整合基因組學(xué)研究發(fā)現(xiàn)銀屑病甲基化標(biāo)記和遺傳調(diào)控位點(diǎn)
發(fā)布時間：2018-07-16 15:52
【摘要】：銀屑病是一類以界限清晰的紅斑、銀色鱗屑為主要表現(xiàn)的慢性免疫性皮膚病。因地理位置和種族差異不同,在世界范圍內(nèi)患病率差別較大,約為0.1-4%�？傮w而言,高加索人群患病率較亞洲人群高。我國銀屑病患病率約為0.123%,患者總數(shù)將近1000萬例,其分布趨勢為城市高于農(nóng)村,北方高于南方,男性高于女性。銀屑病發(fā)病機(jī)制不清,普遍認(rèn)為是遺傳和環(huán)境因素共同作用的結(jié)果。既往研究顯示其遺傳度約為60-90%,然而當(dāng)前基于DNA序列變異的研究僅能解釋13%的疾病發(fā)生,提示表觀學(xué),環(huán)境因素,基因-基因相互作用等可能與疾病相關(guān)。以DNA甲基化和組蛋白修飾為主的表觀遺傳學(xué)是人類基因組學(xué)中重要的調(diào)控因素,甲基化能夠解釋部分DNA序列變異以外的疾病遺傳度。DNA甲基化通過抑制轉(zhuǎn)錄因子與DNA序列的結(jié)合或者募集甲基化結(jié)合蛋白的方式控制基因的表達(dá)水平。甲基化結(jié)合蛋白與其他調(diào)控機(jī)制結(jié)合,如組蛋白乙�；蛉ヒ阴；�,誘發(fā)染色體構(gòu)象變化并控制基因的表達(dá)。DNA甲基化研究已在腫瘤等多種疾病和生物學(xué)通路中被廣泛研究�，F(xiàn)有銀屑病的DNA甲基化研究在兩個層面展開,即針對候選基因啟動子和無偏倚的全基因水平。候選基因研究如p15和p21蛋白啟動子基因在銀屑病組織中甲基化過低；對比特應(yīng)性皮炎患者和正常個體,發(fā)現(xiàn)SHP-1(PTPN6)基因啟動子完全脫甲基化。全基因組甲基化分析病例對照研究發(fā)現(xiàn)一批與免疫、表皮分化復(fù)合體等疾病相關(guān)基因。然而既往研究存在樣本量偏小,基因組覆蓋度偏低,基因表達(dá)數(shù)據(jù)不完整等情況使得大量潛在位點(diǎn)或易感基因沒有被發(fā)現(xiàn)。因此開展大范圍的銀屑病全基因組甲基化研究,整合高精度RNA表達(dá)數(shù)據(jù)將有助于發(fā)現(xiàn)疾病風(fēng)險(xiǎn)基因。目的：在全基因組范圍內(nèi)搜尋銀屑病相關(guān)DNA甲基化位點(diǎn),整合轉(zhuǎn)錄組表達(dá)數(shù)據(jù),發(fā)現(xiàn)疾病風(fēng)險(xiǎn)易感基因。方法：采用IlluminaHuman450K芯片對114例患者皮損,41例非皮損,62例對照個體的皮膚組織DNA分析近450000個位點(diǎn)的CpG甲基化水平。位點(diǎn)甲基化差異分析采用Wilcox中位數(shù)秩和檢驗(yàn)分析,并經(jīng)Benjamini-Hochberg法矯正多重檢驗(yàn)。Spearman相關(guān)性檢驗(yàn)分析甲基化與基因表達(dá)相互關(guān)系。sequenom質(zhì)譜系統(tǒng)驗(yàn)證差異性甲基化位點(diǎn)。結(jié)果：通過分析皮損/(非皮損+對照)DNA的甲基化高低,發(fā)現(xiàn)286個差異性甲基化位點(diǎn),分布于188個基因。整合全基因組轉(zhuǎn)錄組數(shù)據(jù),發(fā)現(xiàn)36個基因表達(dá)與甲基化相關(guān),包括AIM2, TGFBR3, PHYHD1, PHOB, FOLR1, ZC3H12A, LYPD1和ZBP1等。1.比對41對病人皮損和非皮損發(fā)現(xiàn)1638個差異性位點(diǎn),在皮損組織中過高和過低甲基化位點(diǎn)分別為954和684個。2.比對73例病人皮損和62個正常個體發(fā)現(xiàn)434個差異性甲基化位點(diǎn)。同時比較皮損/(非皮損+對照),發(fā)現(xiàn)286個差異甲基化位點(diǎn),位點(diǎn)分布于188個基因上。3.分析286個位點(diǎn)在基因組中的分布情況,發(fā)現(xiàn)位點(diǎn)在特定CpG區(qū)域富集。近60%位點(diǎn)位于開放區(qū)域(Open Sea),42.4%位點(diǎn)位于基因體內(nèi)(Gene body)4.DAVID基因功能注釋顯示,188個顯著性基因中,顯示甲基化過高的基因在蛋白磷酸化、RNA轉(zhuǎn)錄調(diào)節(jié)等方面富集。而低甲基化基因無明顯富集(P0.05)5.相比既往歐美報(bào)道的1108個差異性位點(diǎn),通過IlluminaHuman450K可獲得776個位點(diǎn)數(shù)據(jù),其中456個達(dá)到顯著性水平,較隨機(jī)出現(xiàn)的可能性有顯著差異(Chi-square=276.5,P 2.2×10-16)。比較兩項(xiàng)研究,456個位點(diǎn)中僅1個甲基化位點(diǎn)差異方向相反。6.通過轉(zhuǎn)錄組測序可分析188個基因當(dāng)中178個基因的表達(dá)數(shù)據(jù)。發(fā)現(xiàn)19個(13.3%)DNA甲基化升高伴基因表達(dá)降低,16個(9.4%)甲基化降低伴基因表達(dá)升高。提示約有五分之一DNA甲基化差異與基因表達(dá)相關(guān)。呈現(xiàn)甲基化表達(dá)負(fù)相關(guān)的基因包括：AIM2, TGFBR3, PHYHD1, PHOB, FOLRl, ZC3H12A, LYPD1和ZBP1等。7.構(gòu)建因果關(guān)系模型分析遺傳標(biāo)記(SNP),甲基化,疾病狀態(tài)關(guān)系,發(fā)現(xiàn)3個CpG位點(diǎn)為潛在調(diào)節(jié)SNP作用于疾病的調(diào)控點(diǎn)。結(jié)論：通過非配對病例對照分析發(fā)現(xiàn)286個銀屑病差異性甲基化位點(diǎn),對應(yīng)于188個基因。整合全基因組轉(zhuǎn)錄組表達(dá)數(shù)據(jù),發(fā)現(xiàn)36個DNA甲基化/基因表達(dá)呈現(xiàn)負(fù)相關(guān),包括AIM2, TGFBR3, PHYHD1, PHOB, FOLR1, ZC3H12A, LYPD1和ZBP1等,該批基因可能與銀屑病發(fā)病機(jī)制相關(guān)；通過CIT因果分析發(fā)現(xiàn)C1orf106, DMBXl和SIK3基因可能在調(diào)節(jié)遺傳變異位點(diǎn)對銀屑病的過程中發(fā)揮作用。
