糖尿病大鼠早期肾脏病变相关新基因Dmrs91克隆及其生物信息学分析

对合并早期肾脏病变的糖尿病大鼠肾脏进行cDNARDA获得的新EST序列进行全长cDNA克隆即新基因Dmrs91,并对该基因进行生物信息学分析。     

Analyses of multi-omics differences between patients with high and low PD1/PDL1 expression in lung squamous cell carcinoma

BackgroundImmunotherapy has achieved excellent results in patients with lung squamous cell carcinoma. However, in which population it can exert the greatest effect is still unknown. Some studies have suggested that its effect is related to the expression level of PD1. Analyzing the relationship between PD1 expression level and genetic differences in lung squamous cell carcinoma patients will be helpful in understanding the underlying causes of this immunotherapy effect and provide a reference for clinical practice.MethodsIn this study, we used RNA-seq, miRNA-seq, methylation array, mutation profiles, and copy number variation data from the TCGA database and RNA-seq data from the GEO database to analyze the distinctive genomic patterns associated with PD1 and PDL1 expression. RNA-seq data from 44 LUSC patients who underwent surgery at Zhongshan Hospital were also included in the study.ResultsAfter grouping LUSC patients according to the expression levels of PD1 and PDL1, we found no significant difference in survival between the two groups. However, 178 genes, including IL-21, KLRC3, and KLRC4, were significantly upregulated in both the TCGA and GEO databases in the high expression group, and there was a precise correlation between gene expression and epigenetic changes in the two groups. At the same time, the overall level of somatic mutations was not significantly different between the two groups. It is worth noting that the gene enrichment results showed that the differential pathways were mainly enriched in immune regulation, especially T cell-related immune activities.ConclusionWe found that the differences in gene expression between the two groups were related to immunity, which may affect the effectiveness of immunotherapy. We hope our results can provide a reference for further research and help in finding other targets to improve the efficacy of immunotherapy.     

利什曼原虫感染树突状细胞早期基因表达差异分析及关键基因筛选

目的:分析利什曼原虫感染树突状细胞(DCs)早期的基因表达与信号通路变化,探究DCs感染后应答,寻找利什曼原虫感染后基于DCs的免疫治疗方法。方法:GEO数据库下载利什曼原虫感染前后DCs基因芯片数据,RStudio软件筛选差异表达基因(DEGs),STRING构建DEGs蛋白质相互作用网络(PPI),Cytoscape筛选差异表达蛋白质的核心模块,RStudio软件对DEGs进行GO和KEGG富集分析。结果:共筛选出DEGs 129个,其中IL12B与CXCL10差异最为显著,GO分析共富集23个过程,主要涉及病毒感染过程相关细胞反应及Ⅰ-IFN相关免疫反应;KEGG分析共富集3条信号通路,分别为甲型流感、麻疹及DNA复制信号通路。结论:利什曼原虫感染DCs前后Ⅰ-IFN信号通路和TLR4/NF-κB信号通路激活,影响IL12表达,提示Ⅰ-IFN/IL12信号通路与TLR4/NF-κB/IL12信号通路可作为利什曼原虫感染治疗的靶点,CXCL10也有望成为潜在的治疗靶点;利什曼原虫感染后,出现类似病毒感染现象,推测抗病毒免疫疗法可能在对抗利什曼原虫感染中具有一定疗效。     

基于网络药理学探讨趋化因子-13对间充质干细胞增殖和迁移的影响

目的 以网络药理学技术探讨趋化因子-13（CXCL-13）对人骨髓间充质干细胞（BMSCs）增殖和迁移的影响。 方法 在线数据库预测CXCL-13作用于BMSCs的靶点。Metascape数据库对靶点的基因本体论和京都基因与基因组百科全书(KEGG）信号通路进行富集分析。STRING 11.0数据库进行蛋白质相互作用分析,Cytoscape 3.8的cytoHubba 0.1插件筛选核心基因编码的蛋白质。BMSCs分为对照组、CXCL-13组和PI3K抑制剂组。分别以MTT、流式细胞术和Transwell细胞小室迁移实验检测各组BMSCs的吸光度（A）值、细胞凋亡率和细胞迁移数目情况;ELISA检测各组BMSCs上清液表皮生长因子(EGF)和血管内皮生长因子(VEGF)蛋白含量。Western blotting检测各组BMSCs的Akt、磷酸化Akt（p-Akt）蛋白的表达。 结果 CXCL-13作用于BMSCs 21个靶点。与细胞增殖相关的生物学过程包括干细胞增殖、调节内皮细胞增殖、正向调控平滑肌细胞增殖等32条;与细胞迁移相关的生物学过程包括调节细胞迁移、阿米巴状细胞迁移、调节内皮细胞迁移等22条。KEGG通路包括癌症途径、PI3K-Akt信号通路、MAPK信号通路等40条。核心蛋白包括肿瘤蛋白P53（TP53）、表皮生长因子受体（EGFR）、90kD热休克蛋白αB1（HSP90AB1）、蛋白激酶Cα（PRKCA）、雌激素受体2（ESR2）及前列腺素E受体4（PTGER4）。与其他组相比,CXCL-13组BMSCs的吸光度（A）值和细胞迁移数目均显著增高（P＜0.01,n=15）,细胞凋亡率明显降低（P＜0.01,n=15）;PI3K抑制剂组BMSCs的A值、细胞凋亡率和细胞迁移数目与CXCL-13组相比均呈相反变化（P＜0.01,n=15）。相对于对照组,CXCL-13组BMSCs的EGF和VEGF蛋白含量显著提高（P＜0.01,n=15）,Akt和p-Akt相对表达均明显升高（P＜0.01,n=9）;而PI3K抑制剂组EGF和VEGF蛋白含量、Akt和p-Akt相对表达呈相反变化。 结论 CXCL-13激活PI3K-Akt通路促进BMSCs旁分泌EGF和VEGF蛋白,提高BMSCs增殖和迁移,抑制BMSCs凋亡。     

