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Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from A Data-driven Perspective

Genomics, Proteomics & Bioinformatics 2023年第1期21卷 164-176页

作者： jianlei gu Jiawei Dai Hui Lu Hongyu Zhao SJTU-Yale Joint Center for Biostatistics and Data Science Department of Bioinformatics and BiostatisticsSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Center for Biomedical Informatics Shanghai Engineering Research Center for Big Data in Pediatric Precision MedicineShanghai Children’s HospitalShanghai 200040China Department of Biostatistics Yale UniversityNew HavenCT 06511USA

Comprehensive characterization of spatial and temporal gene expression patterns in humans is critical for uncovering the regulatory codes of the human genome and understanding the molecular mechanisms of human *** expressed genes(UEGs)refer to the genes expressed across a majority of,if not all,phenotypic and physiological conditions of an *** is known that many human genes are broadly expressed across ***,most previous UEG studies have only focused on providing a list of UEGs without capturing their global expression patterns,thus limiting the potential use of UEG *** this study,we proposed a novel data-driven framework to leverage the extensive collection of40,000 human transcriptomes to derive a list of UEGs and their corresponding global expression patterns,which offers a valuable resource to further characterize human *** results suggest that about half(12,234;49.01%)of the human genes are expressed in at least 80%of human transcriptomes,and the median size of the human transcriptome is 16,342 genes(65.44%).Through gene clustering,we identified a set of UEGs,named LoVarUEGs,which have stable expression across human transcriptomes and can be used as internal reference genes for expression *** further demonstrate the usefulness of this resource,we evaluated the global expression patterns for 16 previously predicted disallowed genes in islet beta cells and found that seven of these genes showed relatively more varied expression patterns,suggesting that the repression of these genes may not be unique to islet beta cells.

关键词： Ubiquitous expression Housekeeping gene Disallowed gene Expression specificity Expression variability

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Toll-like receptor 7 deficiency suppresses type 1 diabetes development by modulating B-cell differentiation and function

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Cellular & Molecular Immunology 2021年第2期18卷 328-338页

作者： Juan Huang Jian Peng James Alexander Pearson Georgios Efthimiou Youjia Hu Ningwen Tai Yanpeng Xing Luyao Zhang jianlei gu Jianping Jiang Hongyu Zhao Zhiguang Zhou F.Susan Wong Li Wen National Clinical Research Center for Metabolic Diseases Key Laboratory of Diabetes Immunology(Central South University)Ministry of Educationand Department of Metabolism and EndocrinologyThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina Section of Endocrinology Department of Internal MedicineSchool of MedicineYale UniversityNew HavenCTUSA Division of Infection and Immunity School of MedicineCardiff UniversityCardiffUK Department of Microbiology University of HullHullUK Department of Gastrointestinal Surgery of the First Hospital of Jilin University ChangchunJilinChina Department of Biostatistics Data Science&GeneticsYale School of Public HealthNew HavenCTUSA

Innate immunity mediated by Toll-like receptors(TLRs),which can recognize pathogen molecular patterns,plays a critical role in type 1 diabetes ***7 is a pattern recognition receptor that senses single-stranded RNAs from viruses and host tissue cells;however,its role in type 1 diabetes development remains *** our study,we discovered that Tlr7-deficient(Tlr7^(−/−))nonobese diabetic(NOD)mice,a model of human type 1 diabetes,exhibited a significantly delayed onset and reduced incidence of type 1 diabetes compared with Tlr7-sufficient(Tlr7^(+/+))NOD *** investigations showed that Tlr7 deficiency significantly altered B-cell differentiation and immunoglobulin ***,Tlr7^(−/−)NOD B cells were found to suppress diabetogenic CD4^(+)T-cell responses and protect immunodeficient NOD mice from developing diabetes induced by diabetogenic T *** addition,we found that Tlr7 deficiency suppressed the antigen-presenting functions of B cells and inhibited cytotoxic CD8^(+)T-cell activation by downregulating the expression of both nonclassical and classical MHC class I(MHC-I)molecules on B *** data suggest that TLR7 contributes to type 1 diabetes development by regulating B-cell functions and subsequent interactions with T ***,therapeutically targeting TLR7 may prove beneficial for disease protection.

