BACKGROUND A growing number of clinical examples suggest that coronavirus disease 2019(COVID-19)appears to have an impact on the treatment of patients with liver cancer compared to the normal population,and the preval...BACKGROUND A growing number of clinical examples suggest that coronavirus disease 2019(COVID-19)appears to have an impact on the treatment of patients with liver cancer compared to the normal population,and the prevalence of COVID-19 is significantly higher in patients with liver cancer.However,this mechanism of action has not been clarified.Gene sets for COVID-19(GSE180226)and liver cancer(GSE87630)were obtained from the Gene Expression Omnibus database.After identifying the common differentially expressed genes(DEGs)of COVID-19 and liver cancer,functional enrichment analysis,protein-protein interaction network construction and scree-ning and analysis of hub genes were performed.Subsequently,the validation of the differential expression of hub genes in the disease was performed and the regulatory network of transcription factors and hub genes was constructed.RESULTS Of 518 common DEGs were obtained by screening for functional analysis.Fifteen hub genes including aurora kinase B,cyclin B2,cell division cycle 20,cell division cycle associated 8,nucleolar and spindle associated protein 1,etc.,were further identified from DEGs using the“cytoHubba”plugin.Functional enrichment analysis of hub genes showed that these hub genes are associated with P53 signalling pathway regulation,cell cycle and other functions,and they may serve as potential molecular markers for COVID-19 and liver cancer.Finally,we selected 10 of the hub genes for in vitro expression validation in liver cancer cells.CONCLUSION Our study reveals a common pathogenesis of liver cancer and COVID-19.These common pathways and key genes may provide new ideas for further mechanistic studies.展开更多
Seed weight is a component of seed yield in rapeseed(Brassica napus L.).Although quantitative trait loci(QTL)for seed weight have been reported in rapeseed,only a few causal quantitative trait genes(QTGs)have been ide...Seed weight is a component of seed yield in rapeseed(Brassica napus L.).Although quantitative trait loci(QTL)for seed weight have been reported in rapeseed,only a few causal quantitative trait genes(QTGs)have been identified,resulting in a limitation in understanding of seed weight regulation.We constructed a gene coexpression network at the early seed developmental stage using transcripts of 20,408 genes in QTL intervals and 1017 rapeseed homologs of known genes from other species.Among the 10 modules in this gene coexpression network,modules 1 and 2 were core modules and contained genes involved in source–flow–sink processes such as synthesis and transportation of fatty acid and protein,and photosynthesis.A hub gene SERINE CARBOXYPEPTIDASE-LIKE 19(SCPL19)was identified by candidate gene association analysis in rapeseed and functionally investigated using Arabidopsis T-DNA mutant and overexpression lines.Our study demonstrates the power of gene coexpression analysis to prioritize candidate genes from large candidate QTG sets and enhances the understanding of molecular mechanism for seed weight at the early developmental stage in rapeseed.展开更多
