现已认识到免疫反应、转录因子核因子κB( NF-κB) 的激活、细胞因子、中性粒细胞的激活和肺泡渗入、凝血级联反应、肾素-血管紧张素系统等多种因素构成的复杂网络参与急性肺损伤/急性呼吸窘迫综合征( ALI/ARDS) 的发病过程[ 1-5] 。虽然脓毒症、创伤、肺炎等ALI/ARDS诱发因素很常见, 但仅有部分病人发生ALI/ARDS, 并且具有相似临床特征的ALI/ARDS病人可有截然不同的结果, 这种异质性引起研究者对影响ALI/ARDS 易感性和预后的遗传因子进行鉴别的浓厚兴趣[ 6] 。由于数量庞大的表现型变异, 不完全的基因外显率、复杂的基因-环境相互作用及高度可能的基因座不均一性而使ALI 遗传学的研究受到挑战[ 7] 。近年来基因组学技术被应用于ALI/ARDS 发病机制的研究, 加深了人们对ALI/ARDS的认识并有可能发展出新的治疗策略以降低其发病率和病死率。
Objective To validate the different expressions of human fxyd6 gene between normal bile duct tissues and malignant tumor tissues, and to observe the subcellular localization of human fxyd6 gene in human cholangiocarcinoma cells. MethodsThe different expressions between normal bile duct tissues and malignant tumor tissues were identified by RT-PCR. In situ polymerase chain reaction （IS-RT-PCR） was applied to detect the subcellular localization of fxyd6 gene in paraffin sections of human cholangiocarcinoma cells. Image analysis software was used to semiquantitatively determine the difference between normal and malignant tissues. ResultsHuman fxyd6 gene was highly expressed in cholangiocarcinoma tissues and lowly expressed in normal ones. There was a significant difference between the expressions of carcinoma cells and normal cells （P＜0.05）. IS-RT-PCR showed that fxyd6 gene localized in the kytoplasma of epithelial cells of human cholangiocarcinoma. ConclusionHuman fxyd6 gene may act as an essential component of the malignant transformation process in human cholangiocarcinoma.
ObjectiveTo investigate the expression of Yes-associated protein (YAP) screened by bioinformatics in rats with myocardial-ischemia reperfusion injury and establish the base for further research. MethodsThe difference of gene spectrum of rats with myocardial-ischemia reperfusion injury was analyzed by bioinformatics technique. The related signaling pathways and key genes were screened by KOBAS2.0 and KEGG. Eighteen Sprague Dawley rats were randomly divided into three groups: normal group (n=6), sham operation group (n=6) and myocardial-ischemia reperfusion injury group (n=6). The expression of target gene was detected by immunochemistry, quantitive reverse transcription polymerase chain reaction and western blotting. ResultsA total of 345 differentially expressed genes were found by bioinformatics, among which 181 were up-regulated and 164 were down-regulated. The differential genes were mainly enriched in Wnt, HIPPO, MAPK, Jak-STAT and other signaling pathways. We focused on HIPPO pathway and found that the expression of YAP increased significantly in myocardial-ischemia reperfusion injury group, compared with the normal group and sham operation group (P＜0.05). ConclusionsThe expression of YAP of HIPPO signal pathway is increased in rats with myocardial-ischemia reperfusion injury.
ObjectiveTo investigate the molecular pathogenesis of pulmonary fibrosis induced by bleomycin in a murine model,and provide novel insights for clinical diagnosis and treatment. MethodsFrom Gene Expression Omnibus,we downloaded microarray data extracted from experiments of bleomycin induced pulmonary fibrosis in wild-type mice. With BRB-Array Tools,differentially expressed genes at different time points during disease development were screened,selected and analyzed by DAVID software. ResultsBRB array analysis identified 45101 differentially expressed genes. After induction by bleomycin on 7th day,1164 genes and 735 genes were significantly up-regulated and down-regulated (P<0.05,fold change>2),respectively. On 14th day,731 genes and 390 genes were significantly up-regulated and down-regulated (P<0.05,fold change>2),respectively. DAVID analysis revealed that the up-regulated genes were significantly enriched in cell cycle,p53 signaling and chemokine signaling pathway,damaging reaction and collagen metabolism gene sets. While the down-regulated genes were enriched in the drug metabolism pathway gene set. ConclusionsBioinformatics methodologies are able to efficiently analyze microarray data and extract its underlying information,provide novel insights for major molecular events and shift of cell signaling pathway during pulmonary fibrosis progression,and furthermore,finding molecular markers for early diagnosis and therapeutic targets.
