Investigation of complex miRNA-mRNA interaction networks during JAK inhibitor therapy in rheumatoid arthritis.

Background: MicroRNAs (miRNAs) are small molecules that contribute to the regulation of gene expression by binding to messenger RNAs (mRNAs), controlling the amount of proteins being produced. In the past few decades, biologic and targeted synthetic therapies (e.g., Janus kinase (JAK) inhibitors) have emerged for the treatment of rheumatoid arthritis (RA), which have promised new possibilities for treating the disease. By inhibiting the inflammatory cascade, these drugs are able to moderate further mRNA expression of different pro-inflammatory and inflammatory genes. Since none of the agents provide a uniform solution for all RA patients, a deeper investigation of gene expression processes and regulatory mechanisms, including miRNA-mRNA interaction networks, may facilitate a shift towards personalized medicine. Methods: In our current study, 28 active RA patients were recruited at the Department of Rheumatology, Debrecen, Hungary, blood samples were taken before enrolment and 6 months after continuous JAK inhibitor therapy (T0 and T6). After peripheral blood mononuclear cell isolation, total RNA was extracted, and next-generation sequencing (NGS) was performed to obtain miRNA expression pattern. Previously we examined the mRNA expression profile of the same patient group, using the results of this project, we conducted complex analyses to identify miRNA-mRNA interaction networks. Results: We analyzed the changes in miRNA expression patterns between T0 and T6 and identified 50 differentially expressed miRNAs. Response to treatment was determined by changes in DAS28 score. When comparing responder and non-responder groups, 33 and 30 miRNAs were differentially expressed at T0 and T6, respectively. Moreover miRNA-mRNA interaction network analyses revealed several regulatory mechanisms that may influence the pathogenesis of RA, such as cell proliferation, cytokine signaling, inflammatory response, and JAK/STAT signaling pathway. Conclusion: In all comparisons, several miRNAs were identified that may influence the pathogenesis of RA through the regulation of gene expression. According to responsiveness-related analyses the identified miRNAs were able to separate responder from non-responder at both T0 and T6, miRNA-mRNA interaction analyses identified hundreds of regulatory mechanisms which potentially affect the JAK inhibitor treatment and responsiveness to therapy. Determining the regulatory miRNAs of our previously identified mRNA biomarker candidates places our findings in a broader molecular content.