Background:To provide a reference for the clinical development of drugs to suppress severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).Methods:Retrieving genes related to SARS-CoV-2 with Genecards database an...Background:To provide a reference for the clinical development of drugs to suppress severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).Methods:Retrieving genes related to SARS-CoV-2 with Genecards database and then importing the obtained gene data into the database of Database for Annotation,Visualization and Integrated Discovery(DAVID)(Version 6.8)to collect relevant information on pathways and genes.Genes enriched in the first 20 most significant pathways and genes with gene occurrence frequency≥6 were respectively imported into the STRING database to construct protein-protein interaction(PPI)network diagrams,and the two network diagrams were compared.Results:In the two network graphs,RELA,MAPK1,MAPK3,PIK3CA,PIK3R1,MAPK8,JAK1,STAT1,TNF,IL6,MAPK14,and IL1B ranked higher,and the occurrence frequency of the first 20 pathways was≥10.Conclusion:The pathogenesis of SARS-CoV-2 is associated with multiple pathways such as influenza A,TNF signaling pathway,chemokine signaling pathway,toll-like receptor signaling pathway,T cell receptor signaling pathway et al.RELA,MAPK1,MAPK3,PIK3CA,PIK3R1,MAPK8,JAK1,STAT1,TNF,IL6,MAPK14 and IL1B are closely related to SARS-CoV-2 and need further study.Gene interaction network and pathway analysis of diseaseassociated genes will help us to screen the key target genes of SARS-CoV-2 and provide a reference for the clinical development of effective drugs.展开更多
目的:构建中草药来源的目标微小RNA(microRNA,miR)在小鼠肺组织中的靶基因谱检测方法,利用该方法检测清肺排毒汤所含miR-320—靶基因谱及其生物学功能,为清肺排毒汤治疗病毒性肺炎的分子机制补充miR维度的数据支撑。方法:采用二代高通...目的:构建中草药来源的目标微小RNA(microRNA,miR)在小鼠肺组织中的靶基因谱检测方法,利用该方法检测清肺排毒汤所含miR-320—靶基因谱及其生物学功能,为清肺排毒汤治疗病毒性肺炎的分子机制补充miR维度的数据支撑。方法:采用二代高通量测序测定目标miR(miR-320)在清肺排毒汤中的表达情况,利用“结合态miR—靶基因抓取测序技术(capturing and sequencing of miRNA-target complex technology,CSCT)”初步检测其在小鼠肺组织中的靶基因谱,并采用Alphafold3验证检测结果,取其交集作为目标miR的靶基因谱;进而分析靶基因谱的功能,阐释清肺排毒汤通过miR-320在小鼠肺组织中的调控功能;此外,将检测结果与TargetScan的预测结果进行比对,验证本检测方法(CSCT+Alphafold3序贯检测法)的优势。结果:高通量测序结果表明清肺排毒汤中富含miR-320,其表达含量居前50位。miR-320在小鼠肺组织中可作用于26类靶基因,其中19类为已知基因(18类为mRNA以及1类为转录增强子),其主要通过miR经典作用模式识别靶基因,与26类靶基因具有良好的碱基互补性,最小自由能在-35.8~-21.8 kcal·mol^(-1)之间;Alphafold3预测的靶基因的iPTM和PTM之和最小值为1.1,位于高置信度区域,100%验证了CSCT的检测结果,据此确证26类靶基因为miR-320作用谱;与TargetScan相比,本研究构建的“CSCT+Alphafold3序贯检测法”对于靶基因谱的检测准确率更高。这些靶基因具有多种功能,主要富集于白介素介导的免疫信号通路,在抗原处理与提呈、免疫因子或细胞介导的细胞凋亡、淋巴细胞增殖与活化等生物学过程中发挥作用。结论:清肺排毒汤所含miR-320在小鼠肺组织内主要富集于免疫调节相关通路,这可能是清肺排毒汤治疗病毒性肺炎的miR分子机制之一;本研究构建的“CSCT+Alphafold3”法对于miR靶基因谱的检测具有较高的可靠性和准确性,可作为中药汤剂中miR—靶基因互作谱检测技术。展开更多
文摘BACKGROUND A growing number of clinical examples suggest that coronavirus disease 2019(COVID-19)appears to have an impact on the treatment of patients with liver cancer compared to the normal population,and the prevalence of COVID-19 is significantly higher in patients with liver cancer.However,this mechanism of action has not been clarified.Gene sets for COVID-19(GSE180226)and liver cancer(GSE87630)were obtained from the Gene Expression Omnibus database.After identifying the common differentially expressed genes(DEGs)of COVID-19 and liver cancer,functional enrichment analysis,protein-protein interaction network construction and scree-ning and analysis of hub genes were performed.Subsequently,the validation of the differential expression of hub genes in the disease was performed and the regulatory network of transcription factors and hub genes was constructed.RESULTS Of 518 common DEGs were obtained by screening for functional analysis.Fifteen hub genes including aurora kinase B,cyclin B2,cell division cycle 20,cell division cycle associated 8,nucleolar and spindle associated protein 1,etc.,were further identified from DEGs using the“cytoHubba”plugin.Functional enrichment analysis of hub genes showed that these hub genes are associated with P53 signalling pathway regulation,cell cycle and other functions,and they may serve as potential molecular markers for COVID-19 and liver cancer.Finally,we selected 10 of the hub genes for in vitro expression validation in liver cancer cells.CONCLUSION Our study reveals a common pathogenesis of liver cancer and COVID-19.These common pathways and key genes may provide new ideas for further mechanistic studies.
