Exome-wide association studies on familial and sporadic eosinophilic granulomatosis with polyangiitis

Eosinophilic granulomatosis with polyangiitis (EGPA), formerly known as Churg-Strauss syndrome, is a rare complex systemic disease. Together with granulomatosis with polyangiitis (GPA) and microscopic polyangiitis (MPA), EGPA belongs to the anti neutrophil cytoplasmic autoantibodies (ANCA)-associated vasculitis (AAV). AAVs are characterised by inflammation of blood vessels, tissue damage and development of ANCA autoantibodies, targeting proteinase 3 (PR3) and myeloperoxidase (MPO) proteins. Despite being considered part of the ANCA-associated vasculitis syndromes, EGPA has a small overlap with GPA and MPA and shows unique features, such as severe asthma and high eosinophil levels. Moreover, the majority of affected individuals shows negativity toward ANCA, with just a discrete number of patients presenting an association with MPO-ANCA. Currently, the causes of AAV are far from clear, with particular regards for EGPA. A growing number of studies has proposed multiple factors which may trigger these diseases, being either genetic or environmental. To date, three genome-wide association studies (GWAS) have identified possible candidate genes associated with GPA and MPA. However, only a single GWAS was performed on EGPA; this study identified 11 candidate loci: the strongest associations resulted in the major histocompatibility complex (MHC) region, on the human leukocyte antigen (HLA) gene. The main focus of this thesis is to investigate the genetics of 79 EGPA-affected individuals, comprising 5 families presenting 2 affected individuals each as well as unrelated EGPA-affected individuals, belonging to an Italian cohort of AAV-affected patients who have been sequenced by whole exome sequencing (WES) technology. The five families presenting EGPA-affected individuals were analysed to identify heritable pathogenic variants associated with EGPA, being single nucleotide polymorphisms, small insertions and deletions, and copy number variations. Genomic investigation resulted in a total of 8 candidate genes carrying likely causative variants. The sporadic individuals underwent the first genotype imputation-empowered exome-wide association study (ExWAS) on EGPA. The ExWAS resulted in a total of 11 EGPA-associated loci, showing specificity for MPO-ANCA-positive and ANCA-negative EGPA as well as a common set of gene independent from the ANCA status. Nowadays, genotype imputation is widely used in genomic analyses. However, it is rarely employed on sequencing data, particularly in whole exome sequencing. Hence, the research work presented in this dissertation is preceded by a performance analysis of genotype imputation on in silico WES data from the 1000 Genomes Project, which showed successful results. EGPA largely remains an enigmatic disease, which shows to have features of both a vasculitis and an eosinophilic disease. This dissertation suggested novel candidate genes likely to be associated with EGPA, confirming pathophysiological pathways related to inflammation, immunity and eosinophilia, as well as proposing novel processes likely to be involved in EGPA onset and development. Genomic and multi-omic research will boost the current understanding of EGPA and in general AAV: the discovery of possible therapeutic targets and the development of novel clinical interventions will largely benefit from the identification of the genetic factors associated with EGPA.