Linking Skin and Joint Inflammation in Psoriatic Arthritis through Shared CD8+ T Cell Clones

Abstract

Objective: Psoriatic arthritis (PsA) is an HLA class I-associated inflammatory arthritis that develops in up to 30% of people with psoriasis. We tested the hypothesis that skin and joint inflammation in PsA is linked in terms of CD8⁺ T cell phenotype and clonality.

Methods: Using single-cell RNA sequencing (n = 6 skin samples with n = 5 paired synovial tissue samples and/or n = 5 paired synovial fluid samples) and spatial transcriptomics (n = 1 paired skin and synovial biopsy sample, n = 4 unpaired biopsy samples), we compared the transcriptional signature, T cell receptor repertoire, and cell neighborhoods of T cells from skin and synovial tissue and/or fluid samples from patients with PsA.

Results: We identified an enrichment of type 17 CD8⁺ tissue-resident memory T (Trm) cells in both the skin and joint, with a stronger interleukin-17 signature in the skin than the joint. CD8⁺ Trm cells resided in distinct cell neighborhoods in the skin and joint but were located adjacent to antigen-presenting cells in both sites. Several T cell clones were shared between the skin and joint. Across the six patients, 155 CD8⁺ T cell clones were shared between the two sites, comprising 1,071 CD8⁺ T cells and taking up a median of 13% of the skin and 8% of the joint CD8⁺ T cell receptor repertoire. CD8⁺ skin-joint shared clones tended to have a similar phenotype at both sites, characterized by increased expression of genes associated with a cytotoxic, tissue-resident phenotype.

Conclusion: Our findings support the hypothesis that skin and joint inflammation in PsA is linked in terms of CD8⁺ T cell clonality and that specific T cells migrate between these compartments to propagate inflammation across both sites.

Figure 1

Signature of memory CD8⁺ T cells in PsA. (A) UMAP of integrated analysis of 15,335 memory CD8⁺ T cells from blood, the lesional skin epidermis, and ST and/or SF from an inflamed joint (n = 6 patients). Each dot represents a cell, colored according to the 19 clusters obtained after Seurat clustering. The proximity of the dots to each other indicates similarity of the cells. (B) UMAPs split by tissue of origin. (C) Distribution of CD8⁺ T cells from each tissue across the 19 clusters (n = 6 patients). Clusters are ordered in groups with similar phenotypes. (D and E) Heat maps visualizing averaged expression of specified genes (D) and proteins (E) in each cluster. (F) Dot plot depicting expression of specified genes across CD8⁺ Trm clusters. The size of the dots indicates the percentage of cells within the cluster that express the indicated gene. Color indicates the scaled expression of the indicated gene. (G) Frequency of total memory CD8⁺ T cells from blood, skin, SF, and ST within type 17 (clusters 1 and 4 combined), CD49a⁺ cytotoxic type 17 (cluster 14), and GZMK⁺ cytotoxic (clusters 8 and 15) Trm subsets. Boxplots show the median ± interquartile range. Mixed‐effects analysis comparing skin (n = 6) to blood (n = 6), SF (n = 5) to blood (n = 6), and ST (n = 5) to blood (n = 6) with Dunnett's correction for multiple comparisons. MAIT, mucosal‐associated invariant T; PsA, psoriatic arthritis; SF, synovial fluid; ST, synovial tissue; Tcm, central memory T; Tem, effector memory T; Trm, tissue‐resident memory T; UMAP, uniform manifold approximation and projection.

