Analysis of Significant Genes and Pathways in Esophageal Cancer Based on Gene Expression Omnibus Database

Objective To screen antigen targets for immunotherapy by analyzing over-expressed genes,and to identify significant pathways and molecular mechanisms in esophageal cancer by using bioinformatic methods such as enrichment analysis,protein-protein interaction(PPI)network,and survival analysis based on the Gene Expression Omnibus(GEO)database.Methods By screening with highly expressed genes,we mainly analyzed proteins MUC13 and EPCAM with transmembrane domain and antigen epitope from TMHMM and IEDB websites.Significant genes and pathways associated with the pathogenesis of esophageal cancer were identified using enrichment analysis,PPI network,and survival analysis.Several software and platforms including Prism 8,R language,Cytoscape,DAVID,STRING,and GEPIA platform were used in the search and/or figure creation.Results Genes MUC13 and EPCAM were over-expressed with several antigen epitopes in esophageal squamous cell carcinoma(ESCC)tissue.Enrichment analysis revealed that the process of keratinization was focused and a series of genes were related with the development of esophageal cancer.Four genes including ALDH3A1,C2,SLC6A1,and ZBTB7C were screened with significant P value of survival curve.Conclusions Genes MUC13 and EPCAM may be promising antigen targets or biomarkers for esophageal cancer.Keratinization may greatly impact the pathogenesis of esophageal cancer.Genes ALDH3A1,C2,SLC6A1,and ZBTB7C may play important roles in the development of esophageal cancer.

Gene signatures to therapeutics:Assessing the potential of ivermectin against t(4;14)multiple myeloma

BACKGROUND Multiple myeloma(MM)is a terminal differentiated B-cell tumor disease characterized by clonal proliferation of malignant plasma cells and excessive levels of monoclonal immunoglobulins in the bone marrow.The translocation,(t)(4;14),results in high-risk MM with limited treatment alternatives.Thus,there is an urgent need for identification and validation of potential treatments for this MM subtype.Microarray data and sequencing information from public databases could offer opportunities for the discovery of new diagnostic or therapeutic targets.AIM To elucidate the molecular basis and search for potential effective drugs of t(4;14)MM subtype by employing a comprehensive approach.METHODS The transcriptional signature of t(4;14)MM was sourced from the Gene Expression Omnibus.Two datasets,GSE16558 and GSE116294,which included 17 and 15 t(4;14)MM bone marrow samples,and five and four normal bone marrow samples,respectively.After the differentially expressed genes were identified,the Cytohubba tool was used to screen for hub genes.Then,the hub genes were analyzed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis.Using the STRING database and Cytoscape,protein–protein interaction networks and core targets were identified.Potential small-molecule drugs were identified and validated using the Connectivity Map database and molecular docking analysis,respectively.RESULTS In this study,a total of 258 differentially expressed genes with enriched functions in cancer pathways,namely cytokine receptor interactions,nuclear factor(NF)-κB signaling pathway,lipid metabolism,atherosclerosis,and Hippo signaling pathway,were identified.Ten hub genes(cd45,vcam1,ccl3,cd56,app,cd48,btk,ccr2,cybb,and cxcl12)were identified.Nine drugs,including ivermectin,deforolimus,and isoliquiritigenin,were predicted by the Connectivity Map database to have potential therapeutic effects on t(4;14)MM.In molecular docking,ivermectin showed strong binding affinity to all 10 identified targets,especially cd45 and cybb.Ivermectin inhibited t(4;14)MM cell growth via the NF-κB pathway and induced MM cell apoptosis in vitro.Furthermore,ivermectin increased reactive oxygen species accumulation and altered the mitochondrial membrane potential in t(4;14)MM cells.CONCLUSION Collectively,the findings offer valuable molecular insights for biomarker validation and potential drug development in t(4;14)MM diagnosis and treatment,with ivermectin emerging as a potential therapeutic alternative.