基金provided by the National Natural Science Foundation of China(32201776)the Natural Science Foundation of Chongqing(cstc2019jcyj-bsh X0055,cstc2019jcyj-zdxm X0012)。
文摘Seed weight is a component of seed yield in rapeseed(Brassica napus L.).Although quantitative trait loci(QTL)for seed weight have been reported in rapeseed,only a few causal quantitative trait genes(QTGs)have been identified,resulting in a limitation in understanding of seed weight regulation.We constructed a gene coexpression network at the early seed developmental stage using transcripts of 20,408 genes in QTL intervals and 1017 rapeseed homologs of known genes from other species.Among the 10 modules in this gene coexpression network,modules 1 and 2 were core modules and contained genes involved in source–flow–sink processes such as synthesis and transportation of fatty acid and protein,and photosynthesis.A hub gene SERINE CARBOXYPEPTIDASE-LIKE 19(SCPL19)was identified by candidate gene association analysis in rapeseed and functionally investigated using Arabidopsis T-DNA mutant and overexpression lines.Our study demonstrates the power of gene coexpression analysis to prioritize candidate genes from large candidate QTG sets and enhances the understanding of molecular mechanism for seed weight at the early developmental stage in rapeseed.
文摘Background:To provide a reference for the clinical development of drugs to suppress severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).Methods:Retrieving genes related to SARS-CoV-2 with Genecards database and then importing the obtained gene data into the database of Database for Annotation,Visualization and Integrated Discovery(DAVID)(Version 6.8)to collect relevant information on pathways and genes.Genes enriched in the first 20 most significant pathways and genes with gene occurrence frequency≥6 were respectively imported into the STRING database to construct protein-protein interaction(PPI)network diagrams,and the two network diagrams were compared.Results:In the two network graphs,RELA,MAPK1,MAPK3,PIK3CA,PIK3R1,MAPK8,JAK1,STAT1,TNF,IL6,MAPK14,and IL1B ranked higher,and the occurrence frequency of the first 20 pathways was≥10.Conclusion:The pathogenesis of SARS-CoV-2 is associated with multiple pathways such as influenza A,TNF signaling pathway,chemokine signaling pathway,toll-like receptor signaling pathway,T cell receptor signaling pathway et al.RELA,MAPK1,MAPK3,PIK3CA,PIK3R1,MAPK8,JAK1,STAT1,TNF,IL6,MAPK14 and IL1B are closely related to SARS-CoV-2 and need further study.Gene interaction network and pathway analysis of diseaseassociated genes will help us to screen the key target genes of SARS-CoV-2 and provide a reference for the clinical development of effective drugs.
文摘目的:构建中草药来源的目标微小RNA(microRNA,miR)在小鼠肺组织中的靶基因谱检测方法,利用该方法检测清肺排毒汤所含miR-320—靶基因谱及其生物学功能,为清肺排毒汤治疗病毒性肺炎的分子机制补充miR维度的数据支撑。方法:采用二代高通量测序测定目标miR(miR-320)在清肺排毒汤中的表达情况,利用“结合态miR—靶基因抓取测序技术(capturing and sequencing of miRNA-target complex technology,CSCT)”初步检测其在小鼠肺组织中的靶基因谱,并采用Alphafold3验证检测结果,取其交集作为目标miR的靶基因谱;进而分析靶基因谱的功能,阐释清肺排毒汤通过miR-320在小鼠肺组织中的调控功能;此外,将检测结果与TargetScan的预测结果进行比对,验证本检测方法(CSCT+Alphafold3序贯检测法)的优势。结果:高通量测序结果表明清肺排毒汤中富含miR-320,其表达含量居前50位。miR-320在小鼠肺组织中可作用于26类靶基因,其中19类为已知基因(18类为mRNA以及1类为转录增强子),其主要通过miR经典作用模式识别靶基因,与26类靶基因具有良好的碱基互补性,最小自由能在-35.8~-21.8 kcal·mol^(-1)之间;Alphafold3预测的靶基因的iPTM和PTM之和最小值为1.1,位于高置信度区域,100%验证了CSCT的检测结果,据此确证26类靶基因为miR-320作用谱;与TargetScan相比,本研究构建的“CSCT+Alphafold3序贯检测法”对于靶基因谱的检测准确率更高。这些靶基因具有多种功能,主要富集于白介素介导的免疫信号通路,在抗原处理与提呈、免疫因子或细胞介导的细胞凋亡、淋巴细胞增殖与活化等生物学过程中发挥作用。结论:清肺排毒汤所含miR-320在小鼠肺组织内主要富集于免疫调节相关通路,这可能是清肺排毒汤治疗病毒性肺炎的miR分子机制之一;本研究构建的“CSCT+Alphafold3”法对于miR靶基因谱的检测具有较高的可靠性和准确性,可作为中药汤剂中miR—靶基因互作谱检测技术。
