Affymetrix基因表达谱芯片在新疆维吾尔族与汉族胰腺癌组织样本间差异表达基因筛选中的运用

目的:运用基因表达谱芯片筛选并分析新疆维吾尔族与汉族胰腺癌组织样本间的差异表达基因。方法:收集我院2014年1月至2016年6月间行手术切除的维吾尔族与汉族胰腺导管细胞癌组织并提取总RNA,选取经Nanodrop 2000与Agilent 2100仪器质检合格的样本总RNA采用Affymetrix基因表达谱芯片筛选出差异表达基因并绘制统计图,运用基因本体(GO)分析及信号通路(Pathway)分析对这些差异表达基因的生物信息进行汇总分析。结果:通过基因表达谱芯片分析,新疆维吾尔族与汉族胰腺癌组织样本间共检测到1063个基因存在差异表达,在维吾尔族胰腺癌标本中显著上调表达的基因共281个,差异表达倍数最高的为IGLV1-44基因(差异倍数:9.99)下调表达的基因共782个,差异表达倍数最高的为CPB1基因(差异倍数:33.76);在Gene Ontology数据库中共检索到815个上述差异表达基因具有明确的GO分类,差异表达倍数最高的为CPB1基因(差异倍数:33.76);Pathway分析中共检测到30条信号通路包含有上述差异表达基因,共涉及196个基因,其中以FAK信号通路差异表达基因富集程度最高,差异表达倍数最高的基因为COL11A1基因(差异倍数:5.02)。结论:基因表达谱芯片分析结果显示,在新疆维吾尔族与汉族胰腺癌组织样本间存在大量的差异表达基因,这些基因与胰腺癌的增殖分化、侵袭转移及多药耐药等特性密切相关,且参与了多条生物体内重要信号转导通路的调控。     

Microarray gene expression analysis of Monochamus alternatus (Coleoptera: Cerambycidae) after treatment with a sublethal dose of chloramine phosphorus

Monochamus alternatus Hope (Coleoptera: cerambycidae), the Japanese pine sawyer beetle, is a serious pest management concern in pine stands. A new organophosphorus insecticide, chloramine phosphorus (CP), has been applied as an insecticide in China to control M. alternatus. In this study, we investigated gene expression changes in M. alternatus after 4 h of exposure to CP using a 60-mer oligonucleotide microarray. The results showed that 356 genes were differentially expressed, of which 76 were upregulated and 280 were downregulated. GO enrichment analysis of the differentially expressed genes indicated that those involved in structural molecule activity and transporter activity were among the most highly represented. Within the cellular component category of GO, cell and cell part were the most represented GO terms in upregulated genes. “Cellular process” was the most represented GO term in the biological process category among the downregulated genes. Molecular pathway analysis showed that a large portion of the differentially expressed genes were associated with metabolic pathways. This study sought to identify new biomarkers as nonacetylcholinesterase targets to assess the secondary effects of CP on M. alternatus and will provide a valuable resource for the scientific community to study the molecular toxicology of CP.     

牛痘病毒感染人巨噬细胞基因表达谱的RNA-Seq分析

[目的]利用RNA-Seq,分析人巨噬细胞在牛痘病毒(VACV)感染前后基因表达的变化,探索牛痘病毒与宿主细胞相互作用的机制.[方法]用牛痘病毒感染人巨噬细胞,采用RNA-Seq比较感染组和对照组的差异表达基因,并进行KEGG、GO以及STRING网络分析.[结果]感染组与对照组相比,筛选出显著性差异表达基因4796个...     

Differences in potential key genes and pathways between primary and radiation-associated angiosarcoma of the breast