[Abstract]:Psoriasis is a class of chronic immune dermatosis with distinct red spots and silver scales. The prevalence rate varies widely in the world because of different geographical location and racial differences. The prevalence rate of Caucasus in the Caucasus is higher than that of the Asian population. The prevalence rate of psoriasis in China is about 0.123%, and the total number of patients is nearly 0.123%. 10 million cases, its distribution trend is that the city is higher than the countryside, the north is higher than the south, and the male is higher than the female. The pathogenesis of psoriasis is not clear, and it is generally considered to be the result of the combination of genetic and environmental factors. The previous study shows that its heritability is about 60-90%, however, the current study based on DNA sequence variation can only explain the occurrence of 13% of the disease. Observation, environmental factors, gene gene interaction, etc. may be related to disease. Epigenetics, based on DNA methylation and histone modification, is an important regulatory factor in human genomics. Methylation can explain the combination of.DNA methylation of diseases other than partial DNA sequence variation by inhibiting the binding of transcription factors to DNA sequences. Or collect methylation binding proteins to control the level of gene expression. Methylated binding proteins are combined with other regulatory mechanisms, such as histone acetylation or deacetylation, induced chromosomal conformation changes and the control of gene expression.DNA methylation has been widely studied in a variety of diseases and biological pathways. The DNA methylation study of the chip disease was carried out at two levels, namely, the candidate gene promoter and the total gene level without bias. Candidate gene studies, such as the low methylation of the p15 and p21 promoter genes in the psoriasis tissues, were compared with the patients with atopic dermatitis and normal individuals, and the complete demethylation of the SHP-1 (PTPN6) gene promoter was found. A case control study of genomic methylation has found a number of related genes related to immune and epidermal differentiation complexes. However, previous studies have found that a large number of subpotential sites or susceptible genes have not been found in a large range of psoriasis, which have not been found in a large number of samples, low genome coverage and incomplete gene expression data. Genomic methylation studies and integration of high precision RNA expression data will help to detect the disease risk genes. Objective: to search for the DNA methylation sites in the whole genome, to integrate the transcriptional data and to find the susceptibility genes of the disease risk. Methods: the IlluminaHuman450K chip was used in 114 patients' skin lesions and 41 cases were non skin lesions. DNA analysis of the CpG methylation level of nearly 450000 loci in 62 cases of the skin tissue of the control individuals. The difference analysis of loci methylation was analyzed by the median