Genomic Pathology of SLE-Associated Copy-Number Variation at the FCGR2C/FCGR3B/FCGR2B Locus

Abstract

Reduced FCGR3B copy number is associated with increased risk of systemic lupus erythematosus (SLE). The five FCGR2/FCGR3 genes are arranged across two highly paralogous genomic segments on chromosome 1q23. Previous studies have suggested mechanisms for structural rearrangements at the FCGR2/FCGR3 locus and have proposed mechanisms whereby altered FCGR3B copy number predisposes to autoimmunity, but the high degree of sequence similarity between paralogous segments has prevented precise definition of the molecular events and their functional consequences. To pursue the genomic pathology associated with FCGR3B copy-number variation, we integrated sequencing data from fosmid and bacterial artificial chromosome clones and sequence-captured DNA from FCGR3B-deleted genomes to establish a detailed map of allelic and paralogous sequence variation across the FCGR2/FCGR3 locus. This analysis identified two highly paralogous 24.5 kb blocks within the FCGR2C/FCGR3B/FCGR2B locus that are devoid of nonpolymorphic paralogous sequence variations and that define the limits of the genomic regions in which nonallelic homologous recombination leads to FCGR2C/FCGR3B copy-number variation. Further, the data showed evidence of swapping of haplotype blocks between these highly paralogous blocks that most likely arose from sequential ancestral recombination events across the region. Functionally, we found by flow cytometry, immunoblotting and cDNA sequencing that individuals with FCGR3B-deleted alleles show ectopic presence of FcγRIIb on natural killer (NK) cells. We conclude that FCGR3B deletion juxtaposes the 5'-regulatory sequences of FCGR2C with the coding sequence of FCGR2B, creating a chimeric gene that results in an ectopic accumulation of FcγRIIb on NK cells and provides an explanation for SLE risk associated with reduced FCGR3B gene copy number.

Development and Characterization of Monoclonal Antibodies Specific for Mouse and Human Fcγ Receptors

“…However, in a few donors possessing the known open reading frame for hFcgRIIC (37), as determined by multiplex ligation-dependent probe amplification (37) Cragg, and J.C. Strefford, submitted for publication), the hFcgRIIB mAb 7C07 gave a low level of staining in a small population of NK cells (data not shown) in accordance with their expression of hFcgRIIC (displaying an identical extracellular domain to hFcgRIIB). The regulation and functional relevance of hFcgRIIC expression has been reported previously (37)(38)(39)(40) and is the subject of our ongoing studies. B cells (CD3 2 CD19 + ) expressed high levels of hFcgRIIB, but did not express hFcgRI, -IIA, or -III (Fig.…”

Human gene copy number variation and infectious disease

“…There is a gene dosage effect for FCGR3B, where expression 313 levels on the cell surface reflect gene copy number (Willcocks et al 2008). Deletions of FCGR3B also 314 alters the expression pattern of FCGR2B, which itself is not CNV, causing it to be expressed on 315 natural killer cells ( (Mueller et al 2012;van der Heijden et al 2012), figure 4 example 5)). 316…”

Diversification of IgG effector functions

“…Likewise, genetic variants of FCGR2B that influence receptor expression or activity constitute risk factors for the development of autoimmune pathologies in humans. Since FcγRIIb expression on B cells represents a critical factor for B-cell selection, fluctuations in the FcγRIIb expression levels could readily impact IgG responses (91)(92)(93)(94)(95). Indeed, engagement of CD23 on B cells by sialylated IgG immune complexes up-regulates B-cell FcγRIIb expression, which subsequently raises the threshold for B-cell selection, leading to the generation of high-affinity IgG responses (34).…”