Epigenome association study for DNA methylation biomarkers in buccal and monocyte cells for female rheumatoid arthritis

Abstract

Genetics (i.e., mutations) has been assumed to be the major factor in rheumatoid arthritis (RA) etiology, but accounts for a minority of the variance in disease risk for RA. In contrast to genetics, the environment can have dramatic impacts on epigenetics that associate with disease etiology. The current study used buccal cells and purified blood monocytes from two different clinical cohorts involving Caucasian or African American female populations with or without arthritis. The differential DNA methylation regions (DMRs) between the control and RA populations were identified with an epigenome-wide association study. The DMRs (i.e., epimutations) identified in the buccal cells and monocytes were found to be distinct. The DMR associated genes were identified and many have previously been shown to be associated with arthritis. Observations demonstrate DNA methylation epimutation RA biomarkers are cell type specific and similar findings were observed with the two racial background populations. Rheumatoid arthritis susceptibility epigenetic diagnosis appears feasible and may improve the clinical management of RA and allowpreventative medicine considerations.

Figure 1

Rheumatoid arthritis (RA) DMR identifications. (a) Caucasian control versus RA buccal cell DMR analysis. (b) Caucasian control versus RA monocyte cell DMR analysis. (c) African American (AA) control versus RA buccal cell DMR analysis. (d) Combined Caucasian (CC) and African American (AA) control versus RA buccal cell DMR analysis. The number of DMRs found using different p-value cutoff thresholds. The all window column shows all DMRs. The multiple window column shows the number of DMRs containing at least two adjacent significant windows and the number of DMRs with each specific number of significant windows at a p-value threshold of p < 1e−04. (e) Venn diagram overlap of the RA DMRs at p < 1e−04 for the Caucasian monocyte, buccal and AA buccal, and combined CC and AA (All) buccal. (f) Extended overlap with a comparison of RA DMRs in the different comparison at p < 1e−04 versus horizontal p < 0.05 for the different comparisons. The overlapping DMR numbers and percent (%) of the total is presented. The highlighted overlaps for All buccal and overlaps indicated.

Figure 2

RA DMR chromosomal locations and principal component analysis (PCA). The DMR locations on the individual chromosomes are identified. All DMRs at a p-value threshold of p < 1e−04 are shown with the red arrowheads and clusters of DMRs with the black boxes. (a) Caucasian control versus RA buccal DMRs. (b) Caucasian control versus RA monocyte DMRs. (c) AA control versus RA buccal DMRs. (d) Combined CC and AA for All buccal control versus RA buccal DMRs. All DMRs at a p-value threshold of p < 1e−04.

Figure 3

Control versus RA DMR principal component analysis (PCA). PCA analysis for DMRs at p < 1e−04. (a) Caucasian control versus RA. (b) Caucasian monocyte DMR PCA. (c) AA control versus AA RA buccal DMR PCA. (d) CC and AA all buccal control versus all RA buccal DMR PCA.

Figure 4

RA DMR associated gene categories and pathways. (a) DMR associated gene categories. DMR numbers at a p-value threshold p < 1e−04 are shown. The comparison DMR key is inset. (b) DMR associated gene pathways. The pathways common for two or more comparisons are presented. Number in bracket is number of DMR associated genes in pathway.

Figure 5

DMR associated genes from the current study were compared to genes associated with arthritis in the published literature using Pathway Studio software (Elsevier, Inc.). Those that were in common are depicted. (a) African American (AA) buccal cell RA DMR associated gene disease correlations. (b) Caucasian buccal DMR associated gene disease correlations.

Figure 6

DMR associated genes from the current study were compared to genes associated with arthritis in the published literature using Pathway Studio software (Elsevier, Inc.). Those that were in common are depicted. (a) Combined CC and AA all buccal RA DMR associated gene disease correlations. (b) Caucasian monocyte RA DMR associated gene disease correlations. The gene function symbol index inset.

Figure 7

DMR associated RA genes were correlated with known RA cell processes in the published literature using Pathway Studio software (Elsevier, Inc.). The DMR associated genes from all comparisons were linked to the RA cell processes.