Single-cell characterisation of T lymphocyte immune responses in spondyloarthropathy

The spondyloarthropathies (SpA) are a collection of inflammatory disorders of undetermined etiology affecting the joints and connective tissues, however existing evidence suggests a role for the microbiome, CD4 and CD8 T cells in disease pathogenesis. A CD154 activation based functional assay was first used to quantify and characterise CD4+ memory T cell populations reactive to a panel of 13 microbes found at mucosal barrier sites, predominantly gut bacteria. Peripheral blood mononuclear cells (PBMC) from 31 SpA, 17 rheumatoid arthritis (RA) and 14 healthy controls, as well as synovial fluid mononuclear cells (SFMC) from 9 SpA patients were separated and stimulated overnight with a panel of microbial lysates. Cells were then stained for CD154, TNFα, IFNγ, IL-17A, GM-CSF, IL-22 and IL-2 and analysed by flow cytometry. Single-cell RNA sequencing (scRNA-seq) was then used to characterise S. typhimurium-reactive synovial Th memory cells from a psoriatic arthritis (PsA) patient, in addition to ex vivo CD4 and CD8 memory T cells from the peripheral blood and synovial fluid of 6 PsA patients. The frequency of Th memory cells reactive to microbes capable of inducing a type 17/17.1 response were enriched in SpA synovial fluid relative to blood, and scRNA-seq analysis revealed a trajectory along which Th17.1 cells could differentiate into a "stem-like" memory pool capable of proliferation or into a Th17 regulatory phenotype. Pronounced clonal expansions of ex vivo CD8 memory T-cells within the joints of PsA patients were also identified by scRNA-seq. They exhibited distinct gene expression profiles including cycling, activation, tissue homing and tissue residency markers. Pseudotime analysis of these clonal CD8 populations identified trajectories in which tissue residency can represent an intermediate developmental state giving rise to activated, cycling and exhausted CD8 populations. Comparing T cell clonality across patients further revealed specificity convergence of clones against a putative common antigen. A role for gut microbes in SpA pathogenesis was supported by the higher frequency of Th17 cells reactive to Salmonella typhimurium found in SpA synovial fluid compared with SpA peripheral blood, and characterisation of these cells revealed trajectories of differentiation which could potentially be targeted to skew Th17.1 responses towards a regulatory phenotype. The identification of pro-inflammatory and clonally expanded CD8 T cells by scRNA-seq also suggests an antigen driven expansion of pathogenic CD8 T cells in PsA.