Analysis of differentially expressed genes related to cerebral ischaemia in young rats based on the Gene Expression Omnibus database

BACKGROUND The incidence rate of cerebral infarction in young people is increasing day by day,the age of onset tends to be younger,and its internal pathogenesis and mechanism are very complicated,which leads to greater difficulties in treatment.Therefore,it is essential to analyze the key pathway that affects the onset of cerebral infarction in young people from the perspective of genetics.AIM To compare the differentially expressed genes in the brain tissue of young and aged rats with middle cerebral artery occlusion and to analyse their effect on the key signalling pathway involved in the development of cerebral ischaemia in young rats.METHODS The Gene Expression Omnibus 2R online analysis tool was used to analyse the differentially expressed genes in the GSE166162 dataset regarding the development of cerebral ischaemia in young and aged groups of rats.DAVID 6.8 software was further used to filter the differentially expressed genes.These genes were subjected to Gene Ontology(GO)function analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis to determine the key gene pathway that affects the occurrence of cerebral ischaemia in young rats.RESULTS Thirty-five differentially expressed genes(such as Igf2,Col1a2,and Sfrp1)were obtained;73 GO enrichment analysis pathways are mainly involved in biological processes such as drug response,amino acid stimulation response,blood vessel development,various signalling pathways,and enzyme regulation.They are involved in molecular functions such as drug binding,protein binding,dopamine binding,metal ion binding,and dopamine neurotransmitter receptor activity.KEGG pathway enrichment analysis showed a significantly enriched pathway:The cyclic adenosine monophosphate(c-AMP)signalling pathway.CONCLUSION The c-AMP signalling pathway might be the key pathway in the intervention of cerebral infarction in young people.

Research Progress of miRNA Regulating Cell Signaling Pathways Related to Hepatocarcinogenesis

Hepatocellular carcinoma(HCC)is one of the most common malignant tumors in clinical practice.The pathogenesis of HCC is still unclear.Currently,the clinical treatment of HCC is poorly targeted and the therapeutic effect is poor.MicroRNAs(miRNAs)are closely related to the occurrence of HCC,and they are mainly involved in the occurrence and development of HCC through binding to target genes or acting on related signaling pathways.In recent years,studies have shown that miRNA can be used as a potential biomarker for diagnosis and prognosis of HCC.In addition,studies have also shown that miRNA plays a tumorsuppressing or tumor-promoting role in the process of HCC by regulating the biological processes of tumor cell proliferation,migration,invasion and metastasis.In this paper,the recent studies on miRNA signaling pathways related to the occurrence and development of HCC were reviewed,with a view to providing ideas for the clinical diagnosis and treatment of HCC.

Bioinformatics analysis of ferroptosis in spinal cord injury

Ferroptosis plays a key role in aggravating the progression of spinal cord injury(SCI),but the specific mechanism remains unknown.In this study,we constructed a rat model of T10 SCI using a modified Allen method.We identified 48,44,and 27 ferroptosis genes that were differentially expressed at 1,3,and 7 days after SCI induction.Compared with the sham group and other SCI subgroups,the subgroup at 1 day after SCI showed increased expression of the ferroptosis marker acyl-CoA synthetase long-chain family member 4 and the oxidative stress marker malondialdehyde in the injured spinal cord while glutathione in the injured spinal cord was lower.These findings with our bioinformatics results suggested that 1 day after SCI was the important period of ferroptosis progression.Bioinformatics analysis identified the following top ten hub ferroptosis genes in the subgroup at 1 day after SCI:STAT3,JUN,TLR4,ATF3,HMOX1,MAPK1,MAPK9,PTGS2,VEGFA,and RELA.Real-time polymerase chain reaction on rat spinal cord tissue confirmed that STAT3,JUN,TLR4,ATF3,HMOX1,PTGS2,and RELA mRNA levels were up-regulated and VEGFA,MAPK1 and MAPK9 mRNA levels were down-regulated.Ten potential compounds were predicted using the DSigDB database as potential drugs or molecules targeting ferroptosis to repair SCI.We also constructed a ferroptosis-related mRNA-miRNA-lncRNA network in SCI that included 66 lncRNAs,10 miRNAs,and 12 genes.Our results help further the understanding of the mechanism underlying ferroptosis in SCI.

