Transcriptome Analysis in Women with Rheumatoid Arthritis Who Improve or Worsen during Pregnancy

Background/Purpose: Gene expression changes induced by pregnancy in women with rheumatoid arthritis (RA) and healthy women have not been examined. The few studies previously conducted did not have pre-pregnancy samples available as baseline. We have established a cohort of RA and healthy women followed prospectively from pre-pregnancy. In this study, we aimed to identify pregnancy-induced changes in gene expression among women with RA and healthy women, and to assess how those changes may differ between RA women who improve or worsen during pregnancy. Methods: Clinical data and samples collected from a subset of 11 women with RA and 5 healthy women from our cohort before pregnancy (T0) and at the third trimester (T3) were analyzed. Disease activity scores were used to determine whether the RA women improved or worsened during pregnancy. Global gene expression profiles were generated by RNA sequencing (RNA-seq). The raw RNA-seq reads were pseudo-aligned to the reference transcriptome and expression levels were estimated with kallisto. Differential expression analysis of normalized expression levels was performed using edgeR to identify genes differentially expressed within each group of women (T3 vs T0), using a foldchange cut-off of 2 and a significance threshold of q