关键词： Type 1 diabetes Toll-like receptor 7 B cell

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microRNA对儿童哮喘靶基因调控的生物信息学分析

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临床儿科杂志 2016年第2期34卷 81-87页

作者：董晓艳陆权张慧燕顾坚磊钟南上海市儿童医院上海交通大学附属儿童医院呼吸科上海200062 上海医学遗传研究所上海200040

目的应用生物信息学技术分析尘螨过敏哮喘儿童特异性microRNA(miRNA)及其靶基因筛选,探讨哮喘发病机制。方法采用病例对照研究,在62对尘螨过敏哮喘患儿及同龄正常无过敏儿童中,随机选取12例哮喘患儿及对照者进行microRNA芯片分析,比较... 详细信息

目的应用生物信息学技术分析尘螨过敏哮喘儿童特异性microRNA(miRNA)及其靶基因筛选,探讨哮喘发病机制。方法采用病例对照研究,在62对尘螨过敏哮喘患儿及同龄正常无过敏儿童中,随机选取12例哮喘患儿及对照者进行microRNA芯片分析,比较两组中存在异常表达的miRNAs,并在其余病例中进行RT-qPCR验证和生物信息学分析。结果尘螨过敏哮喘儿童中有6个microRNA表达较对照组下调2倍以上,分别为miRNA-151a-5p、625-5p、126-3p、513a-5p、27b-3p、22-3p,差异均有统计学意义(P<0.05)。进一步的生物信息学富集分析发现,这些microRNAs调控的PPARGC1B、CBL、ONECUT2、ESR1、EGFR、SYK、STAT1与炎症因子信号通路有着显著性关联(P<0.05)。结论 miRNA-625-5p、513a-5p、27b-3p、22-3p可能通过共同调控相关靶基因,形成一个网络通路,参与尘螨诱发儿童哮喘的发生。

关键词： microRNA 哮喘生物信息学信号通路儿童

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基于保留皮肤的“防火带”式引流术治疗肛周坏死性筋膜炎

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中华胃肠外科杂志 2024年第7期27卷 726-730页

作者：叶晓瑞金黑鹰王俊张春霞杨阳顾家博张心怡刘建磊沈彬艳南京中医药大学第二附属医院肛肠科南京210017

目的观察应用一种新型保留皮肤的“防火带”式引流术治疗肛周坏死性筋膜炎的临床疗效。方法本技术适用于就诊时未发生大面积皮肤发黑坏死、可耐受手术的肛周坏死性筋膜炎患者。手术步骤及要点:(1)根据影像学检查及术中探查,确定炎性组... 详细信息

目的观察应用一种新型保留皮肤的“防火带”式引流术治疗肛周坏死性筋膜炎的临床疗效。方法本技术适用于就诊时未发生大面积皮肤发黑坏死、可耐受手术的肛周坏死性筋膜炎患者。手术步骤及要点:(1)根据影像学检查及术中探查,确定炎性组织和正常组织的分界线;(2)沿脓肿波动感最明显的部位切开脓腔,长径3~4 cm,短径1~2 cm;(3)从主切口向感染外缘潜行分离清理坏死组织,每分离3~5 cm作一梭形切口,长径2~3 cm,短径约1 cm,潜行分离直至正常组织处,各相邻切口间挂软管对口引流;(4)各相邻边缘切口间均作潜行分离并挂软管引流,形成“防火带”;(5)反复冲洗创面;(6)如果感染侵及直肠,酌情行结肠造口。回顾性分析2019年7月至2023年2月南京中医药大学第二附属医院收治的11例肛周坏死性筋膜炎患者的病例资料,所有患者均采用保留皮肤的“防火带”式引流术进行了急诊手术清创治疗。结果11例全部治愈,治愈率100%。1例行多次手术。平均住院时间22(11~46)d,平均创面愈合时间43(28~75)d。除了1例外伤患者,其余患者术后均无明显肛门功能损伤,11例患者均痊愈出院,术后中位随访136(115~413)d,无复发。结论基于保留皮肤的“防火带”式引流术治疗肛周坏死性筋膜炎具有创伤小,恢复快等优势,且不造成明显肛门功能损伤。

关键词：肛周坏死性筋膜炎防火带保留皮肤临床疗效

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Phase transferring luminescent gold nanoclusters via single-stranded DNA

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Science China Chemistry 2022年第6期65卷 1212-1220页

作者： Yu Li Hui Lu Zhibei Qu Mingqiang Li Haoran Zheng Peilin gu Jiye Shi Jiang Li Qian Li Lihua Wang Jing Chen Chunhai Fan jianlei Shen Division of Physical Biology CAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of SciencesShanghai201800China University of Chinese Academy of Sciences Beijing100049China School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational MedicineShanghai Jiao Tong UniversityShanghai200240China Shanghai Synchrotron Radiation Facility Zhangjiang LaboratoryShanghai Advanced Research InstituteChinese Academy of SciencesShanghai201210China Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal UniversityShanghai200127China

Atomically precise gold nanoclusters(Au NCs) are an emerging class of quantum-sized nanomaterials with discrete electronic energy levels, which has led to a range of attractive electronic and optical applications. Nevertheless, the lack of general methods to transfer Au NCs protected with hydrophobic ligands to an aqueous solution hampers their use in physiological settings. Here,we developed a single-stranded DNA-based approach that could transfer ~90% hydrophobic Au NCs into an aqueous *** experimentally and theoretically established that multivalent electrostatic and hydrophobic interactions between DNA strands and the hydrophobic ligand layer on Au NCs resulted in monodispersed DNA-coated Au NCs with high physical integrity in an aqueous solution. The fluorescence quantum yield of Au NCs was increased by ~13 fold, and surface-constrained DNA retained the specific recognition ability for biosensing. We further demonstrated the versatility of this phase-transfer approach, which thus holds great potential to advance biological and medical applications of Au NCs.

