NFKB2 haploinsufficiency identified via screening for IFN-α2 autoantibodies in children and adolescents hospitalized with SARS-CoV-2-related complications

Abstract

Background: Autoantibodies against type I IFNs occur in approximately 10% of adults with life-threatening coronavirus disease 2019 (COVID-19). The frequency of anti-IFN autoantibodies in children with severe sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is unknown.

Objective: We quantified anti-type I IFN autoantibodies in a multicenter cohort of children with severe COVID-19, multisystem inflammatory syndrome in children (MIS-C), and mild SARS-CoV-2 infections.

Methods: Circulating anti-IFN-α2 antibodies were measured by a radioligand binding assay. Whole-exome sequencing, RNA sequencing, and functional studies of peripheral blood mononuclear cells were used to study any patients with levels of anti-IFN-α2 autoantibodies exceeding the assay's positive control.

Results: Among 168 patients with severe COVID-19, 199 with MIS-C, and 45 with mild SARS-CoV-2 infections, only 1 had high levels of anti-IFN-α2 antibodies. Anti-IFN-α2 autoantibodies were not detected in patients treated with intravenous immunoglobulin before sample collection. Whole-exome sequencing identified a missense variant in the ankyrin domain of NFKB2, encoding the p100 subunit of nuclear factor kappa-light-chain enhancer of activated B cells, aka NF-κB, essential for noncanonical NF-κB signaling. The patient's peripheral blood mononuclear cells exhibited impaired cleavage of p100 characteristic of NFKB2 haploinsufficiency, an inborn error of immunity with a high prevalence of autoimmunity.

Conclusions: High levels of anti-IFN-α2 autoantibodies in children and adolescents with MIS-C, severe COVID-19, and mild SARS-CoV-2 infections are rare but can occur in patients with inborn errors of immunity.

Keywords: Anti-interferon autoantibody; COVID-19; MIS-C; NFKB2; inborn errors of immunity.

Fig 1

High levels of anti–IFN-α2 autoantibodies in children and adolescents with MIS-C, severe COVID-19, and mild SARS-CoV-2 infections are rare. Levels of anti–IFN-α2 were measured by radioligand binding assay. The dotted line represents the antibody index of the anti-Myc assay–positive control. P denotes the patient with high levels of anti–IFN-α2 autoantibodies. APS-1 was used as positive disease control. Medians and interquartile ranges are shown for the control (n = 8) and APS-1 (n = 6) cohorts.

Fig 2

A, Differentially expressed genes (≥2-fold change, false discovery rate < 0.05) determined via bulk RNA sequencing of whole blood from the single patient with increased levels of anti–IFN-α2 autoantibodies, compared to 5 disease controls (patients with MIS-C of comparable age, disease severity, and treatment). The patient and one of the disease controls (labeled 2) had 2 samples available at the midpoint of their hospitalizations. B,Top, Schematic of NFKB2 with the patient’s variant indicated with a red triangle in ankyrin repeat domain 6 (ANK6). DD, Death domain, with the degron domain needed for p100 processing noted in orange; RHD, Rel homology domain. Bottom, Steric clash (red disks) is predicted to arise from the patient’s substitution of a bulky proline residue for threonine 684. C, Representative immunoblot of full-length p100 and processed p52 in PBMCs from the patient (P) and 2 healthy controls (C1 and C2) with and without anti-CD3 stimulation for 2 days. Bar graphs show densitometric quantitation of indicated proteins pooled from 2 experiments in PBMCs from the patient and 5 controls, with and without 2 days of anti-CD3 stimulation. ∗P < .05, ∗∗P < .01 by Student t test.