Longitudinal Changes in Gene Expression Associated with Disease Activity during Pregnancy and Post-Partum Among Women with Rheumatoid Arthritis

Abstract

Background/Purpose: Many women with rheumatoid arthritis (RA) experience an improvement in disease activity during pregnancy, and a predictable flare in the months after they give birth. The cause of these changes is unknown. We hypothesized that understanding biological changes (through gene expression) that occur from pre-pregnancy through the pregnancy and post-partum periods will contribute important evidence to our knowledge of the drivers of disease activity in RA during and after pregnancy. Methods: We have established a prospective RA pregnancy cohort, with clinical data and blood samples collected at pre-pregnancy (T0), each trimester of pregnancy and every 3 months up to a year post-partum (up to 8 time points). Disease activity at each time point was assessed using disease activity scores (DAS28CRP4); women who showed an improvement during pregnancy were selected for analysis (n=9). Global gene expression profiles for each sample were generated using RNA-sequencing (RNA-seq). Raw reads were pseudo-aligned and quantified using kallisto. Random effects regression models were used to estimate the effects of changes in gene expression on disease activity (a) from T0 through the pregnancy period (P1), and (b) in the post-partum period (P2). The models were adjusted for age, medication status at baseline and batch effects. Significance was assessed using a threshold of q<0.05 (FDR-adjusted). Functional enrichment analysis was performed using WebGestalt. Results: During pregnancy, 1,174 genes had expression patterns significantly associated with disease activity. While these were not significantly enriched in specific pathways, the genes whose increased expression was associated with the largest decrease (improvement) in disease activity during pregnancy were immune-related, and included ERAP1, CSNK2A1 and FAM175B. ERAP1 is involved in trimming peptides for presentation on MHC class I molecules; CSNK2A1 regulates cellular processes including cellular response to viral infection; FAM175B is involved in interferon-signaling. In the post-partum period, 4,693 genes had expression patterns significantly associated with disease activity. These were enriched (p<1x10^(-6)) in numerous immune-related pathways including MAPK signaling, T cell receptor signaling, osteoclast differentiation, hematopoietic cell lineage, B cell receptor signaling, Toll-like receptor signaling and leukocyte trans-endothelial migration, in addition to several pathways related to cancer. The genes whose increased expression were associated with larger increases in disease activity included EI24, CMTM7, PPP2CB and BFAR which are related to tumor suppression and/or regulation of apoptosis. Conclusion: In this pilot RA pregnancy cohort study with longitudinal RNA-seq data, several candidate genes were identified as significantly associated with improvement in disease activity during pregnancy, and others were associated with post-partum flares. These results warrant further investigations into possible roles of these genes in modulating RA disease activity in a larger cohort.

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