Figure 3.

Total RNA was isolated from liver tissues and RNA sequencing analysis was performed as in described in the Materials and Methods section for 8 mice including 3 male and 3 female 21 week-old K/BxN mice and 2 male and 2 female WT mice controls (all on chow diet). The male K/BxN mice had higher arthritis activity compared to K/BxN female mice as shown in Fig. 1. Differences in gene expression between more arthritic male K/BxN mice and less arthritic female K/BxN mice were analyzed after controlling for non-arthritic male/female differences in WT controls. (A) Functional classification of the resulting gene pathways from the PANTHER GO-Slim Biological Process (BP) analysis. (B) PANTHER Overrepresentation Pathway BP analysis including the fold-enrichment values for the pathways. (C) PANTHER Reactome Process pathway overrepresentation analysis, which identified 25 gene pathways, which were significantly enriched in the gene data set. The HDL remodelling pathway was the most highly enriched pathway. (D) Differences in 4 individual genes related to lipid metabolism, which were identified in the HDL remodeling pathway between more arthritic males and less arthritic females after controlling for non-arthritic sex differences. Correlations between raw gene expression counts and HDL cholesterol (HDL-C) levels are shown. Statistical analyses were performed as described in the Materials and Methods section. Software: PANTHER version 14.0: https://www.pantherdb.org.