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Open AccessArticle

Differential Expression Profiles of the Transcriptome and miRNA Interactome in Synovial Fibroblasts of Rheumatoid Arthritis Revealed by Next Generation Sequencing

1
Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
2
Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 80145, Taiwan
3
Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
4
Institute of Biomedical Science, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
*
Authors to whom correspondence should be addressed.
Diagnostics 2019, 9(3), 98; https://doi.org/10.3390/diagnostics9030098
Received: 12 July 2019 / Revised: 8 August 2019 / Accepted: 13 August 2019 / Published: 18 August 2019
(This article belongs to the Section Pathology and Molecular Diagnostics)
Using next-generation sequencing to decipher the molecular mechanisms underlying aberrant rheumatoid arthritis synovial fibroblasts (RASF) activation, we performed transcriptome-wide RNA-seq and small RNA-seq on synovial fibroblasts from rheumatoid arthritis (RA) subject and normal donor. Differential expression of mRNA and miRNA was integrated with interaction analysis, functional annotation, regulatory network mapping and experimentally verified miRNA–target interaction data, further validated with microarray expression profiles. In this study, 3049 upregulated mRNA and 3552 downregulated mRNA, together with 50 upregulated miRNA and 35 downregulated miRNA in RASF were identified. Interaction analysis highlighted contribution of miRNA to altered transcriptome. Functional annotation revealed metabolic deregulation and oncogenic signatures of RASF. Regulatory network mapping identified downregulated FOXO1 as master transcription factor resulting in altered transcriptome of RASF. Differential expression in three miRNA and corresponding targets (hsa-miR-31-5p:WASF3, hsa-miR-132-3p:RB1, hsa-miR-29c-3p:COL1A1) were also validated. The interactions of these three miRNA–target genes were experimentally validated with past literature. Our transcriptomic and miRNA interactomic investigation identified gene signatures associated with RASF and revealed the involvement of transcription factors and miRNA in an altered transcriptome. These findings help facilitate our understanding of RA with the hope of serving as a springboard for further discoveries relating to the disease. View Full-Text
Keywords: rheumatoid arthritis; miRNA; synovial fibroblast rheumatoid arthritis; miRNA; synovial fibroblast
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MDPI and ACS Style

Tseng, C.-C.; Wu, L.-Y.; Tsai, W.-C.; Ou, T.-T.; Wu, C.-C.; Sung, W.-Y.; Kuo, P.-L.; Yen, J.-H. Differential Expression Profiles of the Transcriptome and miRNA Interactome in Synovial Fibroblasts of Rheumatoid Arthritis Revealed by Next Generation Sequencing. Diagnostics 2019, 9, 98.

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