Identification of key genes involved in axon regeneration and Wallerian degeneration by weighted gene co-expression network analysis

Peripheral nerve injury repair requires a certain degree of cooperation between axon regeneration and Wallerian degeneration.Therefore,investigating how axon regeneration and degeneration work together to repair peripheral nerve injury may uncover the molecular mechanisms and signal cascades underlying peripheral nerve repair and provide potential strategies for improving the low axon regeneration capacity of the central nervous system.In this study,we applied weighted gene co-expression network analysis to identify differentially expressed genes in proximal and distal sciatic nerve segments from rats with sciatic nerve injury.We identified 31 and 15 co-expression modules from the proximal and distal sciatic nerve segments,respectively.Functional enrichment analysis revealed that the differentially expressed genes in proximal modules promoted regeneration,while the differentially expressed genes in distal modules promoted neurodegeneration.Next,we constructed hub gene networks for selected modules and identified a key hub gene,Kif22,which was up-regulated in both nerve segments.In vitro experiments confirmed that Kif22 knockdown inhibited proliferation and migration of Schwann cells by modulating the activity of the extracellular signal-regulated kinase signaling pathway.Collectively,our findings provide a comparative framework of gene modules that are co-expressed in injured proximal and distal sciatic nerve segments,and identify Kif22 as a potential therapeutic target for promoting peripheral nerve injury repair via Schwann cell proliferation and migration.All animal experiments were approved by the Institutional Animal Ethics Committee of Nantong University,China(approval No.S20210322-008)on March 22,2021.

Study on the mechanism of cholic acid derivatives in traditional Chinese medicine based on the regulation of gene expression

Objective:To investigate the pharmacological action and mechanism of cholic acid derivatives in traditional Chinese medicine(TCM)based on the regulation of gene expression.Methods:Genome-wide gene expression profiles of Michigan Cancer Foundation-7(MCF-7)cells treated with or without 4 cholic acid derivatives were detected by gene chip technology.Similarities in upregulated and downregulated genes were analyzed using the Connectivity Map(CMap)database.The affinity between cholic acid derivatives and the potential target was confirmed by molecular docking.The cholic acid derivative-regulated pathway enrichment analysis was performed by the STRING database,and the potential pathway was confirmed by in vitro experiments on MD Anderson-Metastatic Breast-231(MDA-MB-231)cells.Results:Compared with the reference genome in the CMap database,the gene expression profiles of cholic acid derivatives were similar to those of antipsychotic,anticancer,anti-inflammatory,and antiinfective drugs.Among them,4 derivatives were associated with antianxiety drugs,and molecular docking results showed that these compounds may act by binding to the ligand-binding site of gammaaminobutyric acid(GABA)receptors.Moreover,the cytoskeletal pathway is one of the pathways enriched in the derivatives.Of them,ursodeoxycholic acid showed significant inhibitory activity on the cytoskeleton formation of MDA-MB-231 cells.Conclusion:The gene expression detection method,combined with CMap and pathway enrichment analysis,could be used to study the mechanism of the active ingredients of TCM.In addition,our research showed that cholic acid derivatives have a potential affinity for membrane receptors,where they can exert anxiolytic activity by modulating opioid receptor,GABA receptor,and dopamine receptor.Moreover,ursodeoxycholic and chenodeoxycholic acid inhibit cytoskeleton formation,probably by acting on membrane proteins to activate the corresponding cytoskeletal pathways.

Bioinformatics-based Identification of Key Pathways and Hub Genes of Traumatic Brain Injury in a Rat Model

Traumatic brain injury(TBI)is a common injury caused by external forces that lead to damaged brain function or pathological changes in the brain tissue.To explore the molecular mechanism and the hub genes of TBI,we downloaded gene expression profiles of the TBI model of rat and the sham control for the subsequent gene set enrichment analysis,pathway analysis and protein-protein interactions analysis.The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that multiple biological pathways,including immune response,inflammatory response and cellular response to interleukin-1,as well as signaling pathways,such as tumor necrosis factor signaling pathway,chcmokine signaling pathway,cytokine-cytokine receptor interaction,Toll-like receptor signaling pathway and nuclear factor kappa B signaling pathway were implicated in the TBI.In conclusion,this study provides insights into the molecular mechanism of TBI by screening the differentially expressed genes and hub genes that can be used as biomarkers and therapeutic targets.

