BACKGROUND The objectives of this study were to identify hub genes and biological pathways involved in lung adenocarcinoma(LUAD)via bioinformatics analysis,and investigate potential therapeutic targets.AIM To determin...BACKGROUND The objectives of this study were to identify hub genes and biological pathways involved in lung adenocarcinoma(LUAD)via bioinformatics analysis,and investigate potential therapeutic targets.AIM To determine reliable prognostic biomarkers for early diagnosis and treatment of LUAD.METHODS To identify potential therapeutic targets for LUAD,two microarray datasets derived from the Gene Expression Omnibus(GEO)database were analyzed,GSE3116959 and GSE118370.Differentially expressed genes(DEGs)in LUAD and normal tissues were identified using the GEO2R tool.The Hiplot database was then used to generate a volcanic map of the DEGs.Weighted gene co-expression network analysis was conducted to cluster the genes in GSE116959 and GSE-118370 into different modules,and identify immune genes shared between them.A protein-protein interaction network was established using the Search Tool for the Retrieval of Interacting Genes database,then the CytoNCA and CytoHubba components of Cytoscape software were used to visualize the genes.Hub genes with high scores and co-expression were identified,and the Database for Annotation,Visualization and Integrated Discovery was used to perform enrichment analysis of these genes.The diagnostic and prognostic values of the hub genes were calculated using receiver operating characteristic curves and Kaplan-Meier survival analysis,and gene-set enrichment analysis was conducted.The University of Alabama at Birmingham Cancer data analysis portal was used to analyze relationships between the hub genes and normal specimens,as well as their expression during tumor progression.Lastly,validation of protein expression was conducted on the identified hub genes via the Human Protein Atlas database.RESULTS Three hub genes with high connectivity were identified;cellular retinoic acid binding protein 2(CRABP2),matrix metallopeptidase 12(MMP12),and DNA topoisomerase II alpha(TOP2A).High expression of these genes was associated with a poor LUAD prognosis,and the genes exhibited high diagnostic value.CONCLUSION Expression levels of CRABP2,MMP12,and TOP2A in LUAD were higher than those in normal lung tissue.This observation has diagnostic value,and is linked to poor LUAD prognosis.These genes may be biomarkers and therapeutic targets in LUAD,but further research is warranted to investigate their usefulness in these respects.展开更多
Background Sterol regulatory element binding protein （SREBP）-2 plays a key role in lipid homeostasis by stimulating gene expression of cholesterol biosynthetic pathways. The insulin-like growth factor binding prote...Background Sterol regulatory element binding protein （SREBP）-2 plays a key role in lipid homeostasis by stimulating gene expression of cholesterol biosynthetic pathways. The insulin-like growth factor binding protein （IGFBP） family regulates growth and metabolism, especially bone cell metabolism, and correlates with osteonecrosis. However, association of their gene polymorphisms with risk of avascular necrosis of the femoral head （ANFH） has rarely been reported. We determined whether SREBP-2 and IGFBP-3 gene polymorphisms were associated with increased ANFH risk in the Chinese population. Methods Two single nucleotide polymorphisms of SREBP2 gene, rs2267439 and rs2267443, and one of IGFBP-3 gene, rs2453839, were selected and genotyped in 49 ANFH patients and 42 control individuals by direct sequencing assay. Results The frequencies of rs2267439 TT and rs2267443 GA of SREBP2 and rs2453839 TT and CT of IGFBP-3 in the ANFH group showed increased and decreased tendencies （against normal control group）, respectively. Interaction analysis of genes revealed that the frequency of carrying rs2267439 TT and rs2267443 GA genotypes of SREBF-2 in ANFH patients was significantly higher than in the control group （P 〈0.05）. Association analysis between polymorphisms and clinical phenotype demonstrated that the disease course in ANFH patients with the rs2453839 TT genotype of IGFBP-3 was significantly shorter than that of CT＋CC carriers （P 〈0.01）. CT＋CC genotype frequency in patients with stage Ill/IV bilateral hip lesions was significantly higher than in those with stage Ill/IV unilateral lesions and stage II/111 bilateral lesions （P 〈0.05-0.02）. Conclusions Our results suggested that interaction of SREBP-2 gene polymorphisms and the relationship between the polymorphisms and clinical phenotype of IGFBP-3 were closely related to increased ANFH risk in the Chinese population. The most significant finding was that the CT＋CC genotype carriers of IGFBP-3 rs2453839 were highly associated with the development of ANFH.展开更多