BackgroundAngiosarcoma of the breast is a high-grade malignant soft tissue tumor, it can be divided into primary and radiation-associated angiosarcoma(secondary). However, the differences between primary and secondary angiosarcomas in terms of pathogenesis, clinical behavior, early diagnosis biomarkers, genetic abnormalities, and therapeutic targets remain to be fully elucidated. At the same time, due to its rarity, most of current information relating to angiosarcoma is provided by case reports. Therefore, exploring the mechanisms of primary and secondary breast angiosarcoma have important value for the discovery of new biomarkers and research into potential therapeutic targets.MethodsThe differentially expressed genes (DEGs) between 36 cases of primary angiosarcoma and 54 cases of secondary angiosarcoma were screened. Then, the DEGs were used to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Then, a protein-protein interaction (PPI) network was constructed using the STRING database.ResultsA total of 18 DEGs were identified, of which 13 were upregulated and 5 were downregulated in secondary breast angiosarcoma. The GO enrichment analysis showed that the DEGs were most enriched in metabolism, energy pathways, and protein metabolism in biological processes. The enriched signaling pathways of DEGs were the transforming growth factor-β (TGF-β), Wnt, Hippo and PI3K-Akt signaling pathways. Then, the PPI network was conducted and hub genes were identified and they were involved in thyroid hormone, Hippo and other signaling pathways.ConclusionThis study lay the foundation for the discovery of effective and reliable molecular biomarkers and essential therapeutic targets for these malignancies.     

Enhanced clinical phenotyping by mechanistic bioprofiling in heart failure with preserved ejection fraction: insights from the MEDIA-DHF study (The Metabolic Road to Diastolic Heart Failure)

Abstract

Background: Heart failure with preserved ejection fraction (HFpEF) is a heterogeneous syndrome for which clear evidence of effective therapies is lacking. Understanding which factors determine this heterogeneity may be helped by better phenotyping. An unsupervised statistical approach applied to a large set of biomarkers may identify distinct HFpEF phenotypes.

Methods: Relevant proteomic biomarkers were analyzed in 392 HFpEF patients included in Metabolic Road to Diastolic HF (MEDIA-DHF). We performed an unsupervised cluster analysis to define distinct phenotypes. Cluster characteristics were explored with logistic regression. The association between clusters and 1-year cardiovascular (CV) death and/or CV hospitalization was studied using Cox regression.

Results: Based on 415 biomarkers, we identified 2 distinct clusters. Clinical variables associated with cluster 2 were diabetes, impaired renal function, loop diuretics and/or betablockers. In addition, 17 biomarkers were higher expressed in cluster 2 vs. 1. Patients in cluster 2 vs. those in 1 experienced higher rates of CV death/CV hospitalization (adj. HR 1.93, 95% CI 1.12–3.32, p?=?0.017). Complex-network analyses linked these biomarkers to immune system activation, signal transduction cascades, cell interactions and metabolism.

Conclusion: Unsupervised machine-learning algorithms applied to a wide range of biomarkers identified 2 HFpEF clusters with different CV phenotypes and outcomes. The identified pathways may provide a basis for future research.

• Clinical significance

• More insight is obtained in the mechanisms related to poor outcome in HFpEF patients since it was demonstrated that biomarkers associated with the high-risk cluster were related to the immune system, signal transduction cascades, cell interactions and metabolism

• Biomarkers (and pathways) identified in this study may help select high-risk HFpEF patients which could be helpful for the inclusion/exclusion of patients in future trials.

• Our findings may be the basis of investigating therapies specifically targeting these pathways and the potential use of corresponding markers potentially identifying patients with distinct mechanistic bioprofiles most likely to respond to the selected mechanistically targeted therapies.

     

肾透明细胞癌预后相关miRNAs的生物信息学分析

目的寻找可作为肾透明细胞癌（ccRCC）生物标志物的miRNA,以及ccRCC与正常组织间miRNA差异表达情况。 方法利用TCGA数据库下载ccRCC中miRNA表达数据,分析肿瘤与正常组织间差异表达miRNA。使用Kaplan-Meier曲线对患者进行生存分析,筛选出表达情况与临床预后相关的miRNA。通过生物信息学对miRNA的靶基因进行预测,然后运用FunRich软件和ClueGO对靶基因进行GO和KEGG富集分析。 结果通过TCGA数据库分析发现,ccRCC较正常组织差异表达miRNA共54个,其中上调33个,下调21个。通过生存分析发现hsa-miR-21和hsa-miR-155与患者预后相关,P≤0.05。进一步通过Perl软件在Targetscan、miRDB、miRTarBase、miRPath这四个数据库中预测miRNA靶基因并将结果取交集,共发现129个靶基因。GO和KEGG分析结果表明,这些靶基因主要与转录因子活性、信号转导以及FoxO、TNF等信号通路密切相关。 结论通过生物信息学分析发现了ccRCC与正常组织的差异表达miRNA;其中hsa-miR-21和hsa-miR-155与患者总体生存率相关,并通过调控靶基因参与相关的信号通路进而影响ccRCC的发生发展进程,提示hsa-miR-21和hsa-miR-155可能是ccRCC潜在的生物标志物。     

