The Study Of Gene Expression For Psoriasis Based On Transcriptom Sequencing

Background: Psoriasis(Ps)is a common chronic inflammatory skin disease,which is characterized by red,scaly skin patches with clear borderline.Given its uncomfortable appearance and varying degrees of itching,psoriasis seriously affect the quality of life of patients,conferring both a physical and psychological burden.Histological analysis reveals patterns of abnormal epidermal hyperplasia and differentiation.Due to geographical location and ethnic differences,the prevalence of psoriasis is slightly different,from 0.1% to 11.4%,affecting 100 million people in the world.Psoriasis is a serious global problem.The prevalence of psoriasis in China was 0.47%,and there was a trend of increasing year by year.The pathogenesis of psoriasis is more complex,affected by genetic and environmental factors,leading to psoriasis-like lesions occur under the interaction of immune cells and keratinocytes.In order to better understand the molecular mechanism of psoriasis,Genome-wide association studies(GWAS)and genome-wide expression profile studies have been developed in different populations.Through GWAS,more than 70 susceptibility loci were found to be associated with psoriasis,revealing the pathogenesis from genetic variation in the genome to a certain extent.Susceptibility loci identified by GWAS mostly locate in non-coding areas,however,how to interpret the regulatory role to gene expression has been the focus of attention.Gene expression profiling based on DNA microarry can analyze the m RNA expression abundance of cells or tissues under a certain condition,and study the expression level of genes at the transcriptional level with high throughput.Many genes were found to be differentially expressed in psoriasis by whole genome expression profiling studies.Because of the low coverage,however,it is difficult to detect low abundance of gene expression using DNA microarry.With the development of next generation sequencing technology,transcriptome sequencing can accurately detect gene expression level,complementing the gene expression profiling based on microarray.However,there are few studies on transcriptome sequencing of psoriasis.Therefore,it is necessary to carry out the study of gene expression based on transcriptome sequencing,and further reveal the gene expression profile of psoriasis in Chinese population.Identification of the differentially expressed genes in psoriasis lesions will shed light on the pathogenesis of psoriasis from the functional genome level,and further advance the molecular diagnosis of disease,drug treatment,prevention and new drug development.Objective To characterize the gene expression profiles of psoriatic skin(PP),non-lesional skin(PN)from psoriasis patients and normal skin(NN)from healthy individuals,and to identify the differentially expressed genes in PP by comparison analysis.Method: we performed RNA-seq analysis of psoriasis on 20 involved PP,20 PN,and 20 NN skin biopsies from Chinese individuals.The data were subjected to strict quality control and the expression of all genes in the samples was measured.The overall gene expression profiles of the three groups were analyzed through the principal component analysis and hierarchical clustering.The differentially expressed genes were identified in PP vs.NN,PP vs.PN and PN vs.NN with the statistical significance threshold at false discovery rate(FDR)< 0.05 and a fold change ≥ 2 or ≤ 0.5(|log2FC| ≥ 1)in the comparison analysis.We performed the hierarchical clustering analysis and bioinformatic analysis based on the differentially expressed genes in PP that can distinguish PN and NN.Results: Analyses of the expression level of all the samples showed that PP,PN and NN had different expression profiles,however,there was a large overlap between PN and NN,indicating that there was a certain degree of similarity between these two group of samples.PP was significantly deviated from PN and NN,indicating that PP had a significantly different gene expression profile compared with the other two groups of samples.We found 1,160 differentially expressed genes between PP and NN,of which,473 genes were significantly up-regulated while 687 ones were down-regulated in PP compared to NN.1,495 genes were differentially expressed in PP versus PN.997 of which were overlapped with the findings discovered from PP versus NN comparison.419 genes were up-regulated and 578 genes were down-regulated.Cluster analysis showed that 997 differentially expressed genes could significantly differentiate PP from PN samples,and PN and NN samples were clustered into one class,further suggesting that PN and NN had a similar gene expression profile.Comparing of PN and NN,we found that only 33 genes showed a significant difference in gene expression,suggesting that PN and NN skin,consistent with the above results,was similar with each other.Biological process enrichment analysis and pathway analysis indicated that up-regulated genes involved biological pathways as follows: response to physical stimulation(stress,trauma),biological stimulation(bacteria,viruses)and other stimulation(chemistry,drugs,etc.),immune response and immune system processes,cell division,differentiation and regulation of keratinocytes.Down-regulated genes were significantly enriched in tissue and organ development,cell differentiation and development,triglyceride transport and fatty acid metabolism.Conclusion: Through the study of transcriptome sequencing on psoriasis,we found that PP has a different gene expression profile compared with PN and NN skin,and PN and NN samples have a very similar gene expression profile,which provide a reference for the study of subsequent gene expression.A number of differentially expressed genes were found to be related with psoriasis by case-control analysis,enriched in biological pathways associated with the pathogenesis of psoriasis,and explained to some extent other comorbid diseases associated with psoriasis,such as metabolic diseases,cardiovascular diseases and other immune diseases.