rank sum test of Wilcox, and the correlation test of multiple test.Spearman was corrected by Benjamini-Hochberg method to analyze the relationship between methylation and gene expression by.Sequenom mass spectrometry system to verify the difference a Results: by analyzing the methylation of DNA, 286 different methylation sites were found to be distributed in 188 genes. Integrated whole genome transcriptome data, 36 genes were found to be associated with methylation, including AIM2, TGFBR3, PHYHD1, PHOB, FOLR1, ZC3H12A, LYPD1, and ZBP1, and 41 pairs of diseases. 1638 difference sites were found in the skin lesions and non skin lesions. The high and low methylation sites in the skin lesions were 954 and 684.2., respectively, and 434 differential methylation sites were found in 73 cases of skin lesions and 62 normal individuals. At the same time, the lesions / (non skin lesions + control) were compared, and 286 methylation sites were found to be distributed in 188 bases. Because of the.3. analysis of the distribution of 286 loci in the genome, the found site is enriched in a specific CpG region. Nearly 60% loci are located in the open region (Open Sea), the 42.4% site is located in the gene (Gene body) 4.DAVID gene function annotation, and 188 significant genes show the hypermethylation gene in protein phosphorylation and RNA transcriptional regulation. There was no obvious enrichment of the low methylation gene (P0.05) 5. compared with the 1108 difference sites reported in the past and the United States, and 776 loci data could be obtained through IlluminaHuman450K, of which 456 reached significant levels, compared with the probability of random occurrence (Chi-square=276.5, P 2.2 x 10-16). Two studies and 456 bits were compared. The difference of 1 methylation sites in the point was opposite to.6. through the transcriptional sequence to analyze the expression data of 178 genes in the 188 genes. 19 (13.3%) DNA methylation was elevated with the decrease of gene expression, 16 (9.4%) methylation decreased with the increase of gene expression. It suggested that about 1/5 DNA methylation was associated with gene expression. AIM2, TGFBR3, PHYHD1, PHOB, FOLRl, ZC3H12A, LYPD1, ZBP1 and other.7. construction causality models were constructed to analyze the genetic markers (SNP), methylation, and the relationship between disease status. The 3 CpG loci were found to be the regulatory point of the potential regulating SNP in the disease. Conclusion: 28 by non matched case control analysis. 6 psoriatic differential methylation sites, corresponding to 188 genes, integrated the whole genome transcriptome expression data, and found that 36 DNA methylation / gene expression showed negative correlation, including AIM2, TGFBR3, PHYHD1, PHOB, FOLR1, ZC3H12A, LYPD1 and ZBP1, which could be related to the pathogenesis of psoriasis, and found C1o through CIT causality analysis. Rf106, DMBXl and SIK3 genes may play a role in psoriasis regulation by regulating genetic variation sites.