Exosomal small RNA sequencing uncovers the microRNA dose markers for power frequency electromagnetic field exposure

Purpose: The potential health risks caused by power frequency electromagnetic field (PFEMF) have led to increase public health concerns. However, the diagnosis and prognosis remain challenging in determination of exact dose of PFEMF exposure.

Materials and methods: Mice were exposed to different magnetic doses of PFEMF for the following isolation of serum exosomes, microRNAs (miRNAs) extraction and small RNA sequencing. After small RNA sequencing, bioinformatic analysis, quantitative real-time PCR (qRT-PCR) validation and serum exosomal miRNA biomarkers were determined.

Results: Significantly changed serum exosomal miRNA as biomarkers of 0.1, 0.5, 2.5?mT and common PFEMF exposure were confirmed. Gene ontology (GO) and Kyoto encyclopaedia of genes and genomes (KEGG) pathway analysis of the downstream target genes of the above-identified exosomal miRNA markers indicated that, exosomal miRNA markers were predicted to be involved in critical pathophysiological processes of neural system and cancer- or other disease-related signalling pathways.

Conclusions: Aberrantly-expressed serum exosomal miRNAs, including miR-128-3p for 0.1?mT, miR-133a-3p for 0.5?mT, miR-142a-5p for 2.5?mT, miR-218-5p and miR-199a-3p for common PFEMF exposure, suggested a series of informative markers for not only identifying the exact dose of PFEMF exposure, also consolidating the base for future clinical intervention.     

肾透明细胞癌Caki-1细胞系差异表达基因的生物信息学分析

目的比较肾透明细胞癌Caki-1细胞系与正常肾上皮细胞系ASE-5063中的差异表达基因（DEGs）,寻找潜在的肾透明细胞癌特异性分子标志物。 方法利用GEO数据库自带的GEO2R在线分析工具分析基因芯片GSE78179,将筛选出的DEGs分别导入Metascape、STRING以及Cytoscape进行综合分析并筛选出核心基因。最后使用FunRich等软件对筛选出的核心基因进行GO和KEGG富集分析。 结果共筛选出562个DEGs,其中上调基因345个,下调基因217个。进一步使用MCODE筛选出36个关键基因,GO功能分析发现这些基因与细胞粘附分子活性、趋化因子活性、细胞通讯和信号转导等密切相关;KEGG通路富集结果则表明差异基因主要集中在趋化因子信号通路、TNF信号通路以及NF-κB信号通路等多种与肿瘤相关的通路上。 结论运用生物信息学方法筛选出肾透明细胞癌Caki-1细胞系中DEGs,其中数个核心基因广泛参与多种肿瘤的病理进程,但尚未在肾透明细胞癌有相关研究报道,提示其可能是治疗肾透明细胞癌的潜在靶点。     

EA15, MIR22, LINC00472 as diagnostic markers for diabetic kidney disease

This study aimed to investigate the molecular mechanisms of diabetic kidney disease (DKD) and to explore new potential therapeutic strategies and biomarkers for DKD. First we analyzed the differentially expressed changes between patients with DKD and the control group using the chip data in Gene Expression Omnibus (GEO) database. Then the gene chip was subjected to be annotated again, so as to screen long noncoding RNAs (lncRNAs) and study expression differences of these lncRNAs in DKD and controlled samples. At last, the function of the differential lncRNAs was analyzed. A total of 252 lncRNAs were identified, and 14 were differentially expressed. In addition, there were 1,629 differentially expressed messenger RNAs (mRNAs) genes, and proliferation and apoptosis adapter protein 15 (PEA15), MIR22, and long intergenic nonprotein coding RNA 472 ( LINC00472) were significantly differentially expressed in DKD samples. Through functional analysis of the encoding genes coexpressed by the three lncRNAs, we found these genes were mainly enriched in type 1 diabetes and autoimmune thyroid disease pathways, whereas in Gene Ontology (GO) function classification, they were also mainly enriched in the immune response, type I interferon signaling pathways, interferon-γ mediated signaling pathways, and so forth. To summary, we identified EA15, MIR22, and LINC00472 may serve as the potential diagnostic markers of DKD.     