Hub genes and their key effects on prognosis of Burkitt lymphoma

BACKGROUND Burkitt lymphoma(BL)is an exceptionally aggressive malignant neoplasm that arises from either the germinal center or post-germinal center B cells.Patients with BL often present with rapid tumor growth and require high-intensity multidrug therapy combined with adequate intrathecal chemotherapy prophylaxis,however,a standard treatment program for BL has not yet been established.It is important to identify biomarkers for predicting the prognosis of BLs and discriminating patients who might benefit from the therapy.Microarray data and sequencing information from public databases could offer opportunities for the discovery of new diagnostic or therapeutic targets.AIM To identify hub genes and perform gene ontology(GO)and survival analysis in BL.METHODS Gene expression profiles and clinical traits of BL patients were collected from the Gene Expression Omnibus database.Weighted gene co-expression network analysis(WGCNA)was applied to construct gene co-expression modules,and the cytoHubba tool was used to find the hub genes.Then,the hub genes were analyzed using GO and Kyoto Encyclopedia of Genes and Genomes analysis.Additionally,a Protein-Protein Interaction network and a Genetic Interaction network were constructed.Prognostic candidate genes were identified through overall survival analysis.Finally,a nomogram was established to assess the predictive value of hub genes,and drug-gene interactions were also constructed.RESULTS In this study,we obtained 8 modules through WGCNA analysis,and there was a significant correlation between the yellow module and age.Then we identified 10 hub genes(SRC,TLR4,CD40,STAT3,SELL,CXCL10,IL2RA,IL10RA,CCR7 and FCGR2B)by cytoHubba tool.Within these hubs,two genes were found to be associated with OS(CXCL10,P=0.029 and IL2RA,P=0.0066)by survival analysis.Additionally,we combined these two hub genes and age to build a nomogram.Moreover,the drugs related to IL2RA and CXCL10 might have a potential therapeutic role in relapsed and refractory BL.CONCLUSION From WGCNA and survival analysis,we identified CXCL10 and IL2RA that might be prognostic markers for BL.

Research Progress in Targeted Therapy of Hepatocellular Carcinoma

Hepatocellular carcinoma(HCC)is one of the most common malignancies,and its treatment is limited.With the understanding of key genes and signaling pathways in the occurrence and development of HCC,targeted drugs with high selectivity and low toxicity have been developed continuously,bringing a variety of options for the treatment of advanced HCC.In this article,the research progress on representative drugs of targeted therapy and potential therapeutic targets for HCC are reviewed.

Quercetin Increased Protein Utilization and Decreased Nitrogen Excretion in Broilers by Activating TOR Signaling Pathway

The study was conducted to investigate the effect and mechanism of dietary quercetin supplementation on protein utilization of Arbor Acres(AA)broilers.A total of 2401-day-old AA broilers were randomly allocated to four treatments with six replicates,comprising 10 broilers each replicate(60 broilers per treatment).Birds were fed either a corn-soybean meal basal diet without quercetin(control)or a basal diet supplemented with 0.2,0.4 or 0.6 g of quercetin per kg feed,and the trial lasted 42 days.Dietary quercetin supplementation tended to increase the apparent metabolic rate of protein(p=0.076)and the content of serum albumin(p=0.062)in AA broilers.Compared with the control,dietary quercetin supplementation increased the contents of protein in breast muscle(p<0.05)and in thigh muscle(p=0.053).In addition,quercetin up-regulated mRNA expression of insulin-like growth factor 1(IGF-1),phosphatidylinositol 3-kinase(PI3K),target of rapamycin(TOR),ribosomal protein S6 kinase 1(S6K1),eukaryotic translation initiation factor 4E(eIF4E),eukaryotic translation initiation factor 4G(eIF4G),eukaryotic elongation factor 2(eEF2)and eukaryotic translation initiation factor 4B(eIF4B)genes and down-regulated mRNA expression of eukaryotic elongation factor 2 kinase(eEF2K)and eukaryotic initiation factor 4E binding protein1(4E-BP1)genes in breast muscle,thigh muscle and liver of AA broilers(p<0.05).The present results suggested that dietary quercetin supplementation enhanced protein utilization in broilers by activating TOR signaling pathway.