日本血吸虫乳酸脱氢酶(SjLDH)结构与功能的生物信息学分析

目的 应用生物信息学分析软件预测日本血吸虫乳酸脱氢酶（SjLDH）氨基酸序列的结构与功能。 方法 应用NCBI、Expasy等在线生物信息学网站及Vector NTI、PCgene等软件包分析SjLDH与其他物种的同源序列，进行多序列同源比对，分析相同的保守位点及催化活性位点，构建分子进化树；预测二级结构、拓扑结构；同源模建预测三级结构；预测主要抗原表位等。 结果 SjLDH与其他物种的同源序列含相同的保守位点及催化活性位点，与华支睾吸虫LDH（CsLDH）同源性最高为75％，与阴道毛滴虫LDH（TvLDH）同源性最低为17%，与人LDH（HsLDH-A，-B，-C）的同源性为58%~60％； SjLDH与果蝇（DmLDH）的进化距离较秀丽隐杆线虫（CeLDH）为近，3种人LDH中与HsLDH-B、-C的进化距离较HsLDH-A为近；该蛋白具有3个跨膜区域，3个高亲水性区域，主要的线性表位98aa~106aa位于膜外，与原虫LDH相同区域差异显著，而与其他LDH有1~3个氨基酸的差异，关键催化位点之一及底物丙酮酸结合区域位于该区域，蛋白质同源模建分析表明该区域位于蛋白表面形成环状结构，3个关键催化位点位于该区域或在其附近。 结论 生物信息学预测结果提示LDH是研究物种分子进化理想的分子；SjLDH可能是免疫诊断、药物作用及疫苗潜在的靶分子。     

基于生物信息学筛选炎症相关结直肠癌基因及其特征分析

目的通过对炎症性肠病差异基因的筛选以及结直肠癌队列生存特征和表达模式的探究,为炎症相关结直肠癌的发生与发展的后续研究提供候选基因。 方法从GEO数据库中选择RNA测序表达谱数据集GSE95473和GSE107597,通过常规转录组表达谱差异分析,筛选出炎症性肠病差异表达基因（DEG）,利用GO数据库获取DEG的功能注释,并利用KEGG数据库进行通路富集分析。同时基于TCGA数据库进一步在结直肠癌数据集中筛选具有预后意义的基因,并评价其在结直肠肿瘤中的表达特征。 结果两个数据集筛选到了共有DEGs 100个,通过主成分分析证实这些基因能够对结直肠癌肿瘤和黏膜区分良好。进一步筛选,获得ALDOB,SPINK4,REG4,IL1B,C2CD4A,CXCL8,NOS2,CXCL3等候选基因。这些基因在结直肠肿瘤中高表达,并且这些基因的高表达往往提示患者预后较好。 结论ALDOB,SPINK4,REG4,IL1B,C2CD4A,CXCL8,NOS2,CXCL3可能在炎症相关结直肠癌的发生发展中发挥重要作用,有待于后续炎癌转化相关功能验证和机制探究。     

Non-alcoholic fatty liver disease and Atherosclerosis at a crossroad:The overlap of a theory of change and bioinformatics

Atherosclerosis(ATH) and non-alcoholic fatty liver disease(NAFLD) are medical conditions that straddle a communal epidemiology, underlying mechanism and a clinical syndrome that has protean manifestations, touching every organ in the body. These twin partners, ATH and NAFLD, are seemingly straightforward and relatively simple topics when considered alone, but their interdependence calls for more thought. The study of the mutual relationship of NAFLD and ATH should involve big data analytics approaches, given that they encompass a constellation of diseases and are related to several recognized risk factors and health determinants and calls to an explicit theory of change, to justify intervention. Research studies on the "association between aortic stiffness and liver steatosis in morbidly obese patients", published recently, sparsely hypothesize new mechanisms of disease, claiming the "long shadow of NAFLD"as a risk factor, if not as a causative factor of arterial stiffness and ATH. This statement is probably overreaching the argument and harmful for the scientific credence of this area of medicine. Despite the verification that NAFLD and cardiovascular disease are strongly interrelated, current evidence is that NAFLD may be a useful indicator for flagging early arteriosclerosis, and not a likely causative factor. Greater sustainable contribution by precision medicine tools, by validated bioinformatics approaches, is needed for substantiating conjectures,assumptions and inferences related to the management of big data and addressed to intervention for behavioral changes within an explicit theory of change.