Myeloid-derived suppressor cell (MDSC) key genes analysis in rat anti-CD28-induced immune tolerance kidney transplantation

BackgroundIn the field of transplantation, inducing immune tolerance in recipients is of great importance. Blocking co-stimulatory molecule using anti-CD28 antibody could induce tolerance in a rat kidney transplantation model. Myeloid-derived suppressor cells (MDSCs) reveals strong immune suppressive abilities in kidney transplantation. Here we analyzed key genes of MDSCs leading to transplant tolerance in this model.MethodsMicroarray data of rat gene expression profiles under accession number {"type":"entrez-geo","attrs":{"text":"GSE28545","term_id":"28545"}}GSE28545 in the Gene Expression Omnibus (GEO) database were analyzed. Running the LIMMA package in R language, the differentially expressed genes (DEGs) were found. Enrichment analysis of the DEGs was conducted in the Database for Annotation, Visualization and Integrated Discovery (DAVID) database to explore gene ontology (GO) annotation and their Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Their protein-protein interactions (PPIs) were provided by STRING database and was visualized in Cytoscape. Hub genes were carried out by CytoHubba.ResultsThree hundred and thirty-eight DEGs were exported, including 27 upregulated and 311 downregulated genes. The functions and KEGG pathways of the DEGs were assessed and the PPI network was constructed based on the string interactions of the DEGs. The network was visualized in Cytoscape; the entire PPI network consisted of 192 nodes and 469 edges. Zap70, Cdc42, Stat1, Stat4, Ccl5 and Cxcr3 were among the hub genes.ConclusionsThese key genes, corresponding proteins and their functions may provide valuable background for both basic and clinical research and could be the direction of future studies in immune tolerance, especially those examining immunocyte-induced tolerance.     

胶质母细胞瘤差异表达基因的生物信息学分析

目的:应用生物信息学方法挖掘胶质母细胞瘤(GBM)的相关基因，进而探讨发病机制，为GBM临床诊断和靶向治疗提供理论依据。方法:从GEO(Gene Expression Omnibus)数据库下载基因芯片数据集GSE4290和GSE15824，应用GEO2R筛选GBM的差异表达基因(DEGs)。采用DAVID数据库进行GO富集和KEGG通路富集分析，分别应用STRING数据库和Cytoscape软件构建蛋白质相互作用网络和关键基因模块，筛选GBM靶基因。进一步运用ONCOMINE数据库验证临床组织样本中靶基因与GBM的关系。结果:共筛选出76个DEGs，富集分析结果显示DEGs在血管生成的正调节、抗原的呈递和处理、信号转导、调节自噬等方面存在显著富集。共挖掘出POSTN、TAGLN、CALD1、EPCAM 4个GBM靶基因，经证实均在临床GBM组织样本中存在显著上调且靶基因的上调与患者的不良预后密切相关。结论:通过生物信息学共挖掘出4个与GBM显著相关的靶基因，可能是未来GBM发病机制、临床诊断、治疗的重要研究靶点。     

RNA-Seq analysis in an avian model of maternal phenylketonuria

Cardiac malformations (CVMs) are a leading cause of infant morbidity and mortality. CVMs are particularly prevalent when the developing fetus is exposed to high levels of phenylalanine in-utero in mothers with Phenylketonuria. Yet, elucidating the underlying molecular mechanism leading to CVMs has proven difficult. In this study we used RNA-Seq to investigate an avian model of MPKU and establish differential gene expression (DEG) characteristics of the early developmental stages HH10, 12, and 14. In total, we identified 633 significantly differentially expressed genes across stages HH10, 12, and 14. As expected, functional annotation of significant DEGs identified associations seen in clinical phenotypes of MPKU including CVMs, congenital heart defects, craniofacial anomalies, central nervous system defects, and growth anomalies. Additionally, there was an overrepresentation of genes involved in cardiac muscle contraction, adrenergic signaling in cardiomyocytes, migration, proliferation, metabolism, and cell survival. Strikingly, we identified significant changes in expression with multiple genes involved in Retinoic Acid (RA) metabolism and downstream targets. Using qRTPCR, we validated these findings and identified a total of 42 genes within the RA pathway that are differentially expressed. Here, we report the first elucidation of the molecular mechanisms of cardiovascular malformations in MPKU conducted at early developmental timepoints. We provide evidence suggesting a link between PHE exposure and the alteration of RA pathway. These results are promising and offer novel findings associated with congenital heart defects in MPKU.     

