Sebastiscus marmoratus is one of the ideal fish species for offshore breeding,and temperature changes directly affect its physiological process.We performed whole-transcriptome sequencing of the liver tissues of S.mar...Sebastiscus marmoratus is one of the ideal fish species for offshore breeding,and temperature changes directly affect its physiological process.We performed whole-transcriptome sequencing of the liver tissues of S.marmoratus under heat stress(25℃),normal condition(20℃,the control),and cold stress(15℃).A total of 376 differentially expressed genes(DEGs),147 differentially expressed lncRNAs(DELs),and 40 differentially expressed miRNAs(DEMis)were detected under heat stress;59 DEGs,59 DELs,and 44 DEMis were detected under cold stress.Furthermore,a competing endogenous RNA regulatory network for the functional interaction of lncRNA-miRNA-mRNA was constructed,and GO and KEGG enrichment analyses showed that genes involved in maintaining homeostasis or adjusting to stress and stimulation were strongly activated during heat stress.Including heat-shock protein-related genes Hsp70,FKBP4,and Hspa4a regulated by dre-mir-205-5p;energy metabolism-related genes GCK,g6pca,and RFK regulated by dre-miR-205-5p,dre-miR-145-5p,novel_441,TCONS_00023692,and tcon_00095578;and immune-related genes SCAF,NLRC3,per1b,herc4,MafG,and KLHL29 regulated by dre-miR-456,novel_640,novel_163,TCONS_00079377,TCONS_00063590,and TCONS_000605708.Our findings provide new insights into the adaptation of S.marmoratus to acute temperature changes.展开更多
Background:Hepatocellular carcinoma(HCC)has a poor long-term prognosis.The competition of circular RNAs(circRNAs)with endogenous RNA is a novel tool for predicting HCC prognosis.Based on the alterations of circRNA reg...Background:Hepatocellular carcinoma(HCC)has a poor long-term prognosis.The competition of circular RNAs(circRNAs)with endogenous RNA is a novel tool for predicting HCC prognosis.Based on the alterations of circRNA regulatory networks,the analysis of gene modules related to HCC is feasible.Methods:Multiple expression datasets and RNA element targeting prediction tools were used to construct a circRNA-microRNA-mRNA network in HCC.Gene function,pathway,and protein interaction analyses were performed for the differentially expressed genes(DEGs)in this regulatory network.In the proteinprotein interaction network,hub genes were identified and subjected to regression analysis,producing an optimized four-gene signature for prognostic risk stratification in HCC patients.Anti-HCC drugs were excavated by assessing the DEGs between the low-and high-risk groups.A circRNA-microRNA-hub gene subnetwork was constructed,in which three hallmark genes,KIF4A,CCNA2,and PBK,were subjected to functional enrichment analysis.Results:A four-gene signature(KIF4A,CCNA2,PBK,and ZWINT)that effectively estimated the overall survival and aided in prognostic risk assessment in the The Cancer Genome Atlas(TCGA)cohort and International Cancer Genome Consortium(ICGC)cohort was developed.CDK inhibitors,PI3K inhibitors,HDAC inhibitors,and EGFR inhibitors were predicted as four potential mechanisms of drug action(MOA)in high-risk HCC patients.Subsequent analysis has revealed that PBK,CCNA2,and KIF4A play a crucial role in regulating the tumor microenvironment by promoting immune cell invasion,regulating microsatellite instability(MSI),and exerting an impact on HCC progression.Conclusions:The present study highlights the role of the circRNA-related regulatory network,identifies a four-gene prognostic signature and biomarkers,and further identifies novel therapy for HCC.展开更多
基金Supported by the Zhejiang Provincial Natural Science Foundation of China(No.LR21D060003)the National Key Research and Development Program of China(No.2017YFA0604904)。
文摘Sebastiscus marmoratus is one of the ideal fish species for offshore breeding,and temperature changes directly affect its physiological process.We performed whole-transcriptome sequencing of the liver tissues of S.marmoratus under heat stress(25℃),normal condition(20℃,the control),and cold stress(15℃).A total of 376 differentially expressed genes(DEGs),147 differentially expressed lncRNAs(DELs),and 40 differentially expressed miRNAs(DEMis)were detected under heat stress;59 DEGs,59 DELs,and 44 DEMis were detected under cold stress.Furthermore,a competing endogenous RNA regulatory network for the functional interaction of lncRNA-miRNA-mRNA was constructed,and GO and KEGG enrichment analyses showed that genes involved in maintaining homeostasis or adjusting to stress and stimulation were strongly activated during heat stress.Including heat-shock protein-related genes Hsp70,FKBP4,and Hspa4a regulated by dre-mir-205-5p;energy metabolism-related genes GCK,g6pca,and RFK regulated by dre-miR-205-5p,dre-miR-145-5p,novel_441,TCONS_00023692,and tcon_00095578;and immune-related genes SCAF,NLRC3,per1b,herc4,MafG,and KLHL29 regulated by dre-miR-456,novel_640,novel_163,TCONS_00079377,TCONS_00063590,and TCONS_000605708.Our findings provide new insights into the adaptation of S.marmoratus to acute temperature changes.
基金This study was supported by grants from the High-level Preresearch Program of Zhejiang Shuren University 2019(KXJ121860)Zhejiang Provincial Natural Science Foundation of China(LQ20H190004)。
文摘Background:Hepatocellular carcinoma(HCC)has a poor long-term prognosis.The competition of circular RNAs(circRNAs)with endogenous RNA is a novel tool for predicting HCC prognosis.Based on the alterations of circRNA regulatory networks,the analysis of gene modules related to HCC is feasible.Methods:Multiple expression datasets and RNA element targeting prediction tools were used to construct a circRNA-microRNA-mRNA network in HCC.Gene function,pathway,and protein interaction analyses were performed for the differentially expressed genes(DEGs)in this regulatory network.In the proteinprotein interaction network,hub genes were identified and subjected to regression analysis,producing an optimized four-gene signature for prognostic risk stratification in HCC patients.Anti-HCC drugs were excavated by assessing the DEGs between the low-and high-risk groups.A circRNA-microRNA-hub gene subnetwork was constructed,in which three hallmark genes,KIF4A,CCNA2,and PBK,were subjected to functional enrichment analysis.Results:A four-gene signature(KIF4A,CCNA2,PBK,and ZWINT)that effectively estimated the overall survival and aided in prognostic risk assessment in the The Cancer Genome Atlas(TCGA)cohort and International Cancer Genome Consortium(ICGC)cohort was developed.CDK inhibitors,PI3K inhibitors,HDAC inhibitors,and EGFR inhibitors were predicted as four potential mechanisms of drug action(MOA)in high-risk HCC patients.Subsequent analysis has revealed that PBK,CCNA2,and KIF4A play a crucial role in regulating the tumor microenvironment by promoting immune cell invasion,regulating microsatellite instability(MSI),and exerting an impact on HCC progression.Conclusions:The present study highlights the role of the circRNA-related regulatory network,identifies a four-gene prognostic signature and biomarkers,and further identifies novel therapy for HCC.
