The Establishment And Study Of OSF Related Gene Differential Expression Profile

Chapterâ… The Establishment and Gene Ontology Analysis of OSFRelated Gene Differential Expression ProfileObjective: (1) To establish the oral submucous fibrosis(OSF) relatedgene differentially Expression profile by human genome-wideoligonucleotide chips;(2)Screening the OSF related gene groups andfurther discuss their role in OSF pathogenisis by Gene Ontology (GO)analysis, so as to provide the primary experimental data for selecte theOSF related gene.Methods:Extracted the total RNA from OSF buccal mucosas andnormal control were reversely transcribed to cDNA with theincorporation of fluorescend-labeled to prepare the hybridizationprobes, and then followed by a hybridization with human genome-wideoligonucleotide chips with 21571 genes.The signals gathered afterhybridization were detected by scanner and analyzed by computer toestablish an OSF related gene differential expression profile for GOanalysis,to screen the OSF related gene group finally.Result:(1)2369 differential expression genes,which got involved inseveral functional gene groups,were collected from all stages of OSF, It revealed a relatively small P-value with GO analysis in cytoskeletalprotein gene group, extracellular matrix and its metabolic related genegroup and immunity related gene group, etc.(2)The expression of collagengene in the early stage of OSF was resembled TGFB1 in patterns,bothhighly-folded increased.(3)TIMP1 gene,TIMP3 gene, PAI-1 gene, whichbelong to the extracellular matrix metabolic related gene group,weredemonstrated significant up-regulated in the intermediate OSF andadvanced stages.OSF.(4)As for immunity related gene group, adifferential expression could be observed among majority of cellimmuno-genes.Conclusions(1)OSF is the common consequence of multiple genes.Several functional gene groups participate and play vital roles in the OSFpathogenisis,such as cytoskeletal protein gene group,extracellular matrixand its metabolic related gene group, immunity related genegroup;(2)Improvement of the collage synthesis is an early stage molecularevent in OSF. And TGFB1 gene is the very critical regulatory factorwhich response to the up-regulated of collagen gene in the early stage,and no doubt to be an important candidate gene;(3)A molecular basis inthe decline of ECM degradation do exist in the intermediate andadvanced stages of OSF. The reason for the attenuation of ECMdegredation is because of the inhibition of associate protein resolvasesdue to the reinforcement gene expression of TIMP1,TIMP3,PAI1,uPAR etc.(4)The immunological factor is of grate importance in thedevelopment of OSF,for which the differential expression of cellimmunity related gene is one of the critical mechanisms leading to OSF. Chapterâ…¡Pathway Analysis of OSF Related Genes DifferentialExpression profileObjective:To make an pathway analysis about OSF relateddifferential expression genes,based on the following three major genedatabanks: BIOCARTA,GENMAPP,KEGG,explore the possiblepathway of OSF related differential expression genes further.Methods: Rely on the OSF related gene differential expressionprofile which had already established, data were collected and preparedunder the requirement of pathway analysis,then visited the website ofwww.biorg.org, A pathway analysis was carried out depend on the threegene databanks: BIOCARTA,GENMAPP,KEGG.Results:(1) 27 gene interaction pathways with significance werecollected in OSF related differential expression genes, in which 19 camefrom BIOCARTA,7 came from KEGG,1 from GENMAPP.(2)8differential expression genes were collected by the pathway ofMetabolism of xenobiotics by cytochrome P450,7 of which revealed adown-regulation in every stage of OSF.(3)15 genes came from TGF-betasignaling pathway, in which the positive regulatory factors such asTGFB1 gene,Smad2 gene,Smad3 gene,ZFYVE9 gene increased in the early stage of OSF, while the negative regulatory factors like LTBP1 geneshowed an up-regulation in the advanced stage of OSF.(4)13 genes camefrom Erk1/Erk2 Mapk Signaling pathway, of which the critical regulatoryfactor: ERK1/ERK2 gene rised in the early stage, and declined in themoderate and advanced stages.(5)14 genes came from Wnt signalingpathway, those genes showed distinct differential expression in differentstages of OSF.Conclusions:(1)Due to the common effects of various genepathways,the pathways of OSF related differential expression genes arereally complex, of which Metabolism of xenobiotics by cytochrome P450pathway, TGF-beta signaling pathway, ERK Signaling pathway and Wntsignaling pathway have intimate relations with OSF.(2)The geneexpression of the pathway of Metabolism of xenobiotics by cytochromeP450 are down-regulated, related to OSF pathogenisis;(3)TGF-betasignaling pathway and ERK Signaling pathway were activated in theearly stage of OSF, which may join in the cooperation roles oftranscriptional control of collagen gene in the early stage of OSF;(4) Anabnormal molecular basis exist in Wnt signaling pathway, which could beinvolved in the malignant potentiality of OSF. Chapterâ…¢The Screening and Study of OSF Related GeneObjective:To select and identify the candidate gene on the basis ofdifferentially expression gene profile, and further discuss their roles inOSF pathogenesis to provide experimental date so as to explore themechanism of oral submucous fibrosis(OSF).Methods:The candidate gene were selected by bioinformation onthe basis of differentially expression gene profile related OSEThe totalRNA, from 28 cases OSF and 10 control groups,were extracted. ThemRNA expression of selected candidate gene in OSF buccal mucosas andcontrol normal buccal mucosas were evaluated by reverse transcriptionpolymerase chain reaction(RT-PCR).Results:Six genes, including TGFB1 gene,S100A7 gene,LOXL1gene,IL6 gene,CXCL9 gene,CCR2 gene,were selected and tested. ThemRNA expression patterns of selected candidate gene were similar tothose in differentially expression gene profile, and highly-foldedexpression.Conclusions: It is feasible to establish the OSF-related genedifferentially expression profile by human genome-wide oligonucleotide chips, and also reliable to select OSF-related gene by gene differentiallyexpression profile. The gene,such TGFB1 gene,S100A7 gene,LOXL1gene,IL6 gene,CXCL9 gene,CCR2 gene,are important OSF-relatedgene,due to which are highly-folded expression in OSF.