Homozygous STAT2 gain-of-function mutation by loss of USP18 activity in a patient with type I interferonopathy

Abstract

Type I interferonopathies are monogenic disorders characterized by enhanced type I interferon (IFN-I) cytokine activity. Inherited USP18 and ISG15 deficiencies underlie type I interferonopathies by preventing the regulation of late responses to IFN-I. Specifically, USP18, being stabilized by ISG15, sterically hinders JAK1 from binding to the IFNAR2 subunit of the IFN-I receptor. We report an infant who died of autoinflammation due to a homozygous missense mutation (R148Q) in STAT2. The variant is a gain of function (GOF) for induction of the late, but not early, response to IFN-I. Surprisingly, the mutation does not enhance the intrinsic activity of the STAT2-containing transcriptional complex responsible for IFN-I–stimulated gene induction. Rather, the STAT2 R148Q variant is a GOF because it fails to appropriately traffic USP18 to IFNAR2, thereby preventing USP18 from negatively regulating responses to IFN-I. Homozygosity for STAT2 R148Q represents a novel molecular and clinical phenocopy of inherited USP18 deficiency, which, together with inherited ISG15 deficiency, defines a group of type I interferonopathies characterized by an impaired regulation of late cellular responses to IFN-I.

The Ever-Increasing Array of Novel Inborn Errors of Immunity: an Interim Update by the IUIS Committee

“…They have also already highlighted the heterogenous phenotypes that can result from variants in the same gene (e.g., CDC42 [ 33 – 39 , 52 ]), indicated that significant diseases can arise from mono-allelic or bi-allelic loss of function ( IL6ST [ 9 ], RIPK1 [ 42 , 43 ]) or bi-allelic loss- or gain-of-function ( CEBPE [ 24 ], STAT2 [ 40 , 41 ]) variants in the same gene, or from autoAb phenocopies of monogenic lesions (e.g., COVID19 and anti-IFN Abs) [ 48 ], and identified novel somatic mutations as pathogenic causes of immune disorders ( UBA1 ) [ 47 ]. Importantly, they have also provided opportunities for therapeutic interventions, such as JAK inhibitors to treat STAT2 gain of function [ 40 , 41 ] or SOCS1 deficiency [ 22 ], IFNγ to treat mycobacterial disease [ 25 , 26 ], or early IFN-β or IFN-α2a treatment of SARS-CoV2 infection in COVID-19 patients with autoantibodies against IFN-α or IFN-ω [ 67 ] or impaired type 1 IFN responses [ 70 ]. This snapshot of genetic discoveries underpinning human immune disorders further highlights the critical contributions of inborn errors of immunity to our broader understanding of basic, translational, and clinical immunology.…”

“…Recently-reported gene defects have been found for most categories of inborn errors of immunity, including novel causes of: SCID ( PAX1 [ 5 , 6 ], SLP76 [ 7 ]); CID ( MCM10 [ 8 ], IL6ST [ 9 – 11 ]); Predominantly antibody deficiencies ( FNIP1 [ 14 , 15 ], PIK3CG [ 16 , 17 ], CTNNBL1 [ 18 ], TNFSF13 [ 19 ]); Autoinflammatory diseases ( SOCS1 [ 20 – 22 ], TET2 [ 23 ], CEBPE [ 24 ], CDC42 [ 33 – 39 ], LSM11 , RNU7–1 [ 32 ], STAT2 [ 40 , 41 ], RIPK1 [ 42 , 43 ], NCKAP1L [ 44 – 46 ]), UBA1 (somatic mutations) [ 47 ]; and Susceptibility to infection with specific pathogens ( MAPK8 [ 31 ]; TBX21 [ 25 ], IFNG [ 26 ], NOS2 [ 28 ], SNORA31 [ 29 ], ATG4A , MAP1LC3B2 [ 30 ]) (Table 1 ). …”