ObjectiveTo analyze the expression profile changes of osteogenic-related genes during spontaneous calcification of rat bone marrow mesenchymal stem cells (BMSCs). MethodsBMSCs were isolated from 3-day-old healthy Sprague Dawley rats;cells at the 4th generation were used to establish the spontaneous calcification model in vitro. Spontaneous calcification process was recorded by inverted phase contrast microscope observation and alizarin red staining after 7 and 14 days of culture. For gene microarray analysis, cell samples were collected at 0, 7, and 14 days after culture; the differentially expressed genes were analyzed by bioinformatics methods and validated by real-time quantitative PCR (RT-qPCR) assay. ResultsRat BMSCs calcified spontaneously in vitro. When cultured for 7 days, the cells began to aggregate and were weakly positive for alizarin red staining. After 14 days of culture, obvious cellular aggregation and typical mineralized nodules were observed, the mineralized nodules were brightly positive for alizarin red staining. A total of 576 gene probe-sets expressed differentially during spontaneous calcification, corresponding 378 rat genes. Among them, 359 gene probe-sets expressed differentially between at 0 and 7 days, while only 13 gene probe-sets expressed differentially between at 7 and 14 days. The 378 differentially expressed genes were divided into 6 modes according to their expression profiles. Moreover, according to their biological functions, differentially expressed genes related to bone cell biology could be classified into 7 major groups:angiogenesis, apoptosis, bone-related genes, cell cycle, development, cell communication, and signal pathways related to osteogenic differentiation. In cell cycle group, 12 down-regulated genes were linked with each other functionally. Matrix metalloproteinase 13 (Mmp13), secreted phosphoprotein 1 (Spp1), Cxcl12, Mmp2, Mmp3, Apoe, and Itga7 had more functional connections with other genes. The results of genes Spp1, Mgp, Mmp13, Wnt inhibitory factor 1, Cxcl12, and cyclin A2 by RT-qPCR were consistent with that of gene microarray. ConclusionThe first 7 days after rat BMSCs were seeded are a key phase determining the fate of spontaneous calcification. Multiple genes related with cell communication, bone-related genes, cell cycle, transforming growth factor-β signaling pathway, mitogen-activated protein kinase signaling pathway, and Wnt signaling pathway are involved during spontaneous calcification.
Objective To investigate specific changes of T cell repertoire in convalescent patients infected by influenza A (H7N9) virus. Methods Peripheral blood samples from 8 convalescent patients infected by H7N9 virus and 10 healthy donors were collected. After extracting whole DNA from these samples, arm-PCR were performed and the products were submitted to Illumina HiSeq2000 platform to produce deep sequencing data of the nucleotide sequences of complementary determining region 3 of T cell receptor β chain (TRB). Differences were compared in TRB diversity and V-D-J gene usage and similarities of sequences between the patients and the healthy donors. Results Frequency of V-D-J gene usage was different between the H7N9 patient group and the healthy group, such as TRBV30, TRBV27, and TRBV18 (Student's t test, P < 05). Main component analysis showed V-J pairing pattern was significantly different between two groups, which may have potential in identifying patients from healthy people. A considerable number of shared CDR3s were found in patient-patient pairs and normal-normal pairs, while seldom were found in patient-normal pairs. The similarity between patients was also confirmed by overlap distance analysis. Indexes for assessing diversity of immune repertoires, Shannon-Weiner index and Simpson index, were both lower in the patients (Student's t test, P < 05), suggesting that the immune system of the patients had not recovered 6 months after H7N9 infection. Compared with the healthy donors, the number of hyper-expression clones increased in the patient group, and some of them showed similarity among patients. Conclusions TRB repertoires are less diverse in patients with increased hyper-expressed clones and identifiable V-J usage pattern, which is identifiable from normal population. These results suggest that there are H7N9-specific changes in TRB repertoires of H7N9 infected patients in convalescent phase, which have potential implication in diagnosis and therapeutic T cell development.