Deoxyribonucleic acid methylation driven aberrations in pancreatic cancer-related pathways

Pancreatic cancer(PanCa)presents a catastrophic disease with poor overall survival at advanced stages,with immediate requirement of new and effective treatment options.Besides genetic mutations,epigenetic dysregulation of signaling pathway-associated enriched genes are considered as novel therapeutic target.Mechanisms beneath the deoxyribonucleic acid methylation and its utility in developing of epi-drugs in PanCa are under trails.Combinations of epigenetic medicines with conventional cytotoxic treatments or targeted therapy are promising options to improving the dismal response and survival rate of PanCa patients.Recent studies have identified potentially valid pathways that support the prediction that future PanCa clinical trials will include vigorous testing of epigenomic therapies.Epigenetics thus promises to generate a significant amount of new knowledge of biological and medical importance.Our review could identify various components of epigenetic mechanisms known to be involved in the initiation and development of pancreatic ductal adenocarcinoma and related precancerous lesions,and novel pharmacological strategies that target these components could potentially lead to breakthroughs.We aim to highlight the possibilities that exist and the potential therapeutic interventions.

基于生物信息学分析的阿尔茨海默病核心基因挖掘及相关通路分析

目的基于生物信息学分析筛选阿尔茨海默病(AD)的核心基因,并对可能的致病信号通路进行分析。方法从基因表达综合(GEO)数据库中下载AD相关基因芯片数据,筛选出GSE227221和GSE162873数据集。应用GEO2R在线分析软件筛选AD组织样本和正常脑组织样本间的差异表达基因(DEGs)。应用R软件DOSE包对DEGs进行疾病本体论(DO)基因富集分析,使用在线数据分析工具DAVID对DEGs进行基因本体论(GO)和京都基因与基因组百科全书(KEGG)富集分析。通过STRING数据库分析基因的蛋白质交互作用,应用Cytoscape软件构建蛋白质-蛋白质相互作用(PPI)网络,并通过MCODE插件对PPI网络进行枢纽基因的分析与筛选。根据MCODE评分,对枢纽基因进一步分析并筛选出核心基因。结果对2个数据集进行比对后,共筛选出参与AD发生和进展的1373个相同变化趋势的DEGs,并筛选验证出核心基因为GIMAP基因(包括GIMAP1、GIMAP4、GIMAP5、GIMAP6、GIMAP7及GIMAP1-GIMAP5)。DO基因富集分析结果显示,DEGs与系统性红斑狼疮、红斑狼疮和动脉硬化这3种疾病最为相关;GO功能富集分析结果显示,DEGs主要富集于3条信号通路,即经典Wnt信号通路、磷脂酶C-活化G蛋白质-耦合受体通路和等离子体外侧膜通路;KEGG信号通路富集分析结果显示,DEGs主要富集于细胞因子-细胞因子受体相互作用、神经元活性配体-受体相互作用、癌症相关的转录失调等通路。结论AD的核心致病基因可能为GIMAP基因,与AD发生相关的通路复杂,可能与免疫功能紊乱有关。

