Immunoprofiling the inflamed tissue in rheumatic diseases using single-cell technologies

Autoimmune rheumatic diseases affect millions of people around the world, causing physical disability and poor quality of life. Current treatments ameliorate the symptoms, without curing the patients. Therefore, there is an urgent need to investigate further the diseases' mechanisms and to gain new knowledge. Here, we chose to work with three of these diseases: rheumatoid arthritis (RA), psoriatic arthritis (PSA) and idiopathic inflammatory myopathies (IIM). The overall aim of this thesis was to deeply characterise immune cells, primarily effector and memory T cells, that reside in the inflamed tissue and may contribute to the disease development and progression (Figure 1). To achieve this on transcriptomic and phenotypic levels, we used a combination of single-cell RNA sequencing (scRNA-seq) and flow cytometry.

In RA, we isolated mononuclear cells from peripheral blood (PB) and synovial fluid (SF) from patients with or without anti-citrullinated protein antibodies (ACPA). We identified a G-protein coupled receptor 56 (GPR56) delineating peripheral helper T (TPH) cells in SF. TPH cells were also characterised by high expression of tissue resident memory and inhibitory receptors. GPR56 expression on CD4+ T cells was higher in ACPA+ RA, and these cells were clonally expanded (study I). Further investigating GPR56 expression, we also identified it on cytotoxic tissue resident memory and effector memory CD8+ T cells in SF of patients with RA and PsA (study II). Comparing the transcriptomic profile between ACPA+ and ACPA- patients revealed significantly higher type I interferon-stimulated gene (ISG) expression and increased interferon score in mononuclear cells in SF, but not PB, of ACPA- RA. This signature was derived from macrophages, conventional dendritic cells 2 (cDC2) and T cells, and was confirmed in synovial tissue of two ACPA- patients from an independent cohort. Interestingly, there were no differences in the IFN-a or -ß production in SF of the two patient groups (study III).

In IIM, we isolated T cells from PB and skeletal muscle tissues of patients at time of diagnosis. We identified the presence of several T-cell populations infiltrating the muscle of IIM, including T cells with cytotoxic and tissue resident memory signatures, that were clonally expanded. In two patients we detected identical T-cell clones in a follow-up muscle biopsy after treatment suggesting their implication in IIM chronicity (study IV).

In summary, our studies identify unique characteristics in the immune profile of inflamed tissues in RA, PsA and IIM, highlighting their importance in disease development and chronicity.

List of scientific papers

I. Single cell sequencing identifies clonally expanded synovial CD4+ TPH cells expressing GPR56 in rheumatoid arthritis Argyriou, A., M. H. Wadsworth, 2nd, A. Lendvai, S. M. Christensen, A. H. Hensvold, C. Gerstner, A. van Vollenhoven, K. Kravarik, A. Winkler, V. Malmström, and K. Chemin. 2022, Nat Commun, 13: 4046.
https://doi.org/10.1038/s41467-022-31519-6

II. G-protein coupled receptor 56 is expressed on tissue resident memory cytotoxic CD8 T cells in the synovial joint of patients with inflammatory arthritis Argyriou, A., B. Horuluoglu, C. Gerstner, L. Alemo Munters, F. Hjelm, C. Wennerstrom, M. Sharaf, V. Malmström, A. Hensvold, V. Oke, A. Antovic and Karine Chemin [Manuscript]

III. Synovial immune cells exhibit a type I IFN gene signature in ACPA-negative rheumatoid arthritis Argyriou, A., M. H. Wadsworth, 2nd, C. Krishna, C. Gerstner, B. Horuluoglu, M. Sijbranda,, L. Rönnblom, M.L. Eloranta, M. Wahren- Herlenius, A. Hensvold, A. Winkler, V. Malmström and K. Chemin. [Submitted]

IV. Single-cell profiling of muscle-infiltrating T cells in idiopathic inflammatory myopathies
Argyriou, A., B. Horuluoglu, A. S. Galindo-Feria, J. S. Diaz-Boada, M. Sijbranda, A. Notarnicola, L. Dani, A. van Vollenhoven, D. Ramsköld, I. Nennesmo, M. Dastmalchi, I. E. Lundberg, L. M. Diaz-Gallo, and K. Chemin. 2023., EMBO Mol Med, 15: e17240.
https://doi.org/10.15252/emmm.202217240