基于网络药理学的生脉散作用机制分析

目的:探讨生脉散的作用机制。方法:本研究选取生脉散中3味中药人参、麦冬、五味子含有的33个活性成分,通过Pharm Mapper服务器预测其活性成分的潜在靶点,进而构建化合物-靶点网络、构建蛋白互作(protein-protein interaction,PPI)网络、进行基因本体(gene ontology,GO)富集分析、进行基于京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes,KEGG)的生物通路富集分析,研究生脉散作用机制。结果:化合物-靶点网络包含249个节点,关键靶点涉及转甲状腺素蛋白(TTR)等。PPI网络包含155个节点,关键靶点涉及酪氨酸蛋白激酶Src(SRC),蛋白激酶Bα(Akt1)等。GO条目95个,其中生物过程相关的条目67个,分子功能相关的条目22个,细胞组成相关的条目6个。KEGG通路8条,涉及肿瘤信号通路(pathways in cancer),前列腺癌(prostate cancer),胰岛素信号通路(insulin signaling pathway)等。结论:本研究结果初步验证了生脉散的基本药理作用及其机制,并为进一步深入揭示其作用机制奠定了良好基础。     

高低剂量X射线照射正常人淋巴母细胞基因表达转录谱的研究

目的 比较高低剂量X射线照射对基因表达影响的差异性,探讨不同剂量辐射生物效应的作用机制.方法 采用包含有45 033个基因的NimbleGen 12×135K芯片分析0.1和5 Gy照射正常人淋巴母细胞AHH-1培养6h后基因表达谱的改变,以差异为2倍以上且两组实验结果一致的标准确定为有效差异表达基因.用real-time PCR和Western blot方法验证了共同表达基因PERP的表达.结果 0.1 Gy照射后,有760个基因表达上调,1222个基因表达下调;5 Gy照射后,上调和下调基因分别是457和744个.在两个剂量照射条件下共同表达上调的基因有55个,同时下调的基因有339个.低剂量组差异表达基因主要参与细胞信号转导、DNA损伤反应等过程,高剂量组主要参与凋亡、细胞增殖分化等过程.real-time PCR和Western blot方法验证了PERP的表达与芯片结果相一致,均表达下调.结论 高低剂量照射后基因表达改变存在质和量的差异,可更好地阐释高低剂量电离辐射生物学效应的作用机制.     

Fabrication and Adsorption Optimization of Novel Magnetic Core-shell Chitosan/Graphene Oxide/β-cyclodextrin Composite Materials for Bisphenols in Aqueous Solutions

A novel magnetic composite material, Fe₃O₄@SiO₂/chitosan/graphene oxide/β-cyclodextrin (MCGC), was prepared by multi-step methods. Various methods were used to systematically characterize the morphology, composition, structure, and magnetic properties of MCGC. The results obtained show that the composite material has good morphology and crystal structure and can be separated quickly by an external magnetic field. The operation is relatively easy, and the raw materials used to prepare this material are economical, easy to obtain, and environmentally friendly. The performance and adsorption mechanism for using this material as an adsorbent to remove bisphenol A (BPA) and bisphenol F (BPF) from water were studied. The adsorption parameters were optimized. Under optimal conditions, MCGC was found to remove more than 90% of BPA and BPF in a mixed solution (20 mg/L, 50 mL); the adsorption process for BPA and BPF on MCGC was found to follow a Redlich–Peterson isotherm model and Pseudo-second-order kinetic model. The adsorption mechanism for MCGC may involve a combination of various forces. Recycling experiments showed that after five uses, MCGC retained a more than 80% removal effect for BPA and BPF, and through real sample verification, MCGC can be used for wastewater treatment. Therefore, MCGC is economical, environmentally friendly, and easy to separate and collect, and has suitable stability and broad application prospects.     

High-content analysis for mitophagy response to nanoparticles: A potential sensitive biomarker for nanosafety assessment

Mitophagy, a selective autophagy of mitochondria, clears up damaged mitochondria to maintain cell homeostasis. We performed high-content analysis (HCA) to detect the increase of PINK1, an essential protein controlling mitophagy, in hepatic cells treated with several nanoparticles (NPs). PINK1 immunofluorescence-based HCA was more sensitive than assays and detections for cell viability and mitochondrial functions. Of which, superparamagnetic iron oxide (SPIO)-NPs or graphene oxide-quantum dots (GO-QDs) was selected as representatives for positive or negative inducer of mitophagy. SPIO-NPs, but not GO-QDs, activated PINK1-dependent mitophagy as demonstrated by recruitment of PARKIN to mitochondria and degradation of injured mitochondria. SPIO-NPs caused the loss of mitochondrial membrane potential, decrease in ATP, and increase in mitochondrial reactive oxide species and Ca²⁺. Blocking mitophagy with PARKIN siRNA aggravated the cytotoxicity of SPIO-NPs. Taken together, PINK1 immunofluorescence-based HCA is considered to be an early, sensitive, and reliable approach to evaluate the bioimpacts of NPs.