眼睑基底细胞癌差异基因的筛选和分析

目的采用RNA测序技术对眼睑基底细胞癌差异基因进行筛选和分析。方法选取2021年7月至11月因眼睑基底细胞癌就诊于河北省眼科医院并行扩大切除及一期眼睑重建的患者6例,分别取切除的部分癌组织及修复缺损时修剪的癌旁正常组织各一块进行研究。通过RNA测序技术进行建库测序。使用DESeq2软件设定P<0.05及|log 2(foldchange)|>1为显著差异表达的阈值。鉴定出差异表达的基因。采用clusterProfiler软件对差异基因集进行GO功能富集分析和KEGG通路富集分析,进一步分析这些特异性基因的生物学意义。结果使用DESeq2软件进行癌组织和癌旁组织之间的差异表达分析,共筛选出1317个差异基因,其中在6例癌组织中表达上调的基因有906个,表达下调的基因有411个。GO富集分析结果中上调最显著的前30个差异基因主要富集于体液免疫反应、免疫球蛋白复合物、B细胞受体信号通路、细胞外基质、抗原结合、受体调节剂活性等方面。下调基因前10位在生物过程、细胞组成、分子功能层面主要与表皮发展相关。KEGG通路富集主要集中在黑色素生成通路及WNT信号通路、免疫相关信号通路等,相关基因通路有8个。根据基因上调的显著性由大到小,最终确定核心基因包括FZD2、PTCH1、WNT7B、TCF3、MMP-9、TEAD2。结论基底细胞癌的发生与各种通路相互影响和共同作用密切相关,各种高表达基因中,FZD2、PTCH1、WNT7B、TCF3、MMP-9、TEAD2在眼睑基底细胞癌患者组织中表达升高最显著,与眼睑基底细胞癌的发生和发展有密切关系。

基于Illumina Bovine SNP 50K芯片对比利时蓝牛的遗传规律解析

为了研究大型肉牛比利时蓝牛生长发育的遗传规律,筛选优异基因,试验基于Illumina Bovine SNP 50K芯片数据,采用PLINK软件对270头比利时蓝牛常染色体数据进行基因组长纯合片段(ROH)检测并基于选择信号分析,通过核苷酸多态性检测取前5%的单核苷酸多态性(single nucleotide polymorphism,SNP)位点,基于牛参考基因组(ARS-UCD1.2)对结果SNPs进行基因注释,对候选基因进行GO功能注释与KEGG信号通路富集分析,并计算染色体上ROH长度占基因组总长度的比例(FROH)。结果表明:在全部270个个体数据中共检测出1893个ROH片段,平均长度13.2311 Mb,平均FROH为0.0392;得到与生长发育相性状相关的基因有NEB、TET2、NEK11、NCKAP1、MYH15、EIF4A2、bta-miR-1248-1、DCAF8、PRORP、DOCK3、SYT15、MYEF2、ZDHHC13,与公牛生育能力相关的基因有CFAP61、DNAL1、BAG1。说明通过对比利时蓝牛生长发育性状相关分子标记的解析可以为比利时蓝牛遗传改良提供理论指导。

MicroRNA changes of bone marrow-derived mesenchymal stem cells differentiated into neuronal-like cells by Schwann cell-conditioned medium

Bone marrow-derived mesenchymal stem cells differentiate into neurons under the induction of Schwann cells. However, key microRNAs and related pathways for differentiation remain unclear. This study screened and identified differentially expressed microRNAs in bone marrow- derived mesenchymal stem cells induced by Schwann cell-conditioned medium, and explored targets and related pathways involved in their differentiation into neuronal-like cells. Primary bone marrow-derived mesenchymal stem cells were isolated from femoral and tibial bones, while primary Schwann cells were isolated from bilateral saphenous nerves. Bone marrow-derived mesenchymal stem cells were cultured in unconditioned (control group) and Schwann cell-conditioned medium (bone marrow-derived mesenchymal stem cell + Schwann cell group). Neuronal differentiation of bone marrow-derived mesenchymal stem cells induced by Schwann cell-conditioned medium was observed by time-lapse imaging. Upon induction, the morphology of bone marrow-derived mesencaymal stem cells changed into a neural shape with neurites. Results of quantitative reverse transcription-polymerase chain reaction revealed that nestin mRNA expression was upregulated from 1 to 3 days and downregulated from 3 to 7 days in the bone marrow-derived mesenchymal stem cell + Schwann cell group. Compared with the control group, microtubule-associated protein 2 mRNA expression gradually increased from 1 to 7 days in the bone marrow-derived mesenchymal stem cell + Schwann cell group. After 7 days of induction, microRNA analysis iden:ified 83 significantly differentially expressed microRNAs between the two groups. Gene Ontology analysis indicated enrichment of microRNA target genes for neuronal projection development, regulation of axonogenesis, and positive regulation of cell proliferation. Kyoto Encyclopedia of Genes and Genomes pathway analysis demonstrated that Hippo, Wnt, transforming growth factor-beta, and Hedgehog signaling pathv/ays were potentially associated with neural differentiation of bone marrow-derived mesenchymal stem cells. This study, which carried out successful microRNA analysis of neuronal-like cells differentiated from bone marrow-derived mesenchymal stem cells by Schwann cell induction, revealed key microRNAs and pathways involved in neural differentiation of bone marrow-derived mesenchymal stem cells. All protocols were approved by the Animal Ethics Committee of Institute of Radiation Medicine, Chinese Academy of Medical Sciences on March 12, 2017 (approval number: DWLI-20170311).