【學(xué)位授予單位】：安徽醫(yī)科大學(xué)
【學(xué)位級別】：博士
【學(xué)位授予年份】：2014
【分類號】：R758.63
，
本文編號：2126877
[Abstract]:Psoriasis is a class of chronic immune dermatosis with distinct red spots and silver scales. The prevalence rate varies widely in the world because of different geographical location and racial differences. The prevalence rate of Caucasus in the Caucasus is higher than that of the Asian population. The prevalence rate of psoriasis in China is about 0.123%, and the total number of patients is nearly 0.123%. 10 million cases, its distribution trend is that the city is higher than the countryside, the north is higher than the south, and the male is higher than the female. The pathogenesis of psoriasis is not clear, and it is generally considered to be the result of the combination of genetic and environmental factors. The previous study shows that its heritability is about 60-90%, however, the current study based on DNA sequence variation can only explain the occurrence of 13% of the disease. Observation, environmental factors, gene gene interaction, etc. may be related to disease. Epigenetics, based on DNA methylation and histone modification, is an important regulatory factor in human genomics. Methylation can explain the combination of.DNA methylation of diseases other than partial DNA sequence variation by inhibiting the binding of transcription factors to DNA sequences. Or collect methylation binding proteins to control the level of gene expression. Methylated binding proteins are combined with other regulatory mechanisms, such as histone acetylation or deacetylation, induced chromosomal conformation changes and the control of gene expression.DNA methylation has been widely studied in a variety of diseases and biological pathways. The DNA methylation study of the chip disease was carried out at two levels, namely, the candidate gene promoter and the total gene level without bias. Candidate gene studies, such as the low methylation of the p15 and p21 promoter genes in the psoriasis tissues, were compared with the patients with atopic dermatitis and normal individuals, and the complete demethylation of the SHP-1 (PTPN6) gene promoter was found. A case control study of genomic methylation has found a number of related genes related to immune and epidermal differentiation complexes. However, previous studies have found that a large number of subpotential sites or susceptible genes have not been found in a large range of psoriasis, which have not been found in a large number of samples, low genome coverage and incomplete gene expression data. Genomic methylation studies and integration of high precision RNA expression data will help to detect the disease risk genes. Objective: to search for the DNA methylation sites in the whole genome, to integrate the transcriptional data and to find the susceptibility genes of the disease risk. Methods: the IlluminaHuman450K chip was used in 114 patients' skin lesions and 41 cases were non skin lesions. DNA analysis of the CpG methylation level of nearly 450000 loci in 62 cases of the skin tissue of the control individuals. The difference analysis of loci methylation was analyzed by the median rank sum test of Wilcox, and the correlation test of multiple test.Spearman was corrected by Benjamini-Hochberg method to analyze the relationship between methylation and gene expression by.Sequenom mass spectrometry system to verify the difference a Results: by analyzing the methylation of DNA, 286 different methylation sites were found to be distributed in 188 genes. Integrated whole genome transcriptome data, 36 genes were found to be associated with methylation, including AIM2, TGFBR3, PHYHD1, PHOB, FOLR1, ZC3H12A, LYPD1, and ZBP1, and 41 pairs of diseases. 1638 difference sites were found in the skin lesions and non skin lesions. The high and low methylation sites in the skin lesions were 954 and 684.2., respectively, and 434 differential methylation sites were found in 73 cases of skin lesions and 62 normal individuals. At the same time, the lesions / (non skin lesions + control) were compared, and 286 methylation sites were found to be distributed in 188 bases. Because of the.3. analysis of the distribution of 286 loci in the genome, the found site is enriched in a specific CpG region. Nearly 60% loci are located in the open region (Open Sea), the 42.4% site is located in the gene (Gene body) 4.DAVID gene function annotation, and 188 significant genes show the hypermethylation gene in protein phosphorylation and RNA transcriptional regulation. There was no obvious enrichment of the low methylation gene (P0.05) 5. compared with the 1108 difference sites reported in the past and the United States, and 776 loci data could be obtained through IlluminaHuman450K, of which 456 reached significant levels, compared with the probability of random occurrence (Chi-square=276.5, P 2.2 x 10-16). Two studies and 456 bits were compared. The difference of 1 methylation sites in the point was opposite to.6. through the transcriptional sequence to analyze the expression data of 178 genes in the 188 genes. 19 (13.3%) DNA methylation was elevated with the decrease of gene expression, 16 (9.4%) methylation decreased with the increase of gene expression. It suggested that about 1/5 DNA methylation was associated with gene expression. AIM2, TGFBR3, PHYHD1, PHOB, FOLRl, ZC3H12A, LYPD1, ZBP1 and other.7. construction causality models were constructed to analyze the genetic markers (SNP), methylation, and the relationship between disease status. The 3 CpG loci were found to be the regulatory point of the potential regulating SNP in the disease. Conclusion: 28 by non matched case control analysis. 6 psoriatic differential methylation sites, corresponding to 188 genes, integrated the whole genome transcriptome expression data, and found that 36 DNA methylation / gene expression showed negative correlation, including AIM2, TGFBR3, PHYHD1, PHOB, FOLR1, ZC3H12A, LYPD1 and ZBP1, which could be related to the pathogenesis of psoriasis, and found C1o through CIT causality analysis. Rf106, DMBXl and SIK3 genes may play a role in psoriasis regulation by regulating genetic variation sites.
【學(xué)位授予單位】：安徽醫(yī)科大學(xué)
【學(xué)位級別】：博士
【學(xué)位授予年份】：2014
【分類號】：R758.63
，
本文編號：2126877
本文鏈接：http://sikaile.net/yixuelunwen/pifb/2126877.html
最近更新
教材專著
