Effects of left ventricular assist device on heart failure patients: A bioinformatics analysis

With the acceleration of demographic aging, heart failure has become a global public health issue. Left ventricular assist device (LVAD) provides a therapeutic option serving as a bridge to transplantation or destination treatment for end-stage heart failure. However, neither the molecular mechanism nor the gene expression profile of LVAD pathophysiology is well understood. Microarray dataset ( GSE21610 ) was retrieved from the online database of the gene expression omnibus (GEO). Differentially expressed genes (DEGs) between microarrays obtained before and after LVAD therapy were analyzed using GEO2R. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis were carried out, followed by protein–protein interaction (PPI) network construction, which was further visualized by the Cytoscape software. Finally, a target gene-microRNA (miRNA) network was built using the NetworkAnalyst to predict potential miRNA interactions. A total of 36 upregulated DEGs and 14 downregulated DEGs were screened out. Five hub genes with the highest degree of connectivity were identified, including CCL2, CX3CR1, CD163, TLR7, and SERPINE1. CCL2 was identified as the most outstanding hub gene which is specially regulated by miR-124, miR-141, and miR-495. Our study indicates that CCL2 is crucial to the LVAD pathophysiology. The identified hub genes may be involved in cardiac inflammatory responses, remodeling, and the chemokine signaling pathway. These DEGs, pathways, hub genes, miRNAs are valuable for further investigations. This study provides a better understanding of the gene expression profile in LVAD pathophysiology.     

淡色库蚊抗溴氰菊酯品系CYP4E2r6基因的克隆与生物信息学分析

目的 从淡色库蚊抗溴氰菊酯品系Ⅳ龄幼虫扩增并分析CYP4E2r6基因，为蚊虫抗药性的研究、检测和防治筛选靶标。方法 根据已扩增的CYP4E2r6基因片段（长470bp，GenBank登录号为CB074945）的序列设计2条特异引物，从淡色库蚊抗溴氰菊酯品系Ⅳ龄幼虫提取RNA，反转录成cDNA，以cDNA为模板，用5’-RACE和3＇-RACE方法，各获得722bp、617bp片段。进行序列拼接并对所得新基因进行登录和生物信息学分析。结果获得了1条3’端含polyA尾，长1025bp的CYP4E2r6基因大片段（GenBank登录号为AY309972），编码289个氨基酸，与果蝇细胞色素P450氨基酸的同源性为55％。编码蛋白的理论分子质量单位为32．9ku，等电点为5．8。结论 获得了CYP4E2r6基因大片段，为进一步获取全长基因并研究该基因的功能奠定了基础。     

头颈部鳞癌程序性死亡配体-1的共表达基因及 调控网络的生物信息学分析

目的 运用生物信息学的方法绘制头颈部鳞癌（HNSCC）中程序性死亡配体-1（PD-L1）共表达基因关系网络,筛选潜在的PD-L1的协同标志物,寻找可能的PD-L1基因调控肿瘤免疫状态的基因和通路。方法 利用癌症和肿瘤基因图谱（TCGA）中的大样本HNSCC的转录组学数据,在cBioPortal数据平台进行基因集的检索,筛选PD-L1共表达基因,在R语言的clusterProfiler中进行GO-BP和KEGG富集分析,再进行分子关系网络分析,提取重要节点基因（hub基因）,再进行生存分析。结果 筛选出共表达基因117个,共表达基因主要富集在免疫调节和病毒反应过程。网络节度分析得到了10个hub基因,依次为STAT1、IFNG、CXCL10、CCR5、FCGR3A、CXCL9、GBP5、CD86、GZMB、IRF1。生存分析显示：CCR5、CXCL9、GZMB是HNSCC预后相关的重要基因。这些基因均参与了免疫过程,其表达与PD-L1相关（Pearson相关系数为0.30、0.35、0.39,P值均小于0.01）。这些基因高表达在HNSCC中均为保护因素。结论 HNSCC中的PD-L1共表达的主要基因均为免疫相关基因,其中CCR5、CXCL9、GZMB与PD-L1存在共表达关系,与预后相关,其可能与程序性死亡受体-1（PD-1）/PD-L1介导的肿瘤免疫逃避相关,为进一步研究PD-1/PD-L1的作用机制和精准靶向治疗提供了新的参考。     

