冠心病急性心肌梗死患者外周血差异基因表达分析及功能

目的探讨冠心病急性心肌梗死患者外周循环血单核细胞中差异基因表达及功能。方法收集2020年9月至2021年9月在昆明市第一人民医院接受冠脉造影的患者,提取外周血单核细胞总RNA,使用DNBSEQ平台进行第2代高通量测序。检测并筛选差异表达基因,进行KEGG及GO富集分析。结果冠心病急性心肌梗死组与冠脉正常组对比,其中差异基因89个,上调基因67个,下调基因22个;其中差异lncRNA14个,差异mRNA72个,差异circRNA3个。完成KEGG pathway富集分析、KEGG disease富集分析、KEGG molecular富集分析。完成GO cell composition富集分析、GO cell function富集分析、GO biological process molecular富集分析。结论筛选出显著差异的10个mRNA、6个lncRNA、2个circRNA。富集分析中涉及感染、转录失调、PI3K-Akt信号通路、脂类合成、吞噬泡腔、细胞外基质、脂多糖结合等,与冠状动脉粥样硬化的发生与发展及急性血栓事件的发生可能相关。

花生种皮抗黄曲霉差异基因表达初步分析(英文)

黄曲霉不同抗性花生种皮存在显著差异,本试验选择经鉴定的高抗黄曲霉花生种质J11与高感种质金花1012为研究材料,以金花1012为对照利用基因芯片技术开展了抗病差异基因表达分析研究。试验共使用61078杂交探针组,结果表明,共有417个差异基因表达量上升,650个差异基因表达量下降。另外,获得抗Phytophathora Sojae真菌病害表达量上升差异基因4个,表达量下降差异基因49个。获得抗Heterodera Glycines Ichinohe真菌病害表达量上升差异基因4个,表达量下降差异基因25个。

加权基因共表达网络分析和差异基因表达分析鉴定氯离子通道附件1基因对结肠癌预后保护作用

目的:结合应用加权基因共表达网络分析(WGCNA)和差异基因表达分析2种方法筛选结肠癌mRNA表达谱中的差异共表达基因,并分析差异共表达基因与预后的关系。方法:基于生物信息学方法从癌症基因组图谱(TCGA)和基因表达综合(GEO)数据库分别下载TCGA结肠腺癌数据集的转录组学数据和GSE68468数据集的芯片表达谱数据,筛选出两者在正常组织与结肠癌组织之间的差异表达基因(DEG)和最显著相关的加权基因模块,通过差异基因和加权基因取交集筛选出结肠癌相关差异共表达基因。构建蛋白质-蛋白质相互作用(PPI)网络,利用最大派系中心度(MCC)计算方法筛选出MCC评分排名前10位的核心差异共表达基因,使用TCGA结肠腺癌数据集验证核心基因在正常组织和结肠癌组织中的表达,采用Kaplan-Meier生存分析探索核心基因与患者总生存期和无病生存期之间的关系。使用人类蛋白质图谱(HPA)数据库,对生存相关的差异共表达基因进行免疫组织化学染色验证。结果:TCGA结肠腺癌数据集中DEG共3481个,GSE68468数据集中DEG共7275个,共获得237个差异共表达基因。使用PPI网络的MCC计算方法得到10个核心的差异共表达基因,分别为氯离子通道附件1(CLCA1)、MAPK3、胰高血糖素(GCG)、溶质载体家族26成员3(SLC26 A3)、核受体亚家族1组H成员4(NR1 H4)、脂肪酸结合蛋白1(FABP1)、鸟苷酸环化酶激活因子2A(GUCA2 A)、二磷酸尿苷葡糖醛酸糖基转移酶家族2成员A3(UGT2 A3)、肉碱棕榈酰转移酶2(CPT2)和跨膜4域A12(MS4 A12)。与正常组织相比,TCGA结肠腺癌数据集结肠癌组织的CLCA1、GCG、SLC26 A3、NR1 H4、FABP1、GUCA2 A、UGT2 A3、CPT2和MS4 A129个核心基因均下调(P均<0.05),其中CLCA1高表达结肠癌患者的总生存期和无病生存期均长于低表达组(P均<0.05),免疫组织化学染色结果在蛋白质水平也验证了结果的准确性。结论:CLCA1可能在结肠癌的发展中起关键作用,可作为进一步诊断和治疗的潜在生物标志物。