Figure 2

Comparison of skin and ST CD8⁺ T cells in PsA. (A) Volcano plot depicting differentially expressed genes between memory CD8⁺ T cells from paired skin and ST samples (n = 5). Differential expression of pooled cells from all patients was calculated with the Wilcoxon signed rank test using FindMarkers() applied to SCTransformed RNA in Seurat. To mitigate potential batch effect/variability, only genes that were also significantly differentially expressed by FindConservedMarkers() (which performs differential gene expression testing for each patient then combines P values using meta‐analysis methods from the MetaDE package) or significantly differentially expressed in three or more of five patients after applying FindAllMarkers to each patient sample individually are labeled. The top 20 increased and decreased genes meeting these criteria are labeled. (B) Violin plots depicting expression of specified genes in skin (n = 6) and ST (n = 5) samples. (C) The percentage of CD8⁺ memory T cells from paired skin and ST (n = 5) that are Trm cells. (D) The percentage of CD8⁺ Trm cells from paired skin and ST (n = 5) belonging to each Trm subset. (E and F) Volcano plots visualizing differentially expressed genes between paired skin and ST within type 17 (E) and GZMK⁺ cytotoxic (F) Trm cells (n = 5). The top 10 increased and decreased genes and genes that are mentioned in the text are labeled. Calculation of differential genes and the criteria for labeling were as described for panel A. Boxplots show the median ± interquartile range (paired t‐tests; two‐tailed, n = 5). NS, not significant; PsA, psoriatic arthritis; ST, synovial tissue; Trm, tissue‐resident memory T. Color figure can be viewed in the online issue, which is available at http://onlinelibrary.wiley.com/doi/10.1002/art.43286/abstract.

Figure 3

Neighborhood analysis in inflamed skin and joints in PsA. (A–J) Tissue sections from paired skin (A, C, D, G, and I) and ST (B, E, F, H, and J) from PsA patient 5. (A and B) Tissue sections imaged on the CosMx analyzer. Grid lines indicate 0.51 × 0.51 mm fields of view selected for data acquisition. Location of CD8⁺ (C and E) and CD4⁺ (D and F) Trm and non‐Trm cells, myeloid cell subsets (G and H), and MHC class I expression (red), HLA–DR expression (green), and coexpression (yellow) (I and J). (K and M) Heat maps depicting significance of contact‐based interactions between cell types in paired skin (K) and ST (M). The color of the square indicates the −Log₁₀ P value (upper tail, one‐sided) for cell types that are more frequently neighbors than expected by chance. (L and N) Force‐directed graphs depicting contact‐based interactions between cell types in paired skin (L) and ST (N). Arrows between cell types indicate that the neighborhoods of the cell type the arrow originates from comprise ≥5% of the cell type that the arrow points to. Yellow circles highlight nodes corresponding to CD8⁺ Trm cells. Selected significantly enriched ligand–receptor interactions between macrophages and CD8⁺ Trm cells and Langerhans cells and CD8⁺ Trm cells are listed in boxes. MHC, major histocompatibility complex; PsA, psoriatic arthritis; ST, synovial tissue; Trm, tissue‐resident memory T. Color figure can be viewed in the online issue, which is available at http://onlinelibrary.wiley.com/doi/10.1002/art.43286/abstract.

Figure 4

T cell clones are shared between the skin and joint. (A) Alluvial plots visualizing CD8⁺ and CD4⁺ TCR repertoires in the skin and joint (SF and ST combined) (n = 6). Each block represents a T cell clone (single/group of T cells with same TCR). The height of the block represents the percentage of skin/joint CD8⁺ TCR repertoires taken up by clones. Alluvials represent the skin–joint shared clones. (B and C) Circle plots visualizing sharing of CD8⁺ T cell clones between the skin (yellow bar), joint (blue), and blood (red) for each patient. The size of the circumferential bar is proportional to the number of TCRs. (B) Skin–joint, skin–blood, and joint–blood shared clones are represented as purple, red, and blue lines, respectively. (C) Clones shared between patients are represented as purple lines. (D) Bar chart visualizing the size (number of cells) and tissue location of the 155 skin–joint shared clones. Each bar represents a skin–joint shared clone. The height of the bar represents the number of CD8⁺ T cells within that clone, and the color represents the tissue location of cells. Clones are ordered by patient then size. (E and F) Inverse Pielou scores (range: 0, indicating polyclonal, to 1, indicating monoclonal population) for blood, skin, and joint CD8⁺ (E) and CD4⁺ (F) T cells. (G and H) The percentage of skin/joint CD8⁺ (G) and CD4⁺ (H) TCR repertoires taken up by shared clones. PsA, psoriatic arthritis; SF, synovial fluid; ST, synovial tissue; TCR, T cell receptor Color figure can be viewed in the online issue, which is available at http://onlinelibrary.wiley.com/doi/10.1002/art.43286/abstract.