Rett syndrome(RTT),an X-linked dominant neurodevelopmental disorder characterized by regression of language,stereotype hand movement and loss of purposeful hand use,is primarily caused by mutation of menthyl-CpG-bindi...Rett syndrome(RTT),an X-linked dominant neurodevelopmental disorder characterized by regression of language,stereotype hand movement and loss of purposeful hand use,is primarily caused by mutation of menthyl-CpG-binding protein 2(MECP2).The 76 kb human MECP2 is characterized by three salient features: a very large intron 2(60 kb),an 8.5 kb 3′-UTR with highly conserved regions and different polyadenylation sites,and a 40 kb intergenic region separating MECP2 from the nearest upstream gene.There are two isoforms of MeCP2,MeCP2e1 and MeCP2e2.The differences between the two isoforms,the function of the 3′-UTR and the long-range cis-regulatory sequences in the intergenic region were extensively studied.In contrast to initial report,recent studies show that MeCP2 binds not only to methylated promoters and silence transcription,but also to the sites outside of genes containing only a few of CpG islands.Furthermore,MeCP2 can function as both an activator and a repressor of transcription.Abstract:SUMM ARY Rett syndrome(RTT),an X-linked dom inant neurodevelopmental d isorder characterized by regression of language,stereotype hand movement and loss of purposeful hand use,is primarily caused by mutation of menthyl-CpG-bind ing protein 2(MECP2).The 76 kb humanMECP2is characterized by three salient features: a very large intron 2(60 kb),an 8.5 kb 3′-UTR with highly conserved regions and d ifferent polyadenylation sites,and a 40 kb intergenic region separatingMECP2from the nearest up-stream gene.There are two isoforms ofMeCP2,MeCP2e1 and MeCP2e2.The d ifferences between the two isoforms,the function of the 3′-UTR and the long-range cis-regulatory sequences in the intergenic re-gion were extensively stud ied.In contrast to initial report,recent stud ies show thatMeCP2 binds not only to methylated promoters and silence transcription,but also to the sites outside of genes containing only a few of CpG islands.Furthermore,MeCP2 can function as both an activator and a repressor of transcrip-tion.展开更多
文摘BACKGROUND The objectives of this study were to identify hub genes and biological pathways involved in lung adenocarcinoma(LUAD)via bioinformatics analysis,and investigate potential therapeutic targets.AIM To determine reliable prognostic biomarkers for early diagnosis and treatment of LUAD.METHODS To identify potential therapeutic targets for LUAD,two microarray datasets derived from the Gene Expression Omnibus(GEO)database were analyzed,GSE3116959 and GSE118370.Differentially expressed genes(DEGs)in LUAD and normal tissues were identified using the GEO2R tool.The Hiplot database was then used to generate a volcanic map of the DEGs.Weighted gene co-expression network analysis was conducted to cluster the genes in GSE116959 and GSE-118370 into different modules,and identify immune genes shared between them.A protein-protein interaction network was established using the Search Tool for the Retrieval of Interacting Genes database,then the CytoNCA and CytoHubba components of Cytoscape software were used to visualize the genes.Hub genes with high scores and co-expression were identified,and the Database for Annotation,Visualization and Integrated Discovery was used to perform enrichment analysis of these genes.The diagnostic and prognostic values of the hub genes were calculated using receiver operating characteristic curves and Kaplan-Meier survival analysis,and gene-set enrichment analysis was conducted.The University of Alabama at Birmingham Cancer data analysis portal was used to analyze relationships between the hub genes and normal specimens,as well as their expression during tumor progression.Lastly,validation of protein expression was conducted on the identified hub genes via the Human Protein Atlas database.RESULTS Three hub genes with high connectivity were identified;cellular retinoic acid binding protein 2(CRABP2),matrix metallopeptidase 12(MMP12),and DNA topoisomerase II alpha(TOP2A).High expression of these genes was associated with a poor LUAD prognosis,and the genes exhibited high diagnostic value.CONCLUSION Expression levels of CRABP2,MMP12,and TOP2A in LUAD were higher than those in normal lung tissue.This observation has diagnostic value,and is linked to poor LUAD prognosis.These genes may be biomarkers and therapeutic targets in LUAD,but further research is warranted to investigate their usefulness in these respects.
