Revealing the changes in signaling pathways caused by tofacitinib in patients with rheumatoid arthritis through RNA sequencing and the correlation with clinical parameters.

Objectives: The current study is to accelerate the understanding of how tofacitinib works in patients with rheumatoid arthritis (RA) due to the lack of relevant information.We selected ten patients with active RA and obtained the expression profile for their peripheral blood mononuclear cells before and after the tofacitinib treatment by RNA sequencing. The gene set enrichment analysis was conducted, and the significantly enriched gene sets were identified. The hub gene highly correlated with clinical parameters in the gene set was selected. We constructed the weighted gene co-expression network, linked modules with clinical indicators, and screened hub genes. The expression of representative hub genes was validated by real-time quantitative PCR (qPCR).Gene set interferon (IFN) α and IFN β signaling was the most significantly down-regulated after tofacitinib treatment. In this gene set, genes <italic>Oas2</italic> and <italic>Oasl</italic> showed a significant positive correlation with morning stiffness. In co-expression network, gene <italic>Vgll3</italic> from the violet module with the highest correlation coefficient, was positively correlated with morning stiffness. Among them, <italic>Oasl</italic> and <italic>Vgll3</italic> have shown significant down-regulation in qPCR validation.Our results highlighted the role of type I IFN, mainly including IFN α and IFN β, in the pathogenesis of RA and action for tofacitinib, and provided a new entry point for further elucidating the mechanism of morning stiffness.<bold>Key Points</bold>• <italic>Gene set IFN α and IFN β signaling was the most significantly down-regulated after tofacitinib treatment in RA patients.</italic>• <italic>Gene Oasl and Vgll3 were correlated with morning stiffness and significantly down-regulated due to the action of tofacitinib.</italic>• <italic>Type I IFN system was highlighted in the action of tofacitinib.</italic><bold>Key Points</bold>• <italic>Gene set IFN α and IFN β signaling was the most significantly down-regulated after tofacitinib treatment in RA patients.</italic>• <italic>Gene Oasl and Vgll3 were correlated with morning stiffness and significantly down-regulated due to the action of tofacitinib.</italic>• <italic>Type I IFN system was highlighted in the action of tofacitinib.</italic>Method: The current study is to accelerate the understanding of how tofacitinib works in patients with rheumatoid arthritis (RA) due to the lack of relevant information.We selected ten patients with active RA and obtained the expression profile for their peripheral blood mononuclear cells before and after the tofacitinib treatment by RNA sequencing. The gene set enrichment analysis was conducted, and the significantly enriched gene sets were identified. The hub gene highly correlated with clinical parameters in the gene set was selected. We constructed the weighted gene co-expression network, linked modules with clinical indicators, and screened hub genes. The expression of representative hub genes was validated by real-time quantitative PCR (qPCR).Gene set interferon (IFN) α and IFN β signaling was the most significantly down-regulated after tofacitinib treatment. In this gene set, genes <italic>Oas2</italic> and <italic>Oasl</italic> showed a significant positive correlation with morning stiffness. In co-expression network, gene <italic>Vgll3</italic> from the violet module with the highest correlation coefficient, was positively correlated with morning stiffness. Among them, <italic>Oasl</italic> and <italic>Vgll3</italic> have shown significant down-regulation in qPCR validation.Our results highlighted the role of type I IFN, mainly including IFN α and IFN β, in the pathogenesis of RA and action for tofacitinib, and provided a new entry point for further elucidating the mechanism of morning stiffness.<bold>Key Points</bold>• <italic>Gene set IFN α and IFN β signaling was the most significantly down-regulated after tofacitinib treatment in RA patients.</italic>• <italic>Gene Oasl and Vgll3 were correlated with morning stiffness and significantly down-regulated due to the action of tofacitinib.</italic>• <italic>Type I IFN system was highlighted in the action of tofacitinib.</italic><bold>Key Points</bold>• <italic>Gene set IFN α and IFN β signaling was the most significantly down-regulated after tofacitinib treatment in RA patients.</italic>• <italic>Gene Oasl and Vgll3 were correlated with morning stiffness and significantly down-regulated due to the action of tofacitinib.