Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.
Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China.
Mol Cell Biochem. 2019 Jun;456(1-2):135-144. doi: 10.1007/s11010-019-03499-7. Epub 2019 Feb 4.
To identify PBMC-expressed genes significant for RA, and to ascertain their upstream regulatory factors, as well as downstream functional effects relevant to RA pathogenesis. We performed peripheral blood mononuclear cells (PBMCs) transcriptome-wide mRNA expression profiling in a case-control discovery sample. Differentially expressed genes (DEGs) were identified and validated in PBMCs in independent samples. We also generated genome-wide SNP genotyping data, and collected miRNA expression data and DNA methylation data from PBMCs of the discovery sample. Pearson correlation analyses were conducted to identify miRNAs/DNA methylations influencing DEG expression. Association analyses were conducted to identify expression-regulating SNPs. The key DEG, SAMD9, which was reported to function as a tumor suppressor gene, was assessed for its effects on T cell proliferation, apoptosis, and inflammatory cytokine expression. A total of 181 DEGs (Fold Change ≥ 2.0, Bonferroni adjusted p ≤ 0.05) were discovered in PBMCs. Four DEGs (SAMD9, CKLF, PARP9, and GUSB), upregulated with RA, were validated independently in PBMCs. Specifically, SAMD9 mRNA expression level was significantly upregulated in PHA-activated Jurkat T cells in vitro, and correlated with 8 miRNAs and associated with 22 SNPs in PBMCs in vivo. Knockdown of SAMD9 could transiently promote Jurkat T cell proliferation within 48 h and significantly induce TNF-α and IL-8 expression in T cells. SAMD9 expression is (epi-) genetically regulated, and significantly upregulated in PBMCs in RA patients and in activated T cells in vitro. SAMD9 might serve as a T cell activation marker but act as an anti-inflammatory factor.
为了鉴定与 RA 相关的 PBMC 表达基因，并确定其上游调控因子以及与 RA 发病机制相关的下游功能效应，我们在病例对照发现样本中进行了外周血单核细胞 (PBMC) 的全转录组 mRNA 表达谱分析。在独立样本中鉴定和验证了差异表达基因 (DEGs)。我们还生成了全基因组 SNP 基因分型数据，并从发现样本的 PBMC 中收集了 miRNA 表达数据和 DNA 甲基化数据。进行 Pearson 相关分析以鉴定影响 DEG 表达的 miRNA/DNA 甲基化。进行关联分析以鉴定表达调控 SNP。关键的 DEG SAMD9 被报道为肿瘤抑制基因，评估其对 T 细胞增殖、凋亡和炎症细胞因子表达的影响。在 PBMC 中发现了总共 181 个 DEG（Fold Change≥2.0，Bonferroni 调整 p≤0.05）。在 PBMC 中独立验证了上调的四个 DEG（SAMD9、CKLF、PARP9 和 GUSB）。具体来说，SAMD9 mRNA 表达水平在体外 PHA 激活的 Jurkat T 细胞中显著上调，并与体内 PBMC 中的 8 个 miRNA 相关，与 22 个 SNP 相关。SAMD9 的敲低可以在 48 小时内短暂促进 Jurkat T 细胞增殖，并显著诱导 T 细胞中 TNF-α和 IL-8 的表达。SAMD9 的表达受（表观）遗传调控，在 RA 患者的 PBMC 和体外激活的 T 细胞中显著上调。SAMD9 可能作为 T 细胞激活标志物，但作为抗炎因子。
