Comparative genomic profiling of synovium versus skin lesions in psoriatic arthritis

Abstract

Objective: To our knowledge, there is no broad genomic analysis comparing skin and synovium in psoriatic arthritis (PsA). Also, there is little understanding of the relative levels of cytokines and chemokines in skin and synovium. The purpose of this study was to better define inflammatory pathways in paired lesional skin and affected synovial tissue in patients with PsA.

Methods: We conducted a comprehensive analysis of cytokine and chemokine activation and genes representative of the inflammatory processes in PsA. Paired PsA synovial tissue and skin samples were obtained from 12 patients on the same day. Gene expression studies were performed using Affymetrix HGU133 Plus 2.0 arrays. Confirmatory quantitative real-time polymerase chain reaction (PCR) was performed on selected transcripts. Cell populations were assessed by immunohistochemistry and immunofluorescence.

Results: Globally, gene expression in PsA synovium was more closely related to gene expression in PsA skin than to gene expression in synovium in other forms of arthritis. However, PsA gene expression patterns in skin and synovium were clearly distinct, showing a stronger interleukin-17 (IL-17) gene signature in skin than in synovium and more equivalent tumor necrosis factor (TNF) and interferon-γ gene signatures in both tissues. These results were confirmed with real-time PCR.

Conclusion: This is the first comprehensive molecular comparison of paired lesional skin and affected synovial tissue samples in PsA. Our results support clinical trial data showing that PsA skin and joint disease are similarly responsive to TNF antagonists, while IL-17 antagonists have better results in PsA skin than in PsA joints. Genes selectively expressed in PsA synovium might direct future therapies for PsA.

Figure 1

Principal components analysis showing that gene expression in psoriatic arthritis (PsA) synovium was much more closely related to gene expression in PsA skin than to gene expression in synovium in other forms of arthritis, after adjustment for organ (skin and synovium) differences. The principal components plot shows gene expression profiles in lesional skin from PsA patients, synovium from PsA patients, synovium from osteoarthritis (OA) patients, synovium from rheumatoid arthritis (RA) patients, synovium from systemic lupus erythematosus (SLE) patients, skin from healthy controls, and synovium from healthy controls after adjustment for organ differences. Lines connecting samples of skin and synovium from PsA patients indicate matched pairs. While skin and synovium from PsA patients are closely related, they are clearly distinct even after accounting for organ-specific genes, showing that there are disease-related differences between the 2 tissues. PC = principal component.

Figure 2

A, Venn diagram showing numbers of differentially expressed probe sets in psoriatic arthritis (PsA) skin (PsA skin versus normal skin) and PsA synovium (PsA synovium versus normal synovium) transcriptomes prior to adjustment for organ differences. Genes listed in boxes indicate biologically relevant genes in the top 60 differentially expressed genes (DEGs) (fold change of >2, false discovery rate [FDR] of <0.05) uniquely or commonly expressed by each tissue. B, Heatmap showing the top 50 genes shared by PsA skin and PsA synovium transcriptomes in which no difference in dysregulation is observed. C, Heatmap showing all the genes shared by PsA skin and PsA synovium transcriptomes in which the magnitude of dysregulation differs between skin and synovium (fold change of >2, FDR of <0.05). D, Heatmap comparing the 50 most up-regulated and 50 most down-regulated genes in PsA skin versus PsA synovium after adjustment for organ-specific genes. Heatmaps show PsA synovium (n = 12), normal synovium (n = 9), PsA skin (n = 6), psoriatic lesional skin (n = 33), and normal skin (n = 30) tissue samples.

Figure 3

A, Ingenuity Pathway Analysis (IPA) Upstream Regulator Analysis showing that IL17 upstream regulators are present only in skin, while IFNγ and TNF are present in both skin and synovium. B, Gene set variation analysis (GSVA) of curated gene sets in psoriatic arthritis (PsA) synovium (PsA synovium versus normal synovium) and PsA skin (PsA skin versus normal skin) transcriptomes. Values are the mean ± SD of the Z score of the given set of genes. P values indicate significance or a trend of each transcriptome (PsA synovium or PsA skin) independently. ∗ = P < 0.1; ∗∗ = P < 0.05; ∗∗∗ = P < 0.01. IL-17 = interleukin-17; TNF = tumor necrosis factor; IFNγ = interferon-γ; RHE = reconstructed human epidermis.

Figure 4

Confirmation of microarray results by quantifying mRNA expression of biologically significant genes by real-time polymerase chain reaction and normalizing expression values to the housekeeping gene hARP. There is significant elevation of mRNA for interleukin-17A (IL-17A) and IL-17F in psoriatic lesional skin compared with inflamed psoriatic synovium (P = 0.01 and P = 0.001, respectively). In addition, the gene DEFB4A and mRNA for IL-1α are significantly increased in psoriatic skin compared with affected synovium (both P < 0.0005). Messenger RNA for IL-6 and CXCL2 is significantly increased in synovium (P < 0.05 and P = 0.05, respectively). Values are the mean ± SD. ∗ = P ≤ 0.05; ∗∗∗ = P ≤ 0.001. IFNγ = interferon-γ; IL-2RA = IL-2 receptor antagonist; TNFα = tumor necrosis factor α; MMP-1 = matrix metalloproteinase 1.