MO062RARE GENETIC VARIANTS IMPLICATED IN INNATE AND ADAPTIVE IMMUNITY CO-SEGREGATE WITH FAMILIAL IGA NEPHROPATHY

Abstract

Introduction and Aims: The pathogenesis of IgA nephropathy (IgAN) is still not clear but familial clustering demonstrates a strong genetic involvement. Aim of our study was to find rare, highly penetrant risk variants, combining family-based linkage analysis with whole exome sequencing (WES). Methods: Genotyping and linkage analyses have been performed on 16 families of the South Italian ancestry. Linkage analysis was carried out under models of locus homogeneity or heterogeneity and chromosome 4q26 gave the strongest signal and several other linkage signals were also detected on other chromosomes. Eight families (two familial cases and one internal control) that showed the strongest evidence to multiple linked regions were selected for WES. Variant calling and annotation were performed with standard procedures. High priority variants were chosen with stringent criteria and based on their co-segregation in affected family members and the presence within linked areas. High-priority variants were followed up using Sanger sequencing and custom TaqMan assays on the initial familial cohort, and on 240 IgAN patients and 113 in-house population controls from the general population. The functional connectivity between variants and the relationship with previously published expression data was evaluated with Ingenuity Pathway Analysis. Results: We confirmed and refined our previously published identified regions on chromosome 4q26, 6q22-23 and17q21 linked with IgAN. Moreover, additional signals were detected on chromosome 1p, 2p, 3p, 5q, 8p, 9p, 20q. Our exome study identified a total of 150,913 variants in at least one of the 24 samples. At the end of the filtering strategy we discovered 45 co-segregating variants in affected individuals. The most functionally relevant variants were validated using Sanger sequencing. Taqman assays were set-up on validated variants to extend our analyses on other familial and sporadic IgAN patients and in-house population controls. We found that the variants were extremely rare and segregated with IgAN status in each family. MAF of candidate variants was also evaluated and checked in 200 population controls. None of the selected variants were present in controls. The co-segregating validated variants within coding or regulatory regions of 22 functionally related genes merged into a common network. Overlaying publicly available expression data, we found that genes whose expression is known to be altered in IgAN, were also included in this specific immune-related network. Conclusions: Our study confirms the polygenic and multiple-susceptibility-gene model for familial IgAN. It identifies many rare, apparently independent segregating variants that are involved in a common pathway. This identified pathway involves innate and adaptive immunity.