基于系统药理学探讨草乌改善Ⅱ型糖尿病的分子机制

目的 基于系统药理学、生物信息学、分子对接及体内外实验探讨草乌影响 2 型糖尿病(diabetes mellitus type 2, T2DM)的潜力及对 T2DM 相关症状的潜在机制。方法 利用数据库检索草乌相关化学成分、预测潜在作用靶点以及干预 相关疾病;GEO 数据库检索 T2DM 相对健康人的差异基因,与草乌作用靶点映射后置于 DAVIDavid 数据库进行生物功能 富集,利用单因素方差分析、二元 Logistic 回归分析及 ROC 曲线分析目标基因对于 T2DM 的敏感性。借助分子对接技术 分析草乌化学成分与靶蛋白的结合位置及相互作用力。通过体内外 T2DM 模型验证草乌及其化学成分对目标蛋白表达的 影响。 结果 通过数据库检索与分析得到草乌干预靶点相关疾病 44 种(P value<0.05,FDR<0.05),选取度值最高的 T2DM(Degree=22)进行分析。T2DM 相对健康人差异基因与草乌潜在作用靶点取交集得到 43 个目标基因,进行单因素方 差分析得到有显著性差异的基因共 9 个,二元 Logistic 回归分析得到 5 个有意义基因,ROC 曲线下面积 AUC>0.5 的基因 共 3 个。分子对接得到草乌化学成分(+)-Isoboldine 与蛋白 APEX1、CASP1、CBFB,Napelline 与蛋白 CBX1、EHMT2 结 合通过氢键相互作用、疏水相互作用、可电离性和静电相互作用等不同作用力结合,从而增加配体靶向作用蛋白的能力。 体内模型经草乌水提物治疗 2 周后,草乌可能通过改善周围神经病变进而缓解 T2DM 症状。并且草乌可以影响大鼠肝组织 中 APEX1、CASP1、CBFB、CBX1、EHMT2 的蛋白表达,草乌中(+)-Isoboldine 和 Napelline 化学成分对体外模型的目标蛋 白的影响与体内实验一致。结论 初步揭示草乌可作为改善 T2DM 周围神经病变的潜在治疗药物,为中蒙药研发以及挖掘 治疗 T2DM 新靶标药物奠定理论基础。     

Investigation of microRNA expression signatures in HCC via microRNA Gene Chip and bioinformatics analysis

BackgroundDysregulation of miRNAs is closely involved with hepatocellular carcinoma (HCC) progression, oncogenesis and signalling pathways. The aim of this study was to investigate differences in expression of miRNAs in HCC tissue in comparison to healthy liver tissue, as well as to explore the key miRNA-targeted genes.MethodsGene Chip microarray analysis was used to analyse differentially expressed miRNAs (DEMs) in tissues, and qRT-PCR was performed to validate the top 9 downregulated miRNAs. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed for target genes using the DAVID database. A protein-protein interaction (PPI) network of the target genes was created by STRING and visualised using Cytoscape. Three online miRNA databases were utilised to aid in the prediction of genes targeted by the top 10 significantly altered DEMs.ResultsIn total, 153 upregulated and 206 downregulated miRNAs were identified in HCC tissue. The genes targeted by the top 10 increased and decreased miRNAs were 6 and 1060, respectively. Moreover, FOXO1 was projected to be regulated by all twenty miRNAs. A PPI network was constructed that consisted of 956 nodes and 1298 edges. Four significant modules, consisting of 66 hub genes, were detected from the PPI system via MCODE. Functional enrichment demonstrated that miRNAs have a vital function in cancer development and advancement.ConclusionIn summary, our study identified DEMs in HCC tissue, major target genes and possible molecular mechanisms that underlie HCC, providing novel insights for treatment approaches.     

Differential expression profile of long noncoding RNAs in chronic HBV infection: New insights into pathogenesis

Increasing studies have revealed that long noncoding RNAs (lncRNAs) might play vital roles in the development and progression of various diseases including viral infectious diseases. However, the expression and biological functions of lncRNAs in chronic hepatitis B virus (HBV) infection remain largely unknown. Therefore, lncRNA microarray was performed to analyze the lncRNAs' and messenger RNAs' (mRNAs) expression profiles in liver tissues from patients with chronic HBV infection. Subsequently, a comprehensive bioinformatics analysis was conducted to investigate the potential functions of the differentially expressed genes. As a result, a total of 203 differentially expressed lncRNAs and 180 mRNAs were identified in chronic HBV infection. The expressions of five differentially expressed lncRNAs were further validated using quantitative real-time polymerase chain reaction. Gene ontology, pathway analysis, and gene set enrichment analysis revealed that differentially expressed lncRNAs might be mainly be involved in cytokine-cytokine receptor interaction and varied biotransformation processes, including fatty acid metabolism, amino acid metabolism, carbon metabolism, and drug metabolism. Additionally, coexpression networks between differentially expressed lncRNAs and mRNAs were constructed to reveal the hub regulator and analyze the functional pathways. This study provided an overview of lncRNA and mRNA expression in liver tissues from patients with chronic HBV infection. These differentially expressed lncRNAs might play crucial roles in the pathogenesis and progression of chronic HBV infection, which deserve further investigation.     

