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SAMD9 is a (epi-) genetically regulated anti-inflammatory factor activated in RA patients

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Abstract

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.

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Acknowledgements

The study was supported by Natural Science Foundation of China (81373010, 81473046, 81541068, 31271336, 81502868, 31401079 and 81401343), the Natural Science Foundation of Jiangsu Province (BK20150346), the Startup Fund from Soochow University (Q413900112, Q413900712) and a Project of the Priority Academic Program Development of Jiangsu Higher Education Institutions.

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Authors and Affiliations

  1. Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, Jiangsu, People’s Republic of China

    Pei He, Long-Fei Wu, Peng-Fei Bing, Wei Xia, Lan Wang, Fang-Fei Xie, Xin Lu, Shu-Feng Lei & Fei-Yan Deng

  2. Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, 215123, Jiangsu, People’s Republic of China

    Pei He, Long-Fei Wu, Peng-Fei Bing, Wei Xia, Lan Wang, Fang-Fei Xie, Xin Lu, Shu-Feng Lei & Fei-Yan Deng

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  1. Pei He
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Correspondence to Fei-Yan Deng.

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The study was approved by the Institutional Research Ethic Board at the Soochow University (ethics approval number: 2012-146). All the participants signed informed consent form.

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He, P., Wu, LF., Bing, PF. et al. SAMD9 is a (epi-) genetically regulated anti-inflammatory factor activated in RA patients. Mol Cell Biochem 456, 135–144 (2019). https://doi.org/10.1007/s11010-019-03499-7

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