Exome Sequencing Identifies a Novel MAP3K14 Mutation in Recessive Atypical Combined Immunodeficiency

Abstract

Primary immunodeficiency disorders (PIDs) render patients vulnerable to infection with a wide range of microorganisms and thus provide good in vivo models for the assessment of immune responses during infectious challenges. Priming of the immune system, especially in infancy, depends on different environmental exposures and medical practices. This may determine the timing and phenotype of clinical appearance of immune deficits as exemplified with early exposure to Bacillus Calmette-Guérin (BCG) vaccination and dissemination in combined immunodeficiencies. Varied phenotype expression poses a challenge to identification of the putative immune deficit. Without the availability of genomic diagnosis and data analysis resources and with limited capacity for functional definition of immune pathways, it is difficult to establish a definitive diagnosis and to decide on appropriate treatment. This study describes the use of exome sequencing to identify a homozygous recessive variant in MAP3K14, NIKVal345Met, in a patient with combined immunodeficiency, disseminated BCG-osis, and paradoxically elevated lymphocytes. Laboratory testing confirmed hypogammaglobulinemia with normal CD19, but failed to confirm a definitive diagnosis for targeted treatment decisions. NIKVal345Met is predicted to be deleterious and pathogenic by two in silico prediction tools and is situated in a gene crucial for effective functioning of the non-canonical nuclear factor-kappa B signaling pathway. Functional analysis of NIKVal345Met- versus NIKWT-transfected human embryonic kidney-293T cells showed that this mutation significantly affects the kinase activity of NIK leading to decreased levels of phosphorylated IkappaB kinase-alpha (IKKα), the target of NIK. BCG-stimulated RAW264.7 cells transfected with NIKVal345Met also presented with reduced levels of phosphorylated IKKα, significantly increased p100 levels and significantly decreased p52 levels compared to cells transfected with NIKWT. Ideally, these experiments would have been conducted in patient-derived immune cells, but we were unable to source these cells from the patient. The functional analysis described in this paper supports previous illustrations of the importance of NIK in human immune responses and demonstrates the involvement of function-altering mutations in MAP3K14 in PIDs. The genomic approach used for this patient demonstrates its value in the diagnosis of an unusual PID and as a tool for detecting rarer mutations to help guide treatment approaches.

Medullary thymic epithelial NF–kB-inducing kinase (NIK)/IKKα pathway shapes autoimmunity and liver and lung homeostasis in mice

“…Of note, a human homozygous loss-offunction NIK Pro565Arg variant is also linked to child death (13). A homozygous NIK Val345Met variant is associated with severe child illness (14). Thus, TEC-intrinsic NIK/IKKα pathways crucially support life in both mice and humans.…”

“…Global inactivation of NIK abrogates thymic medullary development in mice, leading to autoimmune disease (11,12). Importantly, human NIK Pro565Arg and NIK Val345Met variants are linked to profound immune dysfunctions (13,14). Thus, NIK is an essential regulator of the immune system in both mice and humans.…”

Tuberculosis research in South Africa over the past 30 years: From bench to bedside

“…Using an overexpression cell model to mimic the effects of the mutations, we showed that the mutation significantly impaired the ability of NIK to phosphorylate IKKα. [51] Subsequent to this finding, we identified the same mutation in another patient presenting with destructive pneumonia and hypogammaglobulinaemia. Both parents were heterozygous carriers of the mutation.…”

“…PIDs are challenging to diagnose because of their variable clinical presentations but, in many cases, PIDDGEN has already been able to make a definitive diagnosis only through WES. [51,92,93] One such case clearly illustrates the value of WES for diagnosis of PIDs: Patient CE, a young girl from a non-consanguineous marriage, was at two years of age diagnosed with humoral immunodeficiency after presenting with a BCG abscess on the upper leg. CE was placed on intravenous immunoglobulin replacement therapy, but developed BCG meningitis a year later.…”

Immunologic reconstitution following hematopoietic stem cell transplantation despite lymph node paucity in NF-κB–inducing kinase deficiency

“…3 Diagnosing peanut allergy involves diagnostic procedures including careful review of clinical reactions, peanut-specific IgE, skin prick test (SPT), and an oral peanut food challenge (FC), optimally performed using a double-blind placebo-controlled FC approach. In addition, component-resolved allergen diagnosis [4][5][6] (CRD) and possibly also peanut conjunctival allergen provocation test 7 (CAPT) may improve peanut allergy diagnosis. Testing CRD in diagnosis of peanut allergy has been found useful in assessing the likelihood of clinical allergy or cross-reactive allergic manifestations.…”