Fig. 5

Transcriptomic and proteomic analysis of RA-FLSs after treatment with propionate. a Illustration of RNA sequencing of RA-FLSs after treatment with vehicle (PBS) or propionate. b Heatmap of differentially expressed genes in RA-FLSs after treatment with vehicle (PBS) or propionate based on RNA sequencing analysis. c Gene Set Enrichment Analyses (GSEA) of RNA sequencing data showing the downregulated pathways in RA-FLSs after treatment with propionate based on Hallmark Gene Sets. d Illustration of proteomics of RA-FLSs after treatment with vehicle (PBS) or propionate. e Heatmap of differentially expressed proteins in RA-FLSs after treatment with vehicle (PBS) or propionate based on proteomic analysis. f Functional enrichment analysis of proteomic data showing the downregulated pathways in RA-FLSs after treatment with propionate. g Venn diagram showing the overlap (green) of downregulated protein-coding genes between transcriptomic (blue) and proteomics (red) in RA-FLSs after treatment with propionate (P value < 0.05, log₂(Flod Change) < −0.5). h Functional enrichment analysis of the overlapping protein-coding genes in RA-FLSs downregulated by propionate. i Heatmap showing differentially expressed proteins involved in interferon pathway in RA-FLSs after treatment with vehicle (PBS) or propionate. j Relative mRNA expression of FOXK1 in RA-FLSs after treatment with vehicle (PBS) or propionate. k Protein levels of FOXK1, STAT1 and STAT2 in RA-FLSs after transfection with negative control shRNA (sh-NC) or shRNA targeting FOXK1 (sh-FOXK1). Relative mRNA expression of genes involved in interferon pathway (l), inflammatory response genes (m), chemokines and inflammatory cytokines (n) and migration- and invasion-related genes (o) in RA-FLSs after knockdown of FOXK1. p Co-immunoprecipitation for detecting the interaction between FOXK1 and HDAC3 in RA-FLSs. q Level of lysine acetylation of FOXK1 in RA-FLSs after treatment with vehicle (PBS) or 5 μmol/L TSA. r Protein expression of FOXK1 and HDAC3 in RA-FLSs after treatment with vehicle (PBS) or 5 μmol/L TSA for 48 h, in the presence or absence of a proteasome inhibitor MG132 or a lysosome inhibitor BafA1. s Interaction between HDAC3 and FOXK1 in RA-FLSs after treatment with vehicle (PBS) or propionate. t Level of lysine acetylation of FOXK1 in RA-FLSs after treatment with vehicle (PBS) or 1 mmol/L propionate as detected by co-immunoprecipitation assay. u Protein expression of FOXK1, STAT1, STAT2 and HDAC3 in RA-FLSs after treatment with vehicle (PBS) or different concentrations of propionate for 48 h. v A schematic diagram illustrating the mechanism of action of propionate in RA-FLSs. Graphs represented means ± SEM and statistical significance was calculated by Student’s t test (j and l–o) and one-way ANOVA (r, s and u). Experiments were performed in triplicate and repeated three times. ns no significance, *P < 0.05, **P < 0.01, ***P < 0.001 and ****P < 0.000 1