Integration of Genome-Wide DNA Methylation and Transcription Uncovered Aberrant Methylation-Regulated Genes and Pathways in the Peripheral Blood Mononuclear Cells of Systemic Sclerosis.
Integration of Genome-Wide DNA Methylation and Transcription Uncovered Aberrant Methylation-Regulated Genes and Pathways in the Peripheral Blood Mononuclear Cells of Systemic Sclerosis.
复制标题
全基因组 DNA 甲基化和转录的整合揭示了系统性硬化症外周血单核细胞中异常甲基化调节的基因和通路。
DOI：
10.1155/2018/7342472
复制
发表时间：
2018
影响因子：
2.3
通讯作者：
Li QZ
中科院分区：
文献类型：
--
作者：
Zhu H;Zhu C;Mi W;Chen T;Zhao H;Zuo X;Luo H;Li QZ
Objective.系统性硬化症（SSc）是一种病因不明的系统性结缔组织疾病。循环免疫细胞中的异常基因表达和表观遗传修饰与SSc的发病机制有关。本研究旨在阐明SSc患者PBMC中基因转录与DNA甲基化之间的相互作用网络，并鉴定参与SSc发病机制的甲基化调控基因。方法.使用Illumina BeadChips对来自18名SSc患者和19名匹配的正常对照（NC）的PBMC进行全基因组mRNA转录和全局DNA甲基化分析。对差异表达基因（DEG）和差异甲基化位点（DMPs）进行整合分析，以确定甲基化调控基因和相关分子通路。结果转录组分析区分453 DEG（269上调和184下调）在SSc从NC。全局DNA甲基化分析确定了位于618个基因上的925个DMPs。两个列表的整合揭示了仅20个具有负相关DMP的DEG，包括12个上调的基因（ELANE、CTSG、LTBR、C3AR 1、CSTA、SPI1、ODF 3B、SAMD 4A、PLAUR、NFE 2、ZYX和CTSZ）和8个下调的基因（RUNX3、PRF 1、PRKCH、PAG 1、RASSF5、FYN、CXCR 6和F2 R）。这些潜在的甲基化调节的DEG（MeDEG）在与免疫细胞迁移、增殖、活化和炎症活动相关的途径中富集。使用机器学习算法，我们识别了20个MeDEG中的6个，包括F2R，CXCR6，FYN，LTBR，CTSG和ELANE，它们以100%的准确度区分了SSc和NC。4个基因（F2R、FYN、PAG1和PRKCH）在有间质性肺病（ILD）的SSc与无ILD的SSc中差异表达。结论所鉴定的MeDEG可能代表了导致SSc发病机制中免疫调节途径异常激活的新的候选因子。它们也可用作SSc和临床并发症的诊断生物标志物。
Objective. Systemic sclerosis (SSc) is a systemic connective tissue disease of unknown etiology. Aberrant gene expression and epigenetic modifications in circulating immune cells have been implicated in the pathogenesis of SSc. This study is to delineate the interaction network between gene transcription and DNA methylation in PBMC of SSc patients and to identify methylation-regulated genes which are involved in the pathogenesis of SSc. Methods. Genome-wide mRNA transcription and global DNA methylation analysis were performed on PBMC from 18 SSc patients and 19 matched normal controls (NC) using Illumina BeadChips. Differentially expressed genes (DEGs) and differentially methylated positions (DMPs) were integrative analyzed to identify methylation-regulated genes and associated molecular pathways. Results. Transcriptome analysis distinguished 453 DEGs (269 up- and 184 downregulated) in SSc from NC. Global DNA methylation analysis identified 925 DMPs located on 618 genes. Integration of the two lists revealed only 20 DEGs which harbor inversely correlated DMPs, including 12 upregulated (ELANE, CTSG, LTBR, C3AR1, CSTA, SPI1, ODF3B, SAMD4A, PLAUR, NFE2, ZYX, and CTSZ) and eight downregulated genes (RUNX3, PRF1, PRKCH, PAG1, RASSF5, FYN, CXCR6, and F2R). These potential methylation-regulated DEGs (MeDEGs) are enriched in the pathways related to immune cell migration, proliferation, activation, and inflammation activities. Using a machine learning algorism, we identified six out of the 20 MeDEGs, including F2R, CXCR6, FYN, LTBR, CTSG, and ELANE, which distinguished SSc from NC with 100% accuracy. Four genes (F2R, FYN, PAG1, and PRKCH) differentially expressed in SSc with interstitial lung disease (ILD) compared to SSc without ILD. Conclusion. The identified MeDEGs may represent novel candidate factors which lead to the abnormal activation of immune regulatory pathways in the pathogenesis of SSc. They may also be used as diagnostic biomarkers for SSc and clinical complications.