Anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is a rare autoimmune disease with a UK prevalence of 250 per million. The immunopathogenesis includes neutrophil activation by B cell-derived ANCAs, activation of the alternative complement pathway, and dysregulated T cell responses that result in a necrotizing vasculitis of small blood vessels. The central role of B cells is highlighted by the presence of activated B cells in inflammatory lesions, the association of B cell activation status with disease activity and the efficacy of B cell depletion therapy with rituximab as both an induction and maintenance agent. Rituximab, the only licenced therapy for AAV, is associated with a remission failure rate of 10-30%, and for those who achieve remission, repeated doses are needed to prevent relapses, increasing the risk of hypogammaglobulinaemia and susceptibility to infections. Thus, there is an unmet need to develop a treatment regimen that induces prolonged remission without the need for maintenance therapy. This thesis investigates some of the mechanisms, shortfalls and clinical implications of B cell targeted therapies for the treatment of AAV.

As our understanding of rituximab’s mechanism of action has evolved, the concept of rituximab resistance has emerged. In the first section, a combination of flow cytometry and single cell RNA sequencing (scRNA-seq) is used to demonstrate the dissociation between peripheral B cell depletion and the persistence of B cells in the tissue after rituximab using sequential nasal mucosal biopsies in patients with active AAV. Persistent nasal B cells had expression profiles suggesting the capacity for antigen presentation and production of proinflammatory cytokines. Quantification of predicted cell-cell interactions based on receptor-ligand expression revealed several significant predicted interactions between B and T cell ligand and receptor gene expression, highlighting the complex interplay of stimulatory and inhibitory signalling pathways within the tissue microenvironment, and also revealing some potential mechanisms of rituximab resistance.

In the second section, experiments were conducted using COMBIVAS trial (a mechanistic study of rituximab plus belimumab versus rituximab plus placebo in AAV) samples to evaluate the early pharmacodynamic effects of BAFF antagonism with belimumab on B cells and B cell subsets in patients with active AAV. A combination of flow cytometry and scRNA-seq was used with the primary aim of understanding the mechanisms driving the early rise in circulating B cell numbers after belimumab. We report variable elevations in circulating memory B cells after belimumab that were potentially influenced by prior therapies and/or subtherapeutic drug concentrations. Evidence to support the hypothesis of belimumab-induced tissue mobilisation of B cells was supported by the finding of blood B cells from belimumab-treated samples with expression profiles that were compatible with recent tissue residency. Unfortunately, the BCR-seq analysis, which was limited by poor BCR coverage and small sample size, did not corroborate these findings.

In the final section, data from a cohort of rituximab-treated AAV patients was analysed to test whether patient-specific and/or disease-specific risk factors for relapse and infection could be used in combination to generate risk prediction models to help guide decision making regarding extended rituximab maintenance therapy in AAV. While the models had insufficient power to discriminate risk between individual patients, they were able to assign patients into risk groups for both relapse and infection. The ability to identify risk groups may help in decisions regarding the potential benefit of ongoing rituximab treatment.