</italic>• <italic>Type I IFN system was highlighted in the action of tofacitinib.</italic>Results: The current study is to accelerate the understanding of how tofacitinib works in patients with rheumatoid arthritis (RA) due to the lack of relevant information.We selected ten patients with active RA and obtained the expression profile for their peripheral blood mononuclear cells before and after the tofacitinib treatment by RNA sequencing. The gene set enrichment analysis was conducted, and the significantly enriched gene sets were identified. The hub gene highly correlated with clinical parameters in the gene set was selected. We constructed the weighted gene co-expression network, linked modules with clinical indicators, and screened hub genes. The expression of representative hub genes was validated by real-time quantitative PCR (qPCR).Gene set interferon (IFN) α and IFN β signaling was the most significantly down-regulated after tofacitinib treatment. In this gene set, genes <italic>Oas2</italic> and <italic>Oasl</italic> showed a significant positive correlation with morning stiffness. In co-expression network, gene <italic>Vgll3</italic> from the violet module with the highest correlation coefficient, was positively correlated with morning stiffness. Among them, <italic>Oasl</italic> and <italic>Vgll3</italic> have shown significant down-regulation in qPCR validation.Our results highlighted the role of type I IFN, mainly including IFN α and IFN β, in the pathogenesis of RA and action for tofacitinib, and provided a new entry point for further elucidating the mechanism of morning stiffness.<bold>Key Points</bold>• <italic>Gene set IFN α and IFN β signaling was the most significantly down-regulated after tofacitinib treatment in RA patients.</italic>• <italic>Gene Oasl and Vgll3 were correlated with morning stiffness and significantly down-regulated due to the action of tofacitinib.</italic>• <italic>Type I IFN system was highlighted in the action of tofacitinib.</italic><bold>Key Points</bold>• <italic>Gene set IFN α and IFN β signaling was the most significantly down-regulated after tofacitinib treatment in RA patients.</italic>• <italic>Gene Oasl and Vgll3 were correlated with morning stiffness and significantly down-regulated due to the action of tofacitinib.</italic>• <italic>Type I IFN system was highlighted in the action of tofacitinib.</italic>Conclusions: The current study is to accelerate the understanding of how tofacitinib works in patients with rheumatoid arthritis (RA) due to the lack of relevant information.We selected ten patients with active RA and obtained the expression profile for their peripheral blood mononuclear cells before and after the tofacitinib treatment by RNA sequencing. The gene set enrichment analysis was conducted, and the significantly enriched gene sets were identified. The hub gene highly correlated with clinical parameters in the gene set was selected. We constructed the weighted gene co-expression network, linked modules with clinical indicators, and screened hub genes. The expression of representative hub genes was validated by real-time quantitative PCR (qPCR).Gene set interferon (IFN) α and IFN β signaling was the most significantly down-regulated after tofacitinib treatment. In this gene set, genes <italic>Oas2</italic> and <italic>Oasl</italic> showed a significant positive correlation with morning stiffness. In co-expression network, gene <italic>Vgll3</italic> from the violet module with the highest correlation coefficient, was positively correlated with morning stiffness. Among them, <italic>Oasl</italic> and <italic>Vgll3</italic> have shown significant down-regulation in qPCR validation.Our results highlighted the role of type I IFN, mainly including IFN α and IFN β, in the pathogenesis of RA and action for tofacitinib, and provided a new entry point for further elucidating the mechanism of morning stiffness.<bold>Key Points</bold>• <italic>Gene set IFN α and IFN β signaling was the most significantly down-regulated after tofacitinib treatment in RA patients.</italic>• <italic>Gene Oasl and Vgll3 were correlated with morning stiffness and significantly down-regulated due to the action of tofacitinib.</italic>• <italic>Type I IFN system was highlighted in the action of tofacitinib.</italic><bold>Key Points</bold>• <italic>Gene set IFN α and IFN β signaling was the most significantly down-regulated after tofacitinib treatment in RA patients.</italic>• <italic>Gene Oasl and Vgll3 were correlated with morning stiffness and significantly down-regulated due to the action of tofacitinib.</italic>• <italic>Type I IFN system was highlighted in the action of tofacitinib.</italic> [ABSTRACT FROM AUTHOR]