MicroRNAs: a novel promising therapeutic target for cerebral ischemia/reperfusion injury?

To determine the molecular mechanism of cerebral ischemia/reperfusion injury, we examined the micro RNA（mi RNA） expression profile in rat cortex after focal cerebral ischemia/reperfusion injury using mi RNA microarrays and bioinformatic tools to systematically analyze Gene Ontology（GO） function classifications, as well as the signaling pathways of genes targeted by these differentially expressed mi RNAs. Our results show significantly changed mi RNA expression profiles in the reperfusion period after focal cerebral ischemia, with a total of 15 mi RNAs up-regulated and 44 mi RNAs down-regulated. Target genes of these differentially expressed mi RNAs were mainly involved in metabolic and cellular processes, which were identified as hub nodes of a mi RNA-GO-network. The most correlated pathways included D-glutamine and D-glutamate metabolism, the renin-angiotensin system, peroxisomes, the PPAR signaling pathway, SNARE interactions in vesicular transport, and the calcium signaling pathway. Our study suggests that mi RNAs play an important role in the pathological process of cerebral ischemia/reperfusion injury. Understanding mi RNA expression and function may shed light on the molecular mechanism of cerebral ischemia/reperfusion injury.

Single-nucleotide polymorphism screening and RNA sequencing of key messenger RNAs associated with neonatal hypoxic-ischemia brain damage

A single-nucleotide polymorphism(SNP)is an alteration in one nucleotide in a certain position within a genome.SNPs are associated with disease susceptibility.However,the influences of SNPs on the pathogenesis of neonatal hypoxic-ischemic brain damage remain elusive.Seven-day-old rats were used to establish a hypoxic ischemic encephalopathy model.SNPs and expression profiles of mRNAs were analyzed in hypoxic ischemic encephalopathy model rats using RNA sequencing.Genes exhibiting SNPs associated with hypoxic ischemic encephalopathy were identified and studied by gene ontology and pathway analysis to identify their possible involvement in the disease mechanism.We identified 89 up-regulated genes containing SNPs that were mainly located on chromosome 1 and 2.Gene ontology analysis indicated that the up-regulated genes containing SNPs are mainly involved in angiogenesis,wound healing and glutamatergic synapse and biological processing of calcium-activated chloride channels.Signaling pathway analysis indicated that the differentially expressed genes play a role in glutamatergic synapses,long-term depression and oxytocin signaling.Moreover,intersection analysis of high throughput screening following PubMed retrieval and RNA sequencing for SNPs showed that CSRNP1,DUSP5 and LRRC25 were most relevant to hypoxic ischemic encephalopathy.Significant up-regulation of genes was confirmed by quantitative real-time polymerase chain reaction analysis of oxygen-glucose-deprived human fetal cortical neurons.Our results indicate that CSRNP1,DUSP5 and LRRC25,containing SNPs,may be involved in the pathogenesis of hypoxic ischemic encephalopathy.These findings indicate a novel direction for further hypoxic ischemic encephalopathy research.This animal study was approved on February 5,2017 by the Animal Care and Use Committee of Kunming Medical University,Yunnan Province,China(approval No.kmmu2019038).Cerebral tissue collection from a human fetus was approved on September 30,2015 by the Ethics Committee of Kunming Medical University,China(approval No.2015-9).