卵巢高/低级别浆液性癌的定量蛋白质组学比较研究

目的:探讨卵巢高级别浆液性癌和低级别浆液性癌的差异表达蛋白,为阐明卵巢癌发生机制及寻找诊断和预后标志物的提供线索。方法:收集卵巢癌新鲜组织标本冻存于液氮中,经病理学确诊为高级别浆液性癌和低级别浆液性癌,两种类型各收集15例。应用i TRAQ定量蛋白质组学技术筛选及鉴定高/低级别浆液性癌的差异表达蛋白,并进行生物信息学分析。结果:卵巢高级别和低级别浆液性癌组织的定量蛋白质组学比较研究鉴定出差异表达蛋白314个,其中与低级别浆液性癌组比较,高级别浆液性癌组上调蛋白有97种,下调蛋白有217种。GO分析显示这些差异蛋白在分子功能、生物学功能、细胞成分方面均具有一定分布特点。KEGG分析显示这些差异蛋白涉及复杂的信号通路。结论:高/低级别浆液性癌之间存在差异表达蛋白,这些蛋白涉及复杂的功能和信号通路可能在两型卵巢癌发生机制及肿瘤生物学行为差异中具有重要意义。     

基于单细胞转录组的多级别胶质瘤异质性及免疫微环境分析揭示了潜在的预后生物标志物

脑胶质瘤(glioma)是中枢神经系统最常见的内在肿瘤,具有发病率高、预后较差等特点。本研究旨在鉴定多形性胶质母细胞瘤(glioblastoma multiforme,GBM)和低级别胶质瘤(lower-grade gliomas, LGG)之间的差异表达基因(differentially expressed genes, DEGs),以探讨不同级别胶质瘤的预后影响因素。从NCBI基因表达综合数据库中收集了胶质瘤的单细胞转录组测序数据,其中包括来自3个数据集的共29 097个细胞样本。对于不同分级的人脑胶质瘤进行分析,经过滤得到21 071个细胞,通过基因本体分析、京都基因与基因组百科全书途径分析,从差异表达基因中筛选出70个基因,我们通过查阅文献,聚焦到delta样典型Notch配体3 (delta like canonical Notch ligand 3,DLL3)这个基因。基于TCGA的基因表达谱交互分析(gene expression profiling interactive analysis, GEPIA)数据库用于探索LGG和GBM中DLL3基因的表达差异,采用基因表达...     

基于转录组的八角挥发油合成相关基因挖掘与分析

为更好地挖掘八角(Illicium verum)挥发油合成相关基因，该文对挥发油性状差异显著的优良无性系桂角69号及普通品种砧01号叶片进行了转录组测序及组装注释，并对差异表达基因进行了GO分类和KEGG通路分析。结果表明：(1)转录本经组装后获得84 182条序列，使用NR、NT、Swiss-Prot、KEGG、KOG、GO和Pfam数据库进行序列比对，共注释了59 161条序列，筛选出30 572个差异表达基因。与砧01号相比，桂角69号叶片中上调基因有15 025个，下调基因有15 547个。(2)GO分类结果显示共有20 287个差异基因被注释。KEGG分析结果表明，有21 600个差异基因被注释到133条KEGG通路上，其中挥发油合成相关的单萜生物合成通路、萜类骨架生物合成通路、苯丙素合成通路中的芳樟醇合酶、月桂烯合酶、香叶基香叶基焦磷酸合酶、肉桂酰辅酶A还原酶、咖啡酸3-O-甲基转移酶、肉桂醇脱氢酶等关键酶基因呈差异表达。(3)转录因子分析发现差异表达基因分布于31个转录因子家族，其中MYB家族序列数量最多。该文利用转录组测序技术分析八角优良无性系与普通品种叶片的差异基因及...     