文摘Background Sterol regulatory element binding protein （SREBP）-2 plays a key role in lipid homeostasis by stimulating gene expression of cholesterol biosynthetic pathways. The insulin-like growth factor binding protein （IGFBP） family regulates growth and metabolism, especially bone cell metabolism, and correlates with osteonecrosis. However, association of their gene polymorphisms with risk of avascular necrosis of the femoral head （ANFH） has rarely been reported. We determined whether SREBP-2 and IGFBP-3 gene polymorphisms were associated with increased ANFH risk in the Chinese population. Methods Two single nucleotide polymorphisms of SREBP2 gene, rs2267439 and rs2267443, and one of IGFBP-3 gene, rs2453839, were selected and genotyped in 49 ANFH patients and 42 control individuals by direct sequencing assay. Results The frequencies of rs2267439 TT and rs2267443 GA of SREBP2 and rs2453839 TT and CT of IGFBP-3 in the ANFH group showed increased and decreased tendencies （against normal control group）, respectively. Interaction analysis of genes revealed that the frequency of carrying rs2267439 TT and rs2267443 GA genotypes of SREBF-2 in ANFH patients was significantly higher than in the control group （P 〈0.05）. Association analysis between polymorphisms and clinical phenotype demonstrated that the disease course in ANFH patients with the rs2453839 TT genotype of IGFBP-3 was significantly shorter than that of CT＋CC carriers （P 〈0.01）. CT＋CC genotype frequency in patients with stage Ill/IV bilateral hip lesions was significantly higher than in those with stage Ill/IV unilateral lesions and stage II/111 bilateral lesions （P 〈0.05-0.02）. Conclusions Our results suggested that interaction of SREBP-2 gene polymorphisms and the relationship between the polymorphisms and clinical phenotype of IGFBP-3 were closely related to increased ANFH risk in the Chinese population. The most significant finding was that the CT＋CC genotype carriers of IGFBP-3 rs2453839 were highly associated with the development of ANFH.
文摘Rett syndrome(RTT),an X-linked dominant neurodevelopmental disorder characterized by regression of language,stereotype hand movement and loss of purposeful hand use,is primarily caused by mutation of menthyl-CpG-binding protein 2(MECP2).The 76 kb human MECP2 is characterized by three salient features: a very large intron 2(60 kb),an 8.5 kb 3′-UTR with highly conserved regions and different polyadenylation sites,and a 40 kb intergenic region separating MECP2 from the nearest upstream gene.There are two isoforms of MeCP2,MeCP2e1 and MeCP2e2.The differences between the two isoforms,the function of the 3′-UTR and the long-range cis-regulatory sequences in the intergenic region were extensively studied.In contrast to initial report,recent studies show that MeCP2 binds not only to methylated promoters and silence transcription,but also to the sites outside of genes containing only a few of CpG islands.Furthermore,MeCP2 can function as both an activator and a repressor of transcription.Abstract:SUMM ARY Rett syndrome(RTT),an X-linked dom inant neurodevelopmental d isorder characterized by regression of language,stereotype hand movement and loss of purposeful hand use,is primarily caused by mutation of menthyl-CpG-bind ing protein 2(MECP2).The 76 kb humanMECP2is characterized by three salient features: a very large intron 2(60 kb),an 8.5 kb 3′-UTR with highly conserved regions and d ifferent polyadenylation sites,and a 40 kb intergenic region separatingMECP2from the nearest up-stream gene.There are two isoforms ofMeCP2,MeCP2e1 and MeCP2e2.The d ifferences between the two isoforms,the function of the 3′-UTR and the long-range cis-regulatory sequences in the intergenic re-gion were extensively stud ied.In contrast to initial report,recent stud ies show thatMeCP2 binds not only to methylated promoters and silence transcription,but also to the sites outside of genes containing only a few of CpG islands.Furthermore,MeCP2 can function as both an activator and a repressor of transcrip-tion.
