Human IRF7 gene variants in health and disease
Creators: name: Stanley, Maurice
Publisher: name: The Australian National University
Year: 2022

description: Lupus is a complex heterogeneous disease driven by a combination of genetic and environmental factors. Type 1 interferon (T1 IFN) is central to lupus pathogenesis, with 50-75% of adult lupus patients expressing elevated levels of T1 IFN mRNA in blood. Recent research published in the Vinuesa lab demonstrated that rare and novel single nucleotide polymorphisms (SNPs) in systemic lupus erythematosus (SLE) patients result in increased T1 IFN signalling, contributing to disease development and pathogenesis. Interferon Regulatory Factor 7 (IRF7) is a major signalling component in antiviral and T1 IFN responses and has been reproducibly linked to lupus by Genome-Wide Association Studies. Therefore, we sought to identify and study the contribution of rare genetic variants in IRF7 to SLE. While the SLE cohort was enriched for rare IRF7 SNPs, functional testing revealed that these SNPs did not alter IFNB reporter expression significantly from wild type IRF7. However, we found high-frequency SNPs, IRF7 K179E and IRF7 Q412R, co-inherited in the heterozygous or homozygous state in a 1:1 ratio in &gt;99% of the identified carriers of these mutations. The presence of two SNPs collectively referred to as the IRF7 haplotype variants were also prevalent in the adult healthy control cohort. Further genomic analysis found the two SNPs to exist in the Neanderthal genome and absent in Denisovan DNA. Testing these SNPs using an overexpression based IFNB luciferase reporter system demonstrated that the IRF7 K179E increased IFNB expression as a gain-of-function mutant. In contrast, IRF7 Q412R reduced IFNB expression as a partial loss-of-function mutant. The combined IRF7 K179E;Q412R haplotype had modestly reduced IFNB expression, summarily behaving as a hypomorphic allele. No alterations to cellular localisation differences or viral suppressive activity were observed. Notably, differences in phosphorylation patterns were apparent for IRF7 K179E when expressed alone or with IRF7 Q412R as a haplotype and were altered by TBK1 co-expression. To characterise the effect of haplotype SNPs on immune cell responses, we immunophenotyped healthy donor peripheral blood mononuclear cells, which revealed a significant increase in circulating and memory Tfh T cells, CD8+ T effector memory cells and CD56high CD16- Natural Killer cells in the homozygous group when compared to heterozygous IRF7 haplotype carriers. Thus, although these mutations are common in the human population, it is extremely rare for these variants to exist in isolation without the presence of its pathogenic interacting partner. These gain and loss-of-function mutations are likely permitted to exist at such high frequencies as they exert neutralising effects on each other. When found in isolation, either variant is likely to contribute to an autoimmune (IRF7 K179E) or immunodeficient phenotype (IRF7 Q412R). In addition, we identified rare IRF7 variants in patients with immunodeficiency. Rare loss-of-function mutations in IRF7 have been shown to increase the risk of influenza virus infection and hospitalisation. Within our Primary Immune Deficiency (PID) cohort, we identified two novel IRF7 mutations within the DNA binding domain of IRF7, IRF7 R41C and IRF7 L99V. Both these mutations impaired nuclear translocation resulting in the complete inability to induce IFNB expression. As a result of this loss of function, these novel alleles could not suppress herpes simplex virus infection in an overexpression system. Thus, taken together, this thesis helps in broadening our understanding of common and rare variants and illustrates the importance to genomic medicine in characterising all mutations within a given gene. This thesis has also uncovered novel mutations in IRF7 that contribute to human immunodeficiency and increase susceptibility to viral infections.