Genetic analysis of the pathogenic molecular sub-phenotype interferon-alpha identifies multiple novel loci involved in systemic lupus erythematosus

Abstract

Systemic lupus erythematosus (SLE) is a chronic autoimmune disorder characterized by inflammation of multiple organ systems and dysregulated interferon responses. SLE is both genetically and phenotypically heterogeneous, greatly reducing the power of case-control studies in SLE. Elevated circulating interferon-alpha (IFN-α) is a stable, heritable trait in SLE, which has been implicated in primary disease pathogenesis. About 40-50% of patients have high IFN-α, and high levels correspond with clinical differences. To study genetic heterogeneity in SLE, we performed a case-case study comparing patients with high vs low IFN-α in over 1550 SLE cases, including genome-wide association study and replication cohorts. In meta-analysis, the top associations in European ancestry were protein kinase, cyclic GMP-dependent, type I (PRKG1) rs7897633 (P(Meta) = 2.75 × 10(-8)) and purine nucleoside phosphorylase (PNP) rs1049564 (P(Meta) = 1.24 × 10(-7)). We also found evidence for cross-ancestral background associations with the ankyrin repeat domain 44 (ANKRD44) and pleckstrin homology domain containing, family F member 2 gene (PLEKHF2) loci. These loci have not been previously identified in case-control SLE genetic studies. Bioinformatic analyses implicated these loci functionally in dendritic cells and natural killer cells, both of which are involved in IFN-α production in SLE. As case-control studies of heterogeneous diseases reach a limit of feasibility with respect to subject number and detectable effect size, the study of informative pathogenic sub-phenotypes becomes an attractive strategy for genetic discovery in complex disease.

Figure 1

Top signals of association with increased serum IFN-α activity in SLE cases in the discovery phase. A) Manhattan plot shows top association signals by chromosome. B) Q–Q Plot showing association of SLE GWAS SNPs with serum IFN-α.

Figure 2

Tissue specific analysis of gene networks in different immune cells. Networks demonstrate relationships between PNP, PRKG1, ANKRD44 and PLEKHF2 to other molecules in immune cells. Edges with weight (relative confidence) greater than 0.4 are shown. Each network diagram represents a different immune cell type as follows: A: B lymphocyte, B: Dendritic cell, C: Monocyte, D: Neutrophil, E: NK cell, F: T lymphocyte.

Figure 3

Principal component analyses to detect population structure. A. and B. show principal components from all SNPs studied in the SLEGEN GWAS data set. All studied subjects are included, and reference populations from HapMap 3 samples are also included. Each circle represents an individual sample. PC = principal component, SLE=SLEGEN samples, CEU=Utah residents with Northern and Western European ancestry from the CEPH collection, CHB=Han Chinese in Beijing, China, JPT=Japanese in Tokyo, Japan, TSI=Toscani in Italy, YRI=Yoruba in Ibadan, Nigeria, AJ=Ashkenazi Jewish. C. and D. show the principal components derived from the AIMs in the replication cohort. Each symbol represents an individual sample, and colors represent self-reported ancestry.