对参与肺腺癌发生的核心基因的综合生信分析

目的:侵袭性的肺腺癌(LUAD)是引起肺癌死亡的主要原因之一。因此,鉴定重要的LUAD相关基因及进一步分析其预后意义对于LUAD患者的生存率至关重要。方法:采用加权基因共表达网络分析(WGCNA)和差异基因表达分析方法,从TCGA-LUAD数据库和GEO的GSE32863筛选出有差异的共表达基因,对其进行功能富集分析和蛋白质相互作用网络(PPI)分析。此外,通过应用Cytoscape的CytoHubba插件来识别12个核心基因进行生存分析和肿瘤分期相关性的分析。结果:从TCGA和GEO数据库中共提取了358个差异共表达基因。这些基因在GO分析中主要富集于细胞外结构组织,细胞–细胞连接和DNA结合转录酶激活活性。在KEGG分析中,主要富集于药物代谢–细胞色素P450。此外,在PPI网络中鉴定了12个核心基因。在LUAD患者中,ADCY4、VIPR1和TGFBR2的表达水平与临床分期和整体生存率(OS)相对应。结论:ADCY4、VIPR1和TGFBR2可能在肿瘤发生中起重要作用,因此它们可作为LUAD的预后生物标志物和治疗靶点。

药用植物冬凌草高通量转录组测序与分析

目的:得到冬凌草高通量转录组数据,为挖掘冬凌草二萜类生物合成途径关键基因,研究冬凌草ESTSSR分子标记提供数据来源。方法:利用Illumina Hi Seq 4000高通量测序技术,采用Trinity的方法从头组装、序列拼接和去冗余处理;基于BLAST完成Unigene编码蛋白NR功能注释、GO分类、KEGG代谢通路注释和分类、功能基因挖掘,SSR分子标记挖掘。结果:获得冬凌草叶与茎两种不同组织共12 GB转录组数据,得到3 7961个Unigene基因,平均长度1063 bp;得到冬凌草叶和茎转录组有60条unigenes参与萜类化合物骨架合成、6条unigene参与各种萜类化合物合成,有26条unigene参与二萜化合物合成途径,叶与茎两种组织中有差异表达的基因4565个,其中在茎中表达较高的为1668个,在叶中表达较高的有2697个,与二萜类化合物合成相关的差异表达基因有15个。结论:本研究为冬凌草二萜化合物生物合成途径中关键基因的挖掘和分子育种提供了数据信息,为深入研究冬凌草中冬凌草甲素等有效成分的生物合成途径及其调控机制提供基础。

过表达LXRα和RXRA对HepG2全基因组转录的影响

LXRα(Liver Xreceptorα)是一种氧甾醇核受体在免疫和脂类代谢等生物过程中发挥重要作用,为了进一步探究LXRα的生物学功能,本研究对LXRα和RXRA共同过表达的HepG2细胞进行了全基因组转录分析。在HepG2细胞中LXRα和RXRA共同过表达导致451个基因发生差异表达(p<0.05)其中有213个基因表达上调,221个基因表达下调,通过GO(Gene ontology)功能和KEGG(Kyoto encyclopedia of genes and genomics)通路基因富集分析发现这些基因参与调控化合物代谢、转录和免疫防御等生物过程。此外还发现在HepG2细胞中,LXRα和RXRA过表达也导致细胞死亡和凋亡相关基因的部分沉默或激活,证明LXRα也参与调控细胞死亡和凋亡。本研究首次在HepG2细胞中通过同时过表达LXRα和RXRA分析LXRα的靶基因及其所参与的生物过程和信号通路,为后续LXRα的功能发掘和相关疾病的药物开发和治疗提供了理论依据。

Cloning and Differential Expression Analysis of FaGF14-B and FaGF14-C Genes in Tall Fescue

[Objective] The differential expression analysis was performed for FaGF14- B and FaGF14-C genes in tall fescue so as to provide certain basis for follow-up functional analysis of genes. [Method] The sequence fragments of FaGF14-B and FaGF14-C obtained from reverse transcription were used as templates, and the full- length cDNA sequences of FaGF14-B and FaGF14-C were amplified using the 5＇ RACE use 3＇RACE techniques. They were named as FaGF14-B and FaGF14-C, and used for nucleic acid sequence analysis, encoded protein analysis, protein con- served domain analysis, phylogenetic analysis and differential expression analysis. [Result] The FaGF14-B gene has a full length of 1 548 bp. It has a complete open reading frame （ORF, 449-1 228 bp）, and encodes a protein composed of 261 amino acids. The FaGF14-C gene has a full length of 1 250 bp. It also has a complete open reading frame （ORF, 66-848 bp）, and encodes a protein composed of 261 amino acids. The GF14-B and GF14-C proteins all have a typical domain 14-3-3, and their secondary structures all contain 9 conserved co-helical structures and non-conserved N- and C- terminals. The phylogenetic analysis showed that the FaGF14-B and FaGF14-C from tall rescue have high similarities with GF14 protein from gramineous plants, and they are divided into the same clade with closer ge- netic relationship. The real-time fluorescence quantitative PCR analysis showed that the expression of FaGF14-B and FaGF14-C genes is all sensitive to nitrogen stress. [Conclusion] This study will lay a theoretical basis for further screening of low nitrogen-tolerant genes and breeding of low nitrogen-tolerant grass germplasms.

