Background/Purpose: Pregnancy is known to have disease-modifying effects on rheumatoid arthritis (RA). A role for long non-coding (lnc) RNAs in the improvement or worsening of RA during pregnancy has not previously been investigated. We have examined lncRNAs signatures associated with RA before and during pregnancy, when the disease improves or worsens, and their co-expression with protein coding genes.

Methods: Data and samples collected at pre-pregnancy (T0) and 3^rd trimester (T3) from women with RA (n=21) and healthy women (n=14) enrolled in our prospective pregnancy cohort were included in this analysis. Disease activity was assessed using the Clinical Disease Activity Index (CDAI). Total RNA from whole blood were sequenced (RNA-seq). Following mapping of RNA-seq reads (HISAT2) and transcript assembly (StringTie), lnc and coding RNA transcripts were quantified (featureCounts) and normalized. At each time-point, RA-associated expression signatures were identified using differential expression analysis (edgeR), comparing each RA group (subsequently improved or worsened during pregnancy) to healthy women (significance threshold: q< 0.05 and fold-change≥2). lnc and coding RNAs were examined for co-expression. Functional analysis was performed using Cytoscape.

Results: Of the 21 women with RA,15 improved by T3 (RA_improved), while 6 worsened (RA_worsened). At T0, 311 lncRNAs (99 known, 212 novel) were differentially expressed (DE) between RA_improved and healthy women. Of these, 48 were co-expressed (r >0.95) with 264 protein-coding genes, many of which were also DE (RA_improved vs healthy at T0). Several had been previously associated with RA (e.g. FCGR2A, IL1R1, IL1R2, IL6R, S100A6 and TLR4). The co-expressed genes were enriched in gene ontology (GO) terms leukocyte activation (q=1.2×10^-15), immune response (q= 1.4×10^-14) and neutrophil activation (q= 2.4×10^-14). At T3, when RA improved, 287 of the 311 lncRNAs (92%) in the T0 RA signature were no longer DE between RA_improved and healthy women. Among the RA_worsened women, a very different RA lncRNA signature was identified at T0, although disease activity was similar in both RA groups at baseline (p=0.9): 81 lncRNAs (26 known, 55 novel) were DE (RA_worsened vs healthy), of which only 23 overlapped with the RA lncRNA signature of RA_improved women at T0. Many of these lncRNAs (n=57) were co-expressed with protein-coding genes, most of which were not DE. At T3, when RA worsened, only 41 of the 81  (51%) lncRNAs DE at T0 lost their differential expression, and an additional 34 became newly DE.

Conclusion: In our dataset, there was little overlap in pre-pregnancy RA-associated lncRNA expression signatures between women with RA who improved during pregnancy and those who worsened. Further, many of the lnc and coding RNAs DE at T0 in the improved group were co-expressed, and were no longer DE at T3 when RA improved. We speculate that those lncRNAs could have a role in regulating expression of the coding RNAs during pregnancy, contributing to RA improvement.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/pre-pregnancy-long-non-coding-rna-expression-signatures-among-women-with-rheumatoid-arthritis-who-improve-or-worsen-during-pregnancy/