Genetic Interactions Between SNP Variants in C3 Receptor Sub-units in Patients with SLE

Abstract

Background/Purpose: Genome-wide and candidate gene studies have supported a role for genes involved in immune complex processing as being important contributors to development of SLE. The association of ITGAMvariants and SLE highlights the importance of complement and complement receptors in the SLE diathesis. We hypothesized that there may also be statistical interactions between variants in genes that encode proteins in the complement system. We have developed a gene-based analysis strategy and present data that support a role for genetic interactions between variants in genes involved in the complement system.

Methods: A newly developed variation of the Rank Truncated Product (RTP) statistic was used to assess the combined genetic contribution of loci involved in complement component 3 (C3), C3 activation (C2, C3, C4, CFH, CRP, MBL2), and C3 recognition (CR1, CR2, CR3 (ITGAM/ITGB2), CR4 (ITGAX/ITGB2)). The significance of the RTP statistic for each gene pair was assessed using a parametric bootstrap procedure. The study population included 16,105 unrelated SLE affecteds and controls from four different ancestry backgrounds (European (EA), African (AA), Hispanic (Hisp), Asian). All participants were of self-reported sex and race/ethnicity. Affecteds met 1997 American College of Rheumatology revised criteria for the classification of SLE. 347 SNPs in these loci were genotyped on an Illumina iSelect custom array as part of the Large Lupus Association Study 2 (LLAS2).

Results: We identify new SNP associations across multiple race/ethnicities in the C2 locus with SLE (p<10-11/ <10‑7, OR=1.8/1.7 in EA/AA) and confirm trans-racial associations of ITGAM and SLE (P<10-27/10-11/10-12OR=1.7/1.6/2.1 in EA/AA/Hisp respectively).

We hypothesized that there are genetic interactions between variants in genes encoding proteins in the C3 pathway that are known to functionally and/or physically interact. Indeed, significant gene-by-gene genetic interactions were identified between receptor-ligand, between C3 and complement regulators and between C3 receptor loci. Specific interactions included C3-ITGAM (p<0.001 in AA), C3-ITGB2 (p=0.002 in Hisp), C3-CRP (p=0.003 in AA), C3-CFH (p=0.009 in AA), ITGAM-ITGB2 ( p<0.001 in Hisp) and ITGAX-ITGB2(with trans-racial association in both Hisp and EA, p=0.02/0.045).

Conclusion: We demonstrate significant and replicated genetic association of genes in the C3 pathway with SLE. These associations extend beyond the ITGAM locus to include other C3 receptor genes and regulators of C3 activation. The elucidation of genetic interactions between genes in this pathway demonstrates that the contribution of variants in the C3 pathway act both independently and jointly.