Figure 5

Signature of CD8⁺ skin–joint shared clones (A) Scatterplot showing frequency of CD8⁺ T cell clones in the skin and joint from one patient (PsA patient 3). (B and C) Circled clones from panel A are highlighted on UMAPs. (D) UMAP with clusters grouped into meta‐clusters with similar phenotypes. Clusters not defined as Trm, GZMK⁺, CTL, ANXA1 ⁺, or Tcm cells are grouped as “other.” (E) Bar chart depicting meta‐cluster location and tissue origin of cells in each of the 155 skin–joint shared clones. Each vertical bar represents a CD8⁺ T cell clone. Color represents meta‐cluster and tissue location of cells within that clone. (F) Pie charts indicating similarity of skin–joint, skin–blood and joint–blood shared clones. Clones are defined as having the same (all cells located in the same meta‐cluster in both compartments), different (cells located in different meta‐clusters), or similar (at least one cell from each compartment located within the same meta‐cluster) signatures in the two compartments. (G and H) Volcano plot showing differentially expressed genes between skin (G) and joint (H) cells belonging to skin–joint shared clones versus non shared clones. Low frequency of shared clones in some patients limited utility of FindConservedMarkers(); therefore, differentially expressed genes were calculated with the Wilcoxon signed rank test using FindMarkers(). CTL, cytotoxic lymphocyte; NS, not significant; PsA, psoriatic arthritis; Tcm, central memory T; Trm, tissue‐resident memory T; UMAP, uniform manifold approximation and projection. Color figure can be viewed in the online issue, which is available at http://onlinelibrary.wiley.com/doi/10.1002/art.43286/abstract.

Figure 6

Signature of memory CD4⁺ T cells in PsA. (A) Volcano plot depicting differentially expressed genes between memory CD4⁺ T cells from paired skin epidermis and ST samples (n = 5). Differential expression of pooled cells from all patients were calculated with the Wilcoxon signed rank test using FindMarkers() applied to SCTransformed RNA. The top 20 increased and decreased genes that were also identified as significantly differentially expressed by FindConservedMarkers() or in three or more of five patients after applying FindAllMarkers to each patient individually are labeled. (B) Violin plots comparing expression of specified genes in skin (n = 6) and ST (n = 5) samples. (C) The percentage of CD4⁺ memory T cells from paired skin and ST samples (n = 5) located in Trm cell clusters. (D) The percentage of CD4⁺ Trm cells belonging to each Trm subset. (E) Circle plots visualizing sharing of CD4⁺ T cell clones between the skin (yellow bar), joint (blue), and blood (red). The size of the circumferential bar is proportional to the number of TCRs. Skin–joint, skin–blood, and joint–blood shared clones are represented with purple, red, and blue lines, respectively. (F) Bar chart depicting meta‐cluster location and tissue origin of cells in each of the 46 skin–joint shared CD4⁺ T cell clones. Clusters not defined as Trm, Trm‐like Treg, or Treg are grouped as “other.” (G) Pie charts indicating similarity of skin–joint, skin–blood, and joint–blood shared clones. Boxplots show the median ± interquartile range (paired t‐tests; two‐tailed, n = 5). NS, not significant; PsA, psoriatic arthritis; ST, synovial tissue; TCR, T cell receptor; Trm, tissue‐resident memory T. Color figure can be viewed in the online issue, which is available at http://onlinelibrary.wiley.com/doi/10.1002/art.43286/abstract.