miR-150-5p抑制TLR-5/NF-κB p65信号通路对大脑中动脉阻塞模型大鼠的神经保护效应

文题释义： 缺血性脑梗死：临床常见的一种中枢神经系统疾病,是由于脑组织局部供血动脉血流的减少或停止,造成脑组织缺血、缺氧导致脑组织坏死,具有较高的死亡率和致残率,严重威胁人类的健康和生存质量。 微小RNA：是一类长度为18-25 nt的非编码单链小分子RNA,广泛存在于从病毒到人类的各种生物中,能够与mRNA互补结合调控蛋白编码基因的表达,与细胞的生物学行为密切相关。 背景：缺血性脑梗死的病变组织中发生炎症反应,且miR-150-5p表达明显下降,miR-150-5p是否经Toll样受体5/核因子κB途径抑制炎症因子释放并减轻缺血性脑梗死组织损伤尚不清楚。 目的：探讨微小RNA-150-5p(miR-150-5p)在大鼠缺血性脑梗死中的作用及初步机制。 方法：①构建大脑中动脉阻塞模型大鼠,建模后将大鼠分为5组：对照组、miR-150-5p agomir 组、agomir control、miR-150-5p antagomir组和antagomir control组;②对照组大鼠给予生理盐水脑室注射,后4组大鼠脑室分别给予miR150-5p agomir(miR150-5p激动剂)、agomir阴性对照、miR150-5p antagomir (miR150-5p抑制剂)和antagomir阴性对照;③干预7 d后进行神经功能缺损程度(mNNS)评分,磁共振检测法测量脑梗死体积,苏木精-伊红染色观察脑组织病理学变化,qRT-qPCR法、ELISA法和免疫印迹法检测分别检测脑组织中miR-150-5p、白细胞介素6、肿瘤坏死因子α、Toll样受体5和核因子κB p65表达情况,通过检索生物信息学网站Targetscan预测miR-150-5p与Toll样受体5的结合位点,荧光素酶试验验证二者的靶向关系。 结果与结论：①与对照组比较,miR-150-5p agomir组大鼠神经功能损伤评分、脑组织中白细胞介素6、肿瘤坏死因子α水平及Toll样受体5、核因子κB p65蛋白表达明显降低(P < 0.05);miR-150-5p antagomir组生理评分及生化指标均明显升高(P < 0.05);②苏木精-伊红染色显示,对照组神经细胞排列紊乱、轮廓模糊不清,神经细胞明显变性坏死;上述病理变化在miR-150-5p agomir组明显减轻,而在miR-150-5p antagomir组中明显加重。而agomir control 组和antagomir control组与对照组各指标比较差异均无显著差异(P > 0.05);③TargerScan网站预测结果和荧光素酶报告基因分析显示,miR-150-5p与Toll样受体5存在靶向结合位点;④结果证实,miR-150-5p可抑制缺血所致脑损伤过程中Toll样受体5/核因子κB p65炎性信号通路,降低炎性反应,从而减轻神经功能损害,发挥保护作用。 ORCID: 0000-0003-4635-0842(谢媛媛) 中国组织工程研究杂志出版内容重点：组织构建;骨细胞;软骨细胞;细胞培养;成纤维细胞;血管内皮细胞;骨质疏松;组织工程     

The molecular mechanism for effects of TiN coating on NiTi alloy on endothelial cell function

The aim of this study is to systematically investigate the molecular mechanism of different effects of nickel titanium (NiTi) alloy surface and titanium nitride (TiN) coating on endothelial cell function. Release of nickel (Ni) ion from bare and TiN-coated NiTi alloys and proliferation of endothelial cells on the two materials were evaluated, and then influence of the two materials on cellular protein expression profiles was investigated by proteomic technology. Subsequently, proteomic data were analyzed with bioinformatics analyses and further validated using a series of biological experiments. Results showed that although the two materials did not affect cell proliferation, the Ni ions released from bare NiTi alloy generated inhibition on pathways associated with actin cytoskeleton, focal adhesion, energy metabolism, inflammation, and amino acid metabolism. In comparison, TiN coating not only effectively prevented release of Ni ions from NiTi alloy, but also promoted actin cytoskeleton and focal adhesion formation, increased energy metabolism, enhanced regulation of inflammation, and promoted amino acid metabolism. Furthermore, the two processes, “the initial mediation of adsorbed serum protein layer to endothelial cell adhesion and growth on the two materials” from our previous study, and “the following action of the two materials on cellular protein expression profile”, were linked up and comprehensively analyzed. It was found that in stage of cell adhesion (within 4 h), release of Ni ions from bare NiTi alloy was very low, and the activation of adsorbed proteins to cell adhesion and growth related biological pathways (such as regulation of actin cytoskeleton, and focal adhesion pathways) was almost as same as TiN-coated NiTi alloy. This indicated that the released Ni ions did not affect the mediation of adsorbed proteins to endothelial cell adhesion. However, in stage of cell growth and proliferation, the release of Ni ions from bare NiTi alloy increased with time and reached a higher level, which inhibited endothelial cell function at molecular level, whereas TiN coating improved endothelial cell function.