关键词： gold nanoclusters DNA monodispersed phase transfer biological application

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生活垃圾有机质酸化的研究与展望

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环境卫生工程 2007年第4期15卷 15-18页

作者：廖金宝顾坚磊刘伟陈永梅中国矿业大学江苏徐州221008

综述了国内外生活垃圾有机质酸化的研究进展和目前生活垃圾厌氧降解的微生物学研究现状。提出了当前有机垃圾厌氧降解理论上的不足。

关键词：生活垃圾有机质酸化厌氧降解

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依据血流动力学特征指导高血压治疗用药的可行性探索

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中国心血管杂志 2021年第5期26卷 432-437页

作者：王鲁雁王鸿懿顾坚磊马政张之瀛孙宁玲北京大学人民医院高血压研究室 100044 上海交通大学-耶鲁大学生物统计与数据科学联合中心 200240 北京天坛普华医院心内科 100050

目的探索依据血流动力学表型指导降压药物选择的可行性。方法采用前瞻性单中心随机单盲对照研究方法,纳入102例初发未治疗或经治疗血压未达标(≥140/90 mmHg)的高血压患者。采用阻抗心动图(ICG)检查采集血流动力学指标,并分为依据血流... 详细信息

目的探索依据血流动力学表型指导降压药物选择的可行性。方法采用前瞻性单中心随机单盲对照研究方法,纳入102例初发未治疗或经治疗血压未达标(≥140/90 mmHg)的高血压患者。采用阻抗心动图(ICG)检查采集血流动力学指标,并分为依据血流动力学治疗组(A组,51例)和常规经验治疗组(B组,51例),治疗4~12周,主要疗效指标为两组的诊室血压下降幅度。结果与B组比较,A组收缩压[(19.9±10.7)mmHg比(12.0±11.8)mmHg]和舒张压[(11.3±6.2)mmHg比(4.9±9.9)mmHg]较基线降幅更大,A组达标率更高(66.7%比41.2%)(均为P<0.05)。男性、年龄<50岁、经治、基线收缩压<160 mmHg、基线舒张压≥90 mmHg亚组中,A组血压达标率均高于B组(均为P<0.05)。A组患者中,β受体阻滞剂用药后的心排指数较基线显著下降(P=0.044),利尿剂用药后胸腔血容量饱和度显著降低(P=0.001),钙通道拮抗剂使用后大动脉硬化指数(P=0.003)和系统血管阻力指数(P=0.003)均较基线明显降低,而肾素血管紧张素系统抑制剂类药物使用后系统血管阻力指数显著降低(P<0.001)。结论使用血流动力学检查协助判断未控制的高血压患者可能的血压升高机制,并以此为依据选择降压药物可能更有效地降低血压,并提高降压达标率。

关键词：高血压血流动力学药物治疗阻抗心动图

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On the anomalous low-resistance state and exceptional Hall component in hard-magnetic Weyl nanoflakes

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Science China(Physics,Mechanics & Astronomy) 2021年第8期64卷 107-113页

作者： QingQi Zeng GangXu gu Gang Shi jianlei Shen Bei Ding Shu Zhang XueKui Xi Claudia Felser YongQing Li EnKe Liu Beijing National Laboratory for Condensed Matter Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China Department of Physics and Astronomy University of CaliforniaLos Angeles 90095USA Max Planck Institute for Chemical Physics of Solids Dresden D-01187Germany Songshan Lake Materials Laboratory Dongguan 523808China

Magnetic topological materials, which combine magnetism and topology, are expected to host emerging topological states and exotic quantum phenomena. In this study, with the aid of greatly enhanced coercive fields in high-quality nanoflakes of the magnetic Weyl semimetal Co_(3)Sn_(2)S_(2), we investigate anomalous electronic transport properties that are difficult to reveal in bulk Co_(3)Sn_(2)S_(2) or other magnetic materials. When the magnetization is antiparallel to the applied magnetic field, the low longitudinal resistance state occurs, which is in sharp contrast to the high resistance state for the parallel case. Meanwhile, an exceptional Hall component that can be up to three times larger than conventional anomalous Hall resistivity is also observed for transverse transport. These anomalous transport behaviors can be further understood by considering nonlinear magnetic textures and the chiral magnetic field associated with Weyl fermions, extending the longitudinal and transverse transport physics and providing novel degrees of freedom in the spintronic applications of emerging topological magnets.

