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RNA-seq approaches to understand the biological effects of sialic acid on murine synovial fibroblasts

ABSTRACT: The aim of this study was to explore the role sialic acid in synovial fibroblasts using NGS-derived transcriptome analysis (RNA-seq). Methods: Synovial fibroblasts were extracted from the synovium of healthy mice and expanded ex vivo. RNA was extracted from sialidase buffer (NT) and Clostridium perfringens Neuraminidase (CP) treated synovial fibroblast. Methods: Whole Transcriptome Profiling was generated by deep sequencing, in triplicate, using Illumina NextSeq™ 500 platform. Libraries were prepared using polyA selection (TruSeq stranded mRNA kit). Methods: The sequence reads that passed quality filters were aligned to mouse reference genome (GRCM38) using Hisat2 version 2.1.0. we mapped about 30 million sequence reads per sample (75 bp, paired-end) Methods: Featurecounts version 1.4.6 was used to quantify reads counts. Data quality control, non-expressed gene filtering, median ratio normalization (MRN) implemented in DESeq2 package and identification of differentially expressed (DE) genes were done using the R bioconductor project DEbrowser. Results: we detected differentially expressed genes in CP treated synovial fibroblast compared to NT synovial fibroblast, which pass the threshold of >2 fold, adjp <0.01. DE genes reflect increased cellular inflammatory response after CP treatment Conclusions: These findings underline the ability of sialic acid to modulate homeostatic and inflammatory responses in non-immune synovial fibroblasts, suggesting that sialylation plays a key role in perpetuating local inflammation in the arthritic joint.

ORGANISM(S): Mus musculus

PROVIDER: GSE196898 | GEO | 2022/02/19

REPOSITORIES: GEO

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