基于网络药理学探究栀子川芎胶囊防治动脉粥样硬化的作用机制

目的:采用网络药理学、基因芯片分子对接方法探讨栀子川芎胶囊防治动脉粥样硬化(AS)的作用机制。方法:利用14个数据库和基因芯片等预测栀子川芎胶囊防治AS的靶点,构建成分-治疗靶点(C-T)网络、治疗靶点网络(T-D),并计算网络贡献指数、度值、中介中心性、接近中心性和平均最短路径筛选C-T和T-D网络主要核心成分和靶点。对治疗靶点进行富集分析,最后对核心成分和核心靶点做分子对接验证。结果:预测得到治疗靶点162个,根据网络贡献指数、度值、中介中心性、接近中心性和平均最短路径筛选C-T和T-D网络得到叶酸和槲皮素2个核心成分、13个核心靶点。富集分析显示栀子川芎胶囊从炎症反应、氧化应激、脂质和营养物质代谢等多方面防治AS,并且治疗靶点富集于全身多个组织器官。分子对接验证结果表明核心成分与核心靶点间具有较强的结合力。结论:栀子川芎胶囊防治AS具有多成分、多靶点的特点,可以从多层次、多角度防治AS。

基于网络药理学的复方苁蓉益智胶囊治疗血管性痴呆的分子机制研究

目的:对复方苁蓉益智胶囊(Compound Desert Cistanche Intelligence-improving Capsule)治疗血管性痴呆(VaD)的药理作用机制进行探讨。方法:基于网络药理学和分子对接的方法,通过中药系统药理学数据库与分析平台(TCMSP)获取复方苁蓉益智胶囊中各药物的活性成分,并通过SwissTarget Prediction数据库预测药物活性成分的作用靶点;通过GeneCards、在线人类孟德尔遗传数据库(OMIM)、DrugBank数据库获取血管性痴呆的疾病靶点。通过STRING 11.0数据库和Cytoscape 3.8.2构建蛋白质相互作用(PPI)网络并挖掘网络中潜在的蛋白质功能模块及核心网络;通过DAVID数据库进行基因本体(GO)富集分析和京都基因和基因组百科全书(KEGG)通路富集分析,采用Cytoscape 3.8.2构建“药物-活性成分-靶点-通路”网络图,采用分子对接技术对PPI网络及“药物-活性成分-靶点-通路”网络图结果进行验证。结果:筛选出35个主要活性成分,涉及134个靶点,其中主要活性成分包括亚美罂粟碱(Armepavine)、甘草素(DFV)、异鼠李素(Isorhamnetin)等;关键靶点包括淀粉样前体蛋白(APP)、磷脂酰肌醇-3-激酶催化亚单位α(PIK3CA)、酪氨酸蛋白激酶SRC(SRC)、磷脂酰肌醇3-激酶调控亚基1(PIK3R1)、促分裂原活化的蛋白激酶1(MAPK1)、肿瘤蛋白53(TP53)、促分裂原活化的蛋白激酶3(MAPK3)、原癌基因c-Jun(JUN)、丝氨酸/苏氨酸蛋白激酶(AKT1)、血管内皮生长因子A(VEGFA)、表皮生长因子受体(EGFR)、凝血酶F2(F2)等;复方苁蓉益智胶囊治疗血管性痴呆的生物学通路主要作用在癌症信号通路、Rap1信号通路、PI3K-AKT信号通路、黏着斑、Ras信号通路、神经活性配体-受体相互作用等。分子对接结果验证提示主要活性成分与靶点之间具有较好的结合能力。结论:本研究初步揭示了复方苁蓉益智胶囊治疗血管性痴呆的机制可能是通过多组分、多靶点、多途径协同发挥作用,为接下来的深入研究提供参考。