关键词： hard-magnetic material magnetic Weyl semimetal magnetoresistance Hall effect

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Aggregation-induced emission luminogen for specific identification of malignant tumour in vivo

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Science China Chemistry 2020年第3期63卷 393-397页

作者： jianlei Shen Kun Tao Peilin gu Chen gui Dong Wang Zhenyu Tan Lihua Wang Zhiming Wang Anjun Qin Ben Zhong Tang Shisan Bao School of Chemistry and Chemical Engineering Shanghai Jiao Tong UniversityShanghai 200240China Tongren Hospital School of MedicineShanghai Jiao Tong UniversityShanghai 200240China Discipline of Pathology Bosch Institute and School of Medical SciencesCharles Perkins CentreThe University of SydneyAustralia Division of Physical Biology CAS Key Laboratory of Interfacial Physics and TechnologyShanghai Synchrotron Radiation FacilityShanghai Institute of Applied PhysicsChinese Academy of SciencesShanghai 201800China Department of Chemistry HKUST Jockey Club Institute for Advanced StudyInstitute of Molecular Functional MaterialsDivision of Biomedical EngineeringState Key Laboratory of Molecular NeuroscienceDivision of Life ScienceThe Hong Kong University of Science and TechnologyHong KongChina State Key Laboratory of Luminescent Materials and Devices South China University of TechnologyGuangzhou 510640China

Colorectal cancer(CRC)is still a major killer,mainly due to the lack of early detection biomarker with sensitivity/*** histopathology is the gold standard approach in practice,but there are still some issues(false diagnosis and long waiting period).Aggregation-induced emission(AIE)is a novel photophysical phenomenon which has been widely utilized for biological imaging in vitro,including malignant cells,showing remarkable imaging contrast and enhanced emission in high concentrated ***,it is unclear if AIE dyes can identify malignant cells specifically in vivo.A great challenge for specific labeling of malignant cells is probably ascribed to the complex compositions in tumor ***,an AIE dye-based mitochondria-targeted histological staining strategy was employed to localize cancer and the metastatic track in the fresh colorectal *** novel approach holds great potential to revolutionize the clinical diagnosis and intervention for devastating malignancy.

关键词： aggregation-induced emission histological staining colorectal cancer

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加味行健汤联合TACE对胃癌肝转移患者肿瘤局部控制及血清HGF、VEGF水平的影响

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介入放射学杂志 2022年第4期31卷 359-363页

作者：张建磊刘震坤李庆敏刘固全凌峰郴州市第一人民医院介入科湖南423000 郴州市第一人民医院中医科湖南423000 郴州市第一人民医院普外科湖南423000

目的探讨加味行健汤联合TACE对胃癌肝转移患者肿瘤局部控制及血清肝细胞生长因子(HGF)、血管内皮生长因子(VEGF)水平的影响。方法选取2016年3月至2019年3月89例胃癌肝转移患者,随机数字表法分为对照组(n=44)和实验组(n=45)。对照组给... 详细信息

目的探讨加味行健汤联合TACE对胃癌肝转移患者肿瘤局部控制及血清肝细胞生长因子(HGF)、血管内皮生长因子(VEGF)水平的影响。方法选取2016年3月至2019年3月89例胃癌肝转移患者,随机数字表法分为对照组(n=44)和实验组(n=45)。对照组给予TACE(1~3次),实验组给予TACE^(+)加味行健汤(4个化疗周期)。观察两组肿瘤局部控制率、不良反应、生活质量改善率及治疗前、TACE治疗后1个月、3个月血清HGF、VEGF水平、T淋巴细胞亚群、炎性因子水平,并于TACE治疗后12个月统计生存率。结果实验组肿瘤局部控制率为84.44%(38/45),高于对照组65.9%(29/44)(P0.05)。TACE治疗后1个月、3个月实验组血清HGF、VEGF水平低于对照组(P<0.05)。TACE治疗后1个月、3个月实验组CD3^(+)、CD8^(+)、CD4^(+)/CD8^(+)T淋巴细胞水平均优于对照组(P<0.05),实验组免疫功能呈上升趋势,对照组呈下降趋势。TACE治疗后1个月、3个月两组血清IFN-γ、IL-10、IL-2水平均明显改善,实验组改善幅度较高(P<0.05)。实验组生活质量改善率为53.3%(24/45),高于对照组31.8%(14/44)(P<0.05),TACE治疗后12个月随访,两组生存率比较差异无统计学意义。结论加味行健汤联合TACE治疗胃癌肝转移临床效果显著,可控制肿瘤进展,抑制HGF、VEGF等血清因子表达,同时提高机体免疫功能,缓解机体炎症状态,改善患者生活质量,且安全性良好。

关键词：胃癌肝转移加味行健汤随机对照试验

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