A missense variant in NCF1 is associated with susceptibility to multiple autoimmune diseases

Abstract

Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease with a strong genetic component characterized by autoantibody production and a type I interferon signature. Here we report a missense variant (g.74779296G>A; p.Arg90His) in NCF1, encoding the p47^phox subunit of the phagocyte NADPH oxidase (NOX2), as the putative underlying causal variant that drives a strong SLE-associated signal detected by the Immunochip in the GTF2IRD1-GTF2I region at 7q11.23 with a complex genomic structure. We show that the p.Arg90His substitution, which is reported to cause reduced reactive oxygen species (ROS) production, predisposes to SLE (odds ratio (OR) = 3.47 in Asians (P_meta = 3.1 × 10^-104), OR = 2.61 in European Americans, OR = 2.02 in African Americans) and other autoimmune diseases, including primary Sjögren's syndrome (OR = 2.45 in Chinese, OR = 2.35 in European Americans) and rheumatoid arthritis (OR = 1.65 in Koreans). Additionally, decreased and increased copy numbers of NCF1 predispose to and protect against SLE, respectively. Our data highlight the pathogenic role of reduced NOX2-derived ROS levels in autoimmune diseases.

Fig 1. The GTF2IRD1-GTF2I-NCF1 region on 7q11.23

(a) Association plot of Immunochip variants. The locations of 1000 Genomes Project variants are indicated on the top. The allelic P value (−log₁₀P) of each Immunochip variant assessed for association with SLE in Chinese is plotted as a circle according to the location of the variant. A map of the SLE-associated SNPs described in this study is shown in a box outlined by a blue dash line. (b) Large duplications at 7q11.23 containing NCF1, NCF1B and NCF1C. Duplications are highlighted as red boxes in which the location of NCF1, NCF1B or NCF1C is indicated by a triangle. The region shown in panel a is highlighted by a blue dashed box. (c) LD (shown as r²) analyses in African-American (AfrAm), Chinese and Eurorpean-American (EurAm) subjects with a 4:2 ratio of ΔGT/GTGT (n=100 for each ancestral group).

Fig 2. Highly homologous sequence among NCF1, NCF1B and NCF1C

(a) Alignment of the DNA sequences of NCF1B and NCF1C with that of NCF1. Sequences of NCF1B and NCF1C that are not identical to that of NCF1 are shown in red. This figure was generated using the BLAT tool in the UCSC Genome Browser. (b) NCF1 variants GTGT, p.Arg90His and p.Ser99Gly and the corresponding sequences at NCF1B and NCF1C (highlighted in red). Sequences are based on human reference genome build GRCh38/hg38.

Fig 3. Determination of the ΔGT/GTGT ratio

(a) ΔGT/GTGT ratios. (b) Distribution of the ΔGT/GTGT ratio in all studied subjects. (c) Plot of the ΔGT/GTGT ratio in different ancestry groups.