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Integrated analysis of DNA methylation and gene expression profiles identified S100A9 as a potential biomarker in ulcerative colitis.
Bioscience Reports ( IF 4 ) Pub Date : 2020-11-13 , DOI: 10.1042/bsr20202384
Shasha Su 1 , Wenjie Kong 2 , Jing Zhang 1 , Xinguo Wang 1 , Hongmei Guo 1
Affiliation  

UC is a prevalent relapsing-remitting inflammatory bowel disease whose pathogenetic mechanisms remain elusive. In this study, colonic biopsies samples from 3 UC patients treated in the Traditional Chinese Medicine Hospital and 3 healthy controls were obtained. The genome-wide mRNA and lncRNA expression of the samples were profiled through Agilent gene expression microarray. Moreover, the genome-wide DNA methylation dataset of normal and UC colon tissues was also downloaded from GEO for a collaborative analysis. DEMs and DELs in UC samples compared with healthy samples were identified by using limma Bioconductor package. DMPs in UC samples compared with controls were obtained through comparing the average methylation level of CpGs located at promoters by using t-test. Functional enrichment analysis was performed by the DAVID. STRING database was applied to the construction of gene functional interaction network. As a result, 2,090 DEMs and 1,242 DELs were screened out in UC samples which were closely associated with processes related to complement and coagulation cascades, osteoclast differentiation vaccinia and hemorrhagic diseases and etc. A total of 90 DEMs and 72 DELs were retained for the construction of functional network for the promoters of their corresponding genes were identified as DMPs. S100A9, HECW2, SOD3 and HIX0114733 showed high interaction degrees in the functional network, and expression of S100A9 was confirmed to be significantly elevated in colon tissues of UC patients compared with that of controls by qRT-PCR which was consistent with gene microarray analysis. These indicate that S100A9 could potentially be used as predictive biomarkers in UC.

中文翻译:

DNA甲基化和基因表达谱的综合分析确定S100A9为溃疡性结肠炎的潜在生物标志物。

UC是一种流行的复发-缓解型炎症性肠病,其致病机制仍然难以捉摸。在这项研究中,从中医医院治疗的3例UC患者和3例健康对照中获得了结肠活检样品。通过安捷伦基因表达微阵列分析了样品的全基因组mRNA和lncRNA表达。此外,还从GEO下载了正常和UC结肠组织的全基因组DNA甲基化数据集,以进行协作分析。通过使用limma Bioconductor软件包,可以确定UC样品与健康样品相比的DEM和DEL。通过使用t检验比较位于启动子上的CpG的平均甲基化水平,从而获得了与对照组相比UC样品中的DMP。功能富集分析由DAVID进行。将STRING数据库应用于基因功能相互作用网络的构建。结果,在UC样品中筛选出了2,090个DEM和1,242个DEL,它们与补体和凝血级联,破骨细胞分化痘苗病和出血性疾病等过程密切相关。总共保留了90个DEM和72个DEL用于构建。其相应基因的启动子的功能网络的鉴定为DMP。S100A9,HECW2,SOD3和HIX0114733在功能网络中显示出较高的相互作用程度,并且通过qRT-PCR证实与对照相比,UC患者结肠组织中S100A9的表达显着升高,这与基因芯片分析相一致。这些表明S100A9可以潜在地用作UC中的预测性生物标志物。
更新日期:2020-11-18
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