Objective To explore the expression of yes-associated protein 1 (YAP1), as a key protein of Hippo signal pathway, in rats with brain injury. Methods A total of 18 Sprague Dawley rats were randomly divided into three groups: normal group, sham operation group and brain injury group. The expression of YAP1 in rats with brain injury was detected by immunochemistry, quantitative polymerase chainreaction and Western blotting. Result Seventy-two hours after the brain injury, the expression level of YAP1 in protein and gene increased significantly in brain injury group, compared with those in the normal and sham operation group (P<0.05). Conclusion The expression of YAP1 increases in rats with brain injury, which maybe a new target for therapy.
Circular RNA are one kind of non-coding RNA, charactered by covalently closed rings. They can influence biological functions such as cell transduction and protein synthesis. They are associated with pathogenesis of many diseases and become a novel family of biomarkers. Now we try to introduce the origin, structure, function of circular RNA and the involved research methodology. Furthermore, we primarily discuss their application in the tuberculosis research.
ObjectiveTo conduct a bioinformatics analysis of gene expression profiles in frontal lobe of patients with Parkinson disease (PD), in order to explore the potential mechanism related to depression in PD.MethodsAll the bioinformatics data before March 20th 2019 were acquired from Gene Expression Omnibus (GEO) database, using " Parkinson disease” as the key word. The species was limited to human (Homo sapiens), and the detective method was limited to expression profiling by array. ImgGEO (Integrative Gene Expression Meta-Analysis from GEO database), DAVID (the Database for Annotation, Visualization and Integrated Discovery), STRING and Cytoscape 3.6.1 software were utilized for data analysis.ResultsTotally, 45 samples (24 PD cases and 21 healthy controls) were obtained from 2 datasets. We identified 236 differentially expressed genes (DEGs) in the post-mortem frontal lobe between PD cases and healthy controls, in which 146 genes were up-regulated and 90 genes were down-regulated. Based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis, the DEGs were mainly enriched in the structures of postsynaptic membrane, cell membrane component, postsynaptic membrane dense area, and myelin sheath, and were involved in the occurrence of PD, depression, and other diseases. These genes were involved in the biological processes of dopaminergic, glutamate-nergic, GABA-nergic synapses, and some other synapses, as well as several signaling pathways (e.g. mitogen- activated protein kinase signal pathway, p53 signal pathway, and Wnt signal pathway), which were associated with PD and depression pathogenesis. Besides, we found that NFKBIA, NRXN1, and RPL35A were the Hub proteins.ConclusionsGene expression in frontal lobe of patients with PD is associated with the pathogenesis of PD. This study provides a theoretical basis for understanding the mechanism of PD occurrence and progression, as well as the potential mechanism of depression in PD.
ObjectiveTo explore the pathogenesis of tuberculosis and provide new ideas for its early diagnosis and treatment.MethodsGSE54992 gene expression profile was obtained from the gene expression database. Differentially expressed genes (DEGs) were screened using National Center forBiotechnology Information platform, and GO enrichment analysis, pathway analysis, pathway network analysis, gene network analysis, and co-expression analysis were performed to analyze the DEGs.ResultsCompared with the control group, a total of 3 492 genes were differentially expressed in tuberculosis. Among them, 1 686 genes were up-regulated and 1 806 genes were down-regulated. DEGs mainly involved small molecule metabolic processes, signal transduction, immune response, inflammatory response, and innate immune response. Pathway analysis revealed chemokine signaling pathway, tuberculosis, NF-Kappa B signaling pathway, cytokine-cytokine receptor interaction, and so on; gene signal network analysis found that the core genes were AKT3, PLCB1, MAPK8, and NFKB1; co-expression network analysis speculated that the core genes were PYCARD, TNFSF13, PHPT1, COMT, and GSTK1.ConclusionsAKT3, PYCARD, IRG1, CD36 and other genes and their related biological processes may be important participants in the occurrence and development of tuberculosis. Bioinformatics can help us to comprehensively study the mechanism of disease occurrence, which can provide potential targets for the diagnosis and treatment of tuberculosis.