Cluster Analysis of Differentially Expressed Heat Stress Genes in Rat Jejunal Mucosal

[Objective] The aim was to study the heat stress mechanism of differen tially expressed genes in rat jejunal mucosal.[Method] Variable cluster analysis and cluster analysis of samples on the differentially expressed heat stress genes in rat jejunal mucosal were carried out with SAS software,and statistics of distribution of the differentially expressed genes on chromosomes were conducted.[Result] The differentially expressed genes were divided into seven categories,of which,the upregulated genes included three categories （i.e.：Category A：Hspa1a,Hspa1b,Hspb1,Hsph1,Dnaja4,Ahsa2 and P4ha1; Category B：Cyp1a2,Zbtb16,Gucy2g,Fgb,Cyp4a3 and Etv2; and Category C：Cyp1a2,Chac1 and Cyp4b1） and the down-regulated genes included four categories （i.e.：Category D：Tlr2,Noxo1,LOC286989 and Aspg; Category E：RGD1560395,Alb and BQ194726; Category F：Ccl4,Gzmk,Al228153,Anxa10,S100a9 and Ascl5; and Category G：Reg1a and Slc13a1）.The classification,function and reasons of differential expression for each gene category were analyzed.[Conclusion] Most of the three categories of up-regulated genes were related to the heat shock proteins; and most of the four categories of down-regulated genes were related to the immunity,providing reference for discussion of the heat stress mechanism.

Probiotic Lactobacillus rhamnosus downregulates FCER1 and HRH4 expression in human mast cells

AIM:To investigate the effects of four probiotic bacteria and their combination on human mast cell gene expression using microarray analysis.METHODS:Human peripheral-blood-derived mast cells were stimulated with Lactobacillus rhamnosus (L.rhamnosus) GG (LGG),L.rhamnosus Lc705 (Lc705),Propionibacterium freudenreichii ssp.shermanii JS (PJS) and Bifidobacterium animalis ssp.lactis Bb12 (Bb12) and their combination for 3 or 24 h,and were subjected to global microarray analysis using an Affymetrix GeneChip Human Genome U133 Plus 2.0 Array.The gene expression differences between unstimulated and bacteria-stimulated samples were further analyzed with GOrilla Gene Enrichment Analysis and Visualization Tool and MeV Multiexperiment Viewer-tool.RESULTS:LGG and Lc705 were observed to suppress genes that encoded allergy-related high-affinity IgE receptor subunits α and γ (FCER1A and FCER1G,respectively) and histamine H4 receptor.LGG,Lc705 and the combination of four probiotics had the strongest effect on the expression of genes involved in mast cell immune system regulation,and on several genes that encoded proteins with a pro-inflammatory impact,such as interleukin (IL)-8 and tumour necrosis factor alpha.Also genes that encoded proteins with anti-inflammatory functions,such as IL-10,were upregulated.CONCLUSION:Certain probiotic bacteria might diminish mast cell allergy-related activation by downregulation of the expression of high-affinity IgE and histamine receptor genes,and by inducing a pro-inflammatory response.

Identification of differential gene expressions in colorectal cancer and polyp by cDNA microarray

AIM： TO screen the differential expressed genes in colorectal cancer and polyp tissue samples. METHODS： Tissue specimens containing 16 cases of colorectal adenocarcinoma and colorectal polyp vs nor- mal mucosae were collected and subjected to cDNA microarray and bioinformatical analyses. Quantitative reverse transcription-polymerase chain reaction （qRT- PCR） was used to confirm some of the cDNA microarray data.RESULTS： The experimental data showed that eight genes were differentially expressed, most of which were upregulated in adenomatous polyp lesions. Forty-six genes expressions were altered in colorectal cancers, of which 29 were upregulated and 17 downregulated, as compared to the normal mucosae. In addition, 18 genes were similarly altered in both adenomatous polyps and colorectal cancer, qRT-PCR analyses confirmed the cDNA microarray data for four of those 18 genes： MTA1, PDCD4, TSC1 and PDGFRA. CONCLUSION： These differentially expressed genes likely represent biomarkers for early detection of co- Iorectal cancer and may be potential therapeutic targets after confirmed by further studies.

