓控释给药等优势,在药物递送系统中应用甚广。笔者在查阅近年国内外文献的基础上归纳了CSLPHNs的基本特性、制备方法及在眼部给药、肿瘤治疗及临床诊断成像中的最新研究进展。

关键词：核-壳结构脂质-聚合物杂化纳米粒药物递送系统肿瘤靶向

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前列地尔纳米乳冻干工艺研究

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亚太传统医药 2014年第7期10卷 34-37页

作者：冉海东孙宁云张军东李娟廉云飞房秋雨中国药科大学江苏南京210009 上海信谊药厂有限公司上海201206

目的:制备前列地尔冻干纳米乳剂,提高前列地尔纳米乳的稳定性。方法:采用高压均质法制备前列地尔纳米乳,用冷冻干燥法将其冻干,以冻干乳剂的外观、粒径和复溶情况等优化纳米乳冻干保护剂及冻干工艺。结果:所制备的纳米乳剂冻干前平均粒... 详细信息

目的:制备前列地尔冻干纳米乳剂,提高前列地尔纳米乳的稳定性。方法:采用高压均质法制备前列地尔纳米乳,用冷冻干燥法将其冻干,以冻干乳剂的外观、粒径和复溶情况等优化纳米乳冻干保护剂及冻干工艺。结果:所制备的纳米乳剂冻干前平均粒径为(164.7±21.9)nm,多分散系数(PDI)为0.066。采用10%的海藻糖作为冻干保护剂,制剂冻干复溶后粒径为(169.2±20.5)nm,PDI为0.069,并且冻干乳外观良好,复溶速度快,常温放置主药及杂质含量稳定。结论:该方法能能够显著提高前列地尔纳米乳剂的稳定性。

关键词：前列地尔纳米乳冷冻干燥法冻干乳剂

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84消毒液对多头月季“折射”瓶插保鲜效果的影响

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广东农工商职业技术学院学报 2024年第3期40卷 25-29页

作者：岳海林连凯妮钟秋宇陈礼芬谢秀凤黄敏林桂锋林春华广东农工商职业技术学院广东广州510507

以多头月季“折射”为试验材料,采用不同浓度的84消毒液分别加入0.1 g/L蔗糖作为瓶插液,从瓶插寿命、观赏价值、花径变化率、切花鲜重变化率、水分平衡值等方面研究其对多头月季的瓶插保鲜效果。结果表明,与对照相比,除0.2 ml/L 84消毒... 详细信息

以多头月季“折射”为试验材料,采用不同浓度的84消毒液分别加入0.1 g/L蔗糖作为瓶插液,从瓶插寿命、观赏价值、花径变化率、切花鲜重变化率、水分平衡值等方面研究其对多头月季的瓶插保鲜效果。结果表明,与对照相比,除0.2 ml/L 84消毒液+0.1g/L蔗糖外,0.4 ml/L、0.6 ml/L、0.8 ml/L的84消毒液分别加入0.1g/L蔗糖均能有效延长多头月季“折射”的瓶插寿命、提高其观赏价值,取得较好的保鲜效果。其中,0.6ml/L 84消毒液+1%蔗糖的瓶插液处理多头月季“折射”的瓶插寿命比对照延长了3.4 d,综合保鲜效果最好。

关键词：多头月季 84消毒液保鲜剂瓶插保鲜

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