Deepm5C: A deep-learning-based hybrid framework for identifying human RNA N5-methylcytosine sites using a stacking strategy

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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.     

Identification of key genes and pathways in discoid lupus skin via bioinformatics analysis

Discoid lupus erythematosus (DLE) is the most common skin manifestation of lupus; however, the molecular mechanisms underlying DLE remain unknown. Therefore, we aimed to identify key differentially expressed genes (DEGs) in discoid lupus skin and investigate their potential pathways.To identify candidate genes involved in the occurrence and development of the disease, we downloaded the microarray datasets {"type":"entrez-geo","attrs":{"text":"GSE52471","term_id":"52471"}}GSE52471 and {"type":"entrez-geo","attrs":{"text":"GSE72535","term_id":"72535"}}GSE72535 from the Gene Expression Database (GEO). DEGs between discoid lupus skin and normal controls were selected using the GEO2R tool and Venn diagram software (http://bioinformatics.psb.ugent.be/webtools/Venn/). The Database for Annotation, Visualization, and Integrated Discovery (DAVID), Enrichr, and Cytoscape ClueGo were used to analyze the Kyoto Encyclopedia of Gene and Genome pathways and gene ontology. Protein-protein interactions (PPIs) of these DEGs were further assessed using the Search Tool for the Retrieval Interacting Genes version 10.0.Seventy three DEGs were co-expressed in both datasets. DEGs were predominantly upregulated in receptor signaling pathways of the immune response. In the PPI network, 69 upregulated genes were selected. Furthermore, 4 genes (CXCL10, ISG15, IFIH1, and IRF7) were found to be significantly upregulated in the RIG-I-like receptor signaling pathway, from analysis of Enrichr and Cytoscape ClueGo.The results of this study may provide new insights into the potential molecular mechanisms of DLE. However, further experimentation is required to confirm these findings.     

EZH2在乳腺癌中的差异表达及临床意义

目的:利用整合生物信息学手段分析EZH2（enhancer of zeste 2 polycomb repressive complex 2 subunit）基因在乳腺癌中的表达及其临床意义。方法:在肿瘤基因组计划数据库（The Cancer Genome Atlas，TCGA）中下载乳腺癌与正常乳腺组织的基因表达谱数据，进一步利用Ualcan数据库和人类蛋白质图谱（The Human Protein Atlas）数据库数据分析EZH2基因在乳腺癌中的mRNA及蛋白表达水平。利用Ualcan数据库分析EZH2基因的甲基化水平并筛选其共表达基因；对EZH2及其共表达基因进行GO（Gene Ontology）富集分析和KEGG通路分析以明确EZH2的共表达基因参与的生物学过程和相关通路；使用Kaplan-Meier生存分析法分析乳腺癌患者的总生存期、无病生存期、无远处转移生存期及后进展生存期与EZH2基因表达水平的关系并绘制生存曲线。结果:与正常乳腺组织相比，EZH2在乳腺癌组织中的mRNA及蛋白表达量明显升高。而EZH2的甲基化程度在乳腺癌组织与正常乳腺组织中则差异不明显。同时，EZH2的表达水平与年龄、乳腺癌分期及乳腺癌分子分型等因素密切相关。EZH2及其共表达基因主要参与了核碱基的调节、细胞周期调控、染色体分离、DNA复制、DNA修复等生物学过程，并参与了细胞周期、DNA 复制、M/G1期转化、M期、有丝分裂前中期、ATM通路等生物学通路。此外，EZH2基因表达水平高的乳腺癌患者的总生存期、无病生存期、无远处转移生存期及后进展生存期均明显低于EZH2基因低表达的患者。结论:EZH2在乳腺癌组织中高表达并且与患者不良预后密切相关。同时，EZH2的表达水平与乳腺癌的发生、发展密切相关。EZH2在乳腺癌诊断、靶向治疗及预后分析中具有重要的临床意义。     

Construction of a risk model of steroid-induced necrosis of the femoral head and prediction of potential Chinese medicine treatments北大核心