Establishment of an arsenic-resistant human gallbladder carcinoma cell line and analysis of the differential expressions of genes associated with apoptosis

Objective： The aim of the study was to establish an arsenic trioxide （ATO）-resistant cell line of human gallbladder carcinoma, GBC-SD/ATO, and to analyze the differential expressions of its apoptosis-associated genes, so as to investigate a correlation between ATO induced resistance of gallbladder carcinoma and expressions of apoptosis associated genes. Methods： The resistant cell line was obtained in vitro by culture of human gallbladder carcinoma cell line GBC-SD with increasingly stepwise concentrations of ATO. The sensitivities of GBC-SD cells and GBC-SD/ATO cells to ATO were determined by MTT assay respectively, cDNA microarray containing 458 apoptosis-related human genes was used to compare the gene expression profiles of GBC-SD/ATO cells and corresponding sensitive cell line GBC-SD. Results： GBC-SD/ATO cell line was established successfully after 8 months of exposure to increasing concentrations of ATO. Compared with the parental cell line, GBC-SD/ATO was 13.6 times more resistant to ATO. Of the 458 apoptosis-related genes, 17 genes were detected having 〉 2-fold difference of expression between the GBC-SD/ATO and GBC-SD cells, with 6 genes up-regulated and 11 genes down-regulated in GBC-SD/ATO cells. Conclusion： The 17 genes invoJved in the apoptosis pathway might be relevant to the resistance of GBC-SD/ATO cells to ATO, suggesting that the modulation of expression of apoptosis-related genes may be a main mechanism of acquired resistance in GBC-SD/ATO.

Gene-Ontology Analysis on the Differentially Expressed Genes in Maize （Zea mays L.） Ear Rot

To better know FM （Fusarium moniliforme） induced genes in maize ear rot, GO （gene ontology） method was performed to analyze detail physiological functions in the defensive response after pathogen infection. This gene annotation system was widely used to investigate large numbers of genes involving in real active role or regulator in cell response. First of all, differentially expressed genes were isolated by using genechip platform at 96 h post-inoculation with FM in maize inbred Bt-1. In total, 482 differentially expressed unique genes were screened out in inbred Bt-1 when compared to mock-inoculated bract tissues. Then, each gene was annotated to define functional class by GO method. Finally, these large FM-responsive genes with significant differentially change were sorted into cellular component, molecular function and biological process with complicated network by molecular annotation system. The demonstrated information in the GO analysis could provide another view for understanding the molecular mechanism and indicate a deeply complicated network with gene function underlying disease development in the host tissue. The findings in this study provide important bases to probe the molecular processes, the alteration of metabolism and the immune mechanism upon the FM infection in maize.

Analysis of differentially expressed tumor-related genes in Peutz-Jeghers syndrome combined with colorectal carcinoma with cDNA microarrays

Objective:The aim of the study was to screen the differentially expressed genes of Peutz-Jeghers syndrome (PJS) and colorectal carcinoma (CRC).Methods:This study used cDNA microarray to comparatively analyze the gene expression profiles of 4 cases of PJS combined with colorectal adenocarcinoma vs.normal mucosae.The cDNA microarray contained 8064 human genes,and then using RT-PCR to test three genes of all.Results:The experimental data showed that fourteen genes were differentially expressed,which were up-regulated in PJS.Fifty-one genes expressions were altered in CRCs,of which 32 were up-regulated,as compared to the normal mucosae.In addition,5 genes were similarly altered in both PJS and CRCs.RT-PCR analyses confirmed the cDNA microarray data for three of those genes:LATS2,APC and MADH4.Conclusion:LCN2,USP4,GRO3,HYAL1 and APC-these differentially expressed genes likely represent biomarkers for early detection of CRC and may be potential therapeutic targets.

Identification of key genes and related pathways in hepatocarcinoma usingbioinformatics analysis

Objective Various treatments have greatly reduced the mortality of hepatocellular carcinoma （HCC）. However, few therapies could be performed in advanced HCC. Therefore, understanding the characteristics of HCC at the level of the whole transcriptome can help prevent the progression of HCC. Methods： The aim of this study was to identify differently expressed genes and potent pathways between normal liver and HCC tissues. The gene expression profiles of GSE104627 were downloaded from Gene Expression Omnibus database. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed and protein-protein interaction network of the differentially expressed genes were constructed by Cytoscape software. Results： In total, 880 differently expressed genes were identified between normal and tumor tissues, including 554 up-regulated genes and 326 down-regulated genes. Gene Ontology analysis results showed that the up-regulated genes were significantly enriched in establishment of RNA localization, nucleic acid transport, RNA transport, RNA localization and nucleobase, nucleoside, nucleotide and nucleic acid transport. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed the up-regulated genes were enriched in axon guidance, dorso-ventral axis formation and pathways in cancer. The top 10 hub genes were identified from the protein - protein interaction network, and sub-networks revealed these genes were involved in significant pathways, including G protein-coupled receptors signaling pathway, signaling pathway via MAPK and extracellular matrix organization. Conclusion： The present study described the differently expressed genes between normal tissues and HCC tissues from the level of gene transcription. The possible signaling pathways involved in the development of HCC and related molecules involved were analyzed. However, further laboratory and clinical validation is still needed.