A Novel De Novo NFKBIA Missense Mutation Associated to Ectodermal Dysplasia with Dysgammaglobulinemia

Abstract

Background: Inborn errors of immunity (IEIs) are comprised of heterogeneous groups of genetic disorders affecting immune function. In this report, a 17-month-old Malay patient suspected of having Hyper IgM syndrome, a type of IEIs, was described. However, the diagnosis of Hyper IgM syndrome was excluded by the normal functional studies and the mild features of ectodermal dysplasia observed from a further clinical phenotype inspection. Methods: Whole-exome sequencing (WES) was performed to unravel the causative mutation in this patient. Results: The variant analysis demonstrated a novel missense mutation in NFKBIA (NM_020529:c.94A > T,NP_065390:p.Ser32Cys) and was predicted as damaging by in silico prediction tools. The NFKBIA gene encodes for IκBα, a member of nuclear factor kappa B (NF-κB) inhibitors, playing an important role in regulating NF-κB activity. The mutation occurred at the six degrons (Asp31-Ser36) in IκBα which were evolutionarily conserved across several species. Prediction analysis suggested that the substitution of Ser32Cys may cause a loss of the phosphorylation site at residue 32 and a gain of the sumoylation site at residue 38, resulting in the alteration of post-translational modifications of IκBα required for NF-κB activation. Conclusion: Our analysis hints that the post-translational modification in the NFKBIA Ser32Cys mutant would alter the signaling pathway of NF-κB. Our findings support the usefulness of WES in diagnosing IEIs and suggest the role of post-translational modification of IκBα.

Keywords: IκBα; NF-κB; NFKBIA; hyper IgM-like phenotype; post-translational modification.

Figure 1

Whole-exome sequencing (WES) findings and variant validation. (a) WES filtering diagram. (b) Conservation analysis of NF-κB inhibitor α (IκBα). The red bracket indicates the mutation site (p.Ser32). A fully conserved residue is indicated by an asterisk sign (*). A colon sign (:) indicates conservation between groups of strongly similar properties, while a period sign (.) indicates conservation between groups of weakly similar properties. (c) Familial segregation analysis by Sanger sequencing. The red bracket shows the mutation site (c.94A). The patient had a de novo heterozygous Ser32Cys (c.94A > T) mutation.

Figure 2

The close-up image of superimposed structure of wild-type and mutant residues. (a) Ser32Cys. (b) Ser32Ile. (c) Ser32Gly. (d) Ser32Asn. (e) Ser32Arg. The protein core is shown in gray while the amino acid side chain of the wild-type (green) and the mutant (red) residue are represented as sticks.

Figure 3

Post-translational modification prediction by a deep-learning algorithm. (a) A segment of human NF-κB inhibitor α (IκBα) wild-type protein sequence (residues Met1-Cys96 are shown). (b) A segment of human IκBα mutant protein (Ser32Cys) sequence (residues Met1-Cys96 are shown). The symbol pc denotes the pyrrolidone carboxylic acid site, ub denotes the ubiquitination site, su denotes the sumoylation site, and p denotes the phosphorylation site. The mutation was predicted to abolish the phosphorylation site at residue 32 and gain a sumoylation site at residue 38 (these two residues are indicated in the red line boxes).

Figure 4

Schematic diagram illustrating the nuclear factor kappa B (NF-κB) signaling pathway mediated by the NF-κB inhibitor α (IκBα) protein. (a) The constitutive NF-κB activation is mediated by the degradation of the IκBα protein. (b) The mutant Ser32Cys IκBα protein (star symbol) is speculated to exhibit changes in the post-translational modifications. The loss of phosphorylation site at residue 32 and introduction of a new sumoylation site at residue 38 may facilitate the nuclear transport of NF-κB to the cytoplasm, resulting in the inhibition of NF-κB activation. TLR, toll-like receptor; IL1R, interleukin-1 receptor; BCR, B cell receptor; TNFR, tumor necrosis factor receptor; EDAR, ectodysplasin A receptor; NEMO, NF-κB essential modulator; IKKα, IkappaB kinase α subunit; IKKβ, IkappaB kinase β subunit; NF-κB, nuclear factor kappa B; IκBα, NF-κB inhibitor α. Created with BioRender.com, accessed on 30 July 2022.