小麦叶锈菌休眠与萌发夏孢子的差异表达

【目的】小麦叶锈菌引起的小麦叶锈病是小麦的重要病害之一,孢子萌发和侵入气孔是保证叶锈菌正常侵染寄主的重要前提。本研究旨在研究小麦叶锈菌夏孢子萌发的差异表达特性,为揭示萌发的机制及其与致病的关系提供依据。【方法】利用小麦叶锈菌致病类型THTT的休眠夏孢子和萌发夏孢子进行RNA-seq分析。【结果】在萌发夏孢子中筛选出相比休眠夏孢子上调表达的基因为4400个,下调基因5325个。GO富集分析发现,上调差异基因主要涉及细胞进程、有机物代谢、信号传导、单个有机体过程、催化酶活性等;下调基因主要涉及单组织过程、单个有机体细胞过程、有机物代谢过程、催化活性调节等过程。利用KEGG分析发现,差异基因共参与109条通路,从中筛选出两条与孢子萌发相关的通路——丝裂原活化蛋白激酶(MAPK)信号通路和囊泡运输中的SNARE蛋白交流。10个基因的定量分析结果与基因数字表达谱分析结果一致。【结论】研究获得了叶锈菌孢子萌发及侵入气孔过程中的重要差异基因,研究结果为研究叶锈菌致病机制奠定基础。     

利用木质纤维素类生物质产微生物絮凝剂Pseudomonas boreopolis GO2的全基因组测序及比较基因组学分析

【目的】Pseudomonas boreopolis GO2可以利用木质纤维素类生物质为唯一碳源发酵产微生物絮凝剂。解析菌株GO2的全基因组特征可为利用木质纤维素类生物质定向合成多糖型微生物絮凝剂提供分子基础。【方法】利用Illumina NovaSeq测序平台对菌株GO2进行测序,用SMRT等软件进行基因组组装、系统发育分析、基因预测和功能注释,并与4株近缘模式株进行了比较基因组分析。【结果】菌株GO2基因组大小为4 498 896 bp,GC含量为69.5%,共编码3 906个基因。菌株GO2与Pseudomonas boreopolis JCM 13306的16S r RNA基因相似性、平均核苷酸一致性(average nucleotide identity, ANI)、DNA-DNA杂交(DNA-DNA hybridization, DDH)值最高,分别为99.93%、98.36%和88.00%,将菌株GO2命名为Pseudomonas boreopolis GO2。比较基因组分析发现,GO2与4个近缘模式菌株共有2 348个直系同源核心基因,主要参与碳水化合物代谢、氨基酸代谢...     

Prognostic value of metabolic genes in lung adenocarcinoma via integrative analyses

BackgroundLung adenocarcinoma (LUAD) is the most common malignant lung tumor. Metabolic pathway reprogramming is an important hallmark of physiologic changes in cancers. However, the mechanisms through which these metabolic genes and pathways function in LUAD as well as their prognostic values have not been fully established.MethodsFour publicly available datasets from GEO and TCGA were used to identify differentially expressed genes (DEGs) in LUAD, which were then subjected to GO and KEGG pathway enrichment analysis. Associations between metabolic gene expressions with overall survival, tumor stage, TP53 mutation status, and infiltrated immune cells were investigated. Protein-protein interactions were evaluated using GeneMANIA and Metascape.ResultsBy integrating four public datasets, 247 DEGs were identified in LUAD. These DEGs were significantly enriched in regulation of chromosome segregation, centromeric region, and histone kinase activity GO terms, as well as in cell cycle, p53 signaling pathway, metabolic pathways, and other KEGG pathways. Elevated expressions of ten metabolic genes in LUAD were significantly associated with poor survival outcomes. These metabolic genes were highly expressed in more advanced tumor stage and TP53 mutated patients. Moreover, expression levels were significantly correlated with tumor-infiltrating immune cells. PPI interaction analysis revealed that the top 20 genes interacting with each metabolic gene were significantly enriched in DNA replication, response to radiation, and central carbon metabolism in cancer.ConclusionThis study elucidates on molecular changes in metabolic genes in LUAD, which may inform the development of genetically oriented diagnostic approaches and effective treatment options.