背景:随着疾病治疗模式的改变,人们已经意识到中医药在激素性股骨头坏死治疗过程中的重要性,因此利用生物信息学从分子水平分析激素性股骨头坏死的发病机制,构建疾病风险模型,并预测具有潜在治疗作用的中药,为后期中医药治疗激素性股骨头坏死提供一定的理论依据。目的:基于生物信息学挖掘激素性股骨头坏死的竞争性内源RNA(ceRNA)调控网络,分析其在激素性股骨头坏死中的分子调控机制,预测相关疾病靶点并构建疾病风险模型,同时预测具有潜在治疗作用的中药。方法:检索GEO数据库,下载激素性股骨头坏死的矩阵文件GSE123568和基因注释文件GPL15207。借助R语言等软件分析得到差异表达的长链非编码RNA与mRNA,并通过公共数据库预测与差异表达长链非编码RNA关联的miRNA-mRNA,再将预测到的mRNA与差异表达mRNA取交集,整合得到ceRNA网络。随后采用STRING数据库和Cytoscape软件筛选关键基因,利用R语言分析关键基因的功能与相关通路,并挖掘关键ceRNA网络。最后根据关键基因构建激素性股骨头坏死的风险模型,并进行中药预测。结果与结论:(1)与健康对照相比,激素性股骨头坏死患者共有7个长链非编码RNA和1763个mRNAs存在差异表达;(2)筛选出STAT3、KAT2B、AGO4、JAK2、JAK1、PTGS2共6个关键基因;(3)关键基因所富集的功能包括对肽激素的反应、白细胞介素6介导的信号通路、细胞对白细胞介素6的反应等生物学过程,涉及JAK-STAT、脂肪细胞因子、催乳素等信号通路;(4)4种mi RNAs(mi R-135a-5p、mi R-137、mi R-17-5p、miR-20b-5p)和2种长链非编码RNA(SNHG11、C20orf197)可能在导致激素性股骨头坏死发生发展过程中发挥关键作用;(5)KAT2B最有可能是激素性股骨头坏死发生发展的风险因子;(6)郁金、淫羊藿、黄芪具备治疗激素性股骨头坏死疾病靶点的可能。通过对激素性股骨头坏死相关长链非编码RNA介导的ceRNA网络进行分析,识别出潜在的疾病靶点、信号通路及潜在治疗中药,为进一步阐明其发病机制,并为后续的实验研究提供参考依据。     

急性白血病的基因表达谱分析与亚型分类特征的鉴别

本研究基于生物信息学理论，运用模式识别方法和计算技术，对急性白血病的基因表达谱数据进行分析，研究急性白血病的亚型识别与分类信息基因选取问题。首先去除无关基因，然后利用浮动顺序搜索算法搜索特征空间生成候选特征子集，最后以支持向量机作为分类器进行急性白血病的亚型识别，并以误识率为依据鉴别出了5个包含完整分类信息的基因。实验结果表明，本研究鉴别出的5个信息基因能以100％的正确率准确识别急性白血病亚型。     

Multiomics uncovers developing immunological lineages in human

The development of the human immune system during embryonic and fetal life has historically been difficult to research due to limited access to human tissue. Experimental animal models have been widely used to study development but cellular and molecular programmes may not be conserved across species. The advent of multiomic single-cell technologies and an increase in human developmental tissue biobank resources have facilitated single-cell multiomic studies focused on human immune development. A critical question in the near future is "How do we best reconcile scientific findings across multiple omic modalities, developmental time, and organismic space?" In this review, we discuss the application of single-cell multiomic technologies to unravel the major cellular lineages in the prenatal human immune system. We also identify key areas where the combined power of multiomics technologies can be leveraged to address specific immunological gaps in our current knowledge and explore new research horizons in human development.     

人CD226基因SNP和启动子序列分析

目的 研究人CD226（PTA1）启动子及其5‘上游调控序列。方法 应用计算机软件预测启动子序列，并分析人CD226基因5‘上游调控序列以及通过RT－PCR的方法研究开放读框中的单核苷酸多态性。结果 CD226基因在－375bp处和－130bp处可能有两个启动子，含有AP－1，Ets-1,Spl,P300,PU.1,PEA3等转录因子结合序列，在编码胞浆区的序列中存在一个单核苷酸多态性位点。结论 CD226基因表达受到多种转录因子和5‘端上游调控序列的调控。     

华支睾吸虫ATP合酶B亚基全长基因的生物信息学分析

目的从华支睾吸虫全长cDNA质粒文库中识别ATP合酶B亚基,利用生物信息学方法预测其结构和功能特征,用以指导实验研究。方法利用生物信息学网站的各种在线分析工具和Vector NT Isuite软件包,识别华支睾吸虫ATP合酶B亚基基因并预测编码蛋白质的各种结构与功能特征,并根据该基因构建种系分子进化树。结果Blastx分析该基因为全长基因,属于ATP合酶B亚基家族,其分子进化树与种系进化过程非常吻合。该基因全长1008bp,编码300个氨基酸,含有线粒体转运肽、两个跨膜区、一个核定位序列和多个磷酸化位点,具有较稳定的理化性质。结论ATP合酶B亚基是一个理想的真核种系进化的分子标志。华支睾吸虫ATP合酶B亚基具有线粒体和细胞核的双重定位序列,提示该蛋白可能在华支睾吸虫的能量代谢途径中发挥独特的调节作用。