“…Autoinflammatory diseases ( SOCS1 [ 20 – 22 ], TET2 [ 23 ], CEBPE [ 24 ], CDC42 [ 33 – 39 ], LSM11 , RNU7–1 [ 32 ], STAT2 [ 40 , 41 ], RIPK1 [ 42 , 43 ], NCKAP1L [ 44 – 46 ]), UBA1 (somatic mutations) [ 47 ]; and…”

“…Notably, several of these genes are already included in previous IUIS updates, namely IL6ST , STAT2 , CEBPE , and RIPK1 [ 2 , 3 ]. However, they are listed here because the variant identified is pathogenic via a distinct mechanism and/or different mode of inheritance; i.e., autosomal recessive (AR) vs autosomal dominant for IL6ST [ 9 ] or RIPK1 [ 42 , 43 ], partial deficiency vs complete deficiency for IL6ST [ 10 , 11 ], or AR loss of function vs AR gain of function for CEBPE [ 24 ] or STAT2 [ 40 , 41 ] . Furthermore, the GOF variants reported for CEBPE appear to represent the first described germline neomorphic mutation in inborn errors of immunity where the variant allele has completely novel functions not seen for the wild type gene [ 24 ].…”

“…• ↑ serum levels of IL1, IL18, IFN-γ, ferritin, sCD25, CRP etc. • Recurrent GIT/RT infection; • Neurodevelopmental delay, FTT • Mutation affects actin function; • Treated with Anakinra/ IFN-γ mAb ↓NK function (cytox), Table 7 Subtable 1 [ 33 – 39 ] STAT2 (GOF, 3 patients; all deceased; 2 additional deceased sibs but not genotyped; 2 unrelated families) AR (GOF) • Low frequency of NK, ↑ frequency of T cells (esp naïve), normal NK degranulation • Total B cell frequencies within age-matched controls’ ranges • slight ↑ transitional and naïve B cells %‘s • Low/normal • Severe fatal early-onset autoinflammation (skin ulceration, fever, seizures, intracranial calcification, multiorgan dysfunction, abnormal neurodevelopment; phenocopy of USP18 deficiency) • ↑ serum IFN-α, IL6, TNFα • IFN-opathy gene signature (impaired regulation of late cellular responses to type 1 IFN), Validation • Study of the mutant STAT2 alleles in STAT2 deficient human cell line, and patient’s immortalized fibroblasts • Patient cells hyper-sensitive to IFN-α → prolonged JAK/STAT signaling/transcriptional activation • Biochemical confirmation that mutant allele is GOF in homozygous, but not heterozygous, combination • Impaired interaction of GOF STAT2 protein with USP18, a negative regulator of type 1 IFN responses Table 7 Subtable 1 [ 40 , 41 ] RIPK1 (12 patients; 5 families, 2 papers) AD • Normal T and NK cell numbers • Low/normal CD4 + T cells • Normal/hi CD8 + T cells • ↑ DN T cells • Normal B cells ND • Autoinflamm disorder: regular/prolonged fevers, lymphadenopathy, spleno/hepatomegaly, ulcers, arthralgia, GI features, • ↑ inflamm markers, ↑ pro-inflamm cytokines/gene signature; • Responsive to Tocilizumab (not IL1/TNF blockade) Table 7 Subtable 2 [ 42 , 43 ] NCKAP1L (9 patients; 7 families, 3 papers) AR (LOF) • Normal T cell numbers • ↑T CM , exhausted cells; • Possibly immature NK cells but intact function • Normal B cells and naïve/memory subsets • ↑ CD21 lo cells • Normal/ ↑ Ig levels • autoAbs • Recurrent URTI, skin rashes/abscesses, ulcers, • Anti dsDNA Abs, SLE-like, lymphadenopathy, fever, HLH-like • FTT • Immunodeficiency coupled with atopy, lymphoproliferation, hyperinflammation ,and cytokine overproduction (↑ Th1)...…”