Updates on new monogenic inborn errors of immunity

Abstract

Inborn errors of immunity (IEI), also referred to as primary immunodeficiencies (PID), are disorders that, for the most part, result from mutations in genes involved in immune host defense and immune regulation. Thanks to the increased availability of high-throughput DNA sequencing and the improvement in genomic data interpretation, the number of newly identified genes associated with IEI has exponentially increased over the last decade. We reviewed four recently described monogenic IEI and discussed the clinical and immunologic features of these new conditions.

1 |. INTRODUCTION

Inborn errors of immunity (IEI), also referred to as primary immunodeficiencies (PID), are disorders that, for the most part, result from mutations in genes involved in immune host defense and immunoregulation. These conditions are characterized by various combinations of recurrent infections, autoimmunity, lymphoproliferation, inflammatory manifestations, atopy, and malignancy.

The most recent classification from the International Union of Immunological Societies (IUIS) includes 430 IEI with 65 gene defects discovered or better characterized in the past two years.¹ In addition to the identification of novel genes, it is now clear that distinct clinical phenotypes may be sustained by gain-of-function (GoF) or loss-of-function (LoF) mutations in the same gene.² Moreover, different activity degrees of mutant proteins due to hypomorphic and hypermorphic mutations may also cause EIE phenotypic variability. In this context, we reviewed four recently described IEI, discussing the clinical and immunologic features of these new conditions.

2 |. PAX1 DEFICIENCY

PAX1 is a member of the paired box (PAX) family of transcription factors and has an essential role during embryogenesis. It is expressed in the pharyngeal pouches that give rise to the thymus, tonsils, parathyroid glands, thyroid, and middle ear development during human embryogenesis. Homozygous mutations in PAX1 were previously identified in patients with otofaciocervical syndrome type 2 (OTFCS2), a rare disorder characterized by peculiar syndromic features.³ Yamazaki et al. provided an in-depth clinical, biochemical, and immunologic description of six patients from three unrelated families with biallelic, loss-of-function PAX1 mutations, demonstrating that PAX1 is essential for development and function of the human thymus.⁴ All the patients presented with OTFCS2 and severe T-cell immunodeficiency (five patients with T⁻ B⁺NK⁺ SCID and one patient with Omenn syndrome). Because of the severe immunologic abnormalities, hematopoietic stem cell transplantation was attempted in four of the six patients, before the gene defect was known. Despite engraftment in three of them, HSCT failed to correct the T-cell immunodeficiency. As for other severe T-cell immunodeficiencies characterized by a primary thymic defect (complete DiGeorge syndrome, CHARGE syndrome, and FOXN1 deficiency), it is now clear that thymus transplantation represents the treatment of choice to correct the immunodeficiency related to these conditions, allowing for de novo generation of a polyclonal repertoire of naïve T cells.⁵

3 |. FOXN1 HAPLOINSUFFICIENCY

FOXN1 (forkhead box N1), a member of the FOX family of transcription factors, is the master regulator of thymic epithelium development. Biallelic LoF FOXN1 mutations lead to alopecia, nail dystrophy, and thymic aplasia accounting for the nude/severe combined immunodeficiency (nu/SCID) phenotype in mice and humans.⁶ Recently, Du et al have demonstrated that certain biallelic FOXN1 mutations may cause SCID without hair or nail abnormalities.⁷ Moreover, Bosticardo et al reported that heterozygous LoF FOXN1 gene variants are responsible for low levels of T-cell receptor excision circles (TRECs) and T-cell lymphopenia at birth, and persistent lymphopenia and increased susceptibility to infections in infancy.⁸ CD8⁺ T-cell lymphopenia and isolated nail dystrophy have been observed in adults. A dramatic reduction in the frequency and absolute count of early thymic progenitors and a severe reduction in the expression of all main transcriptional targets of FOXN1 in the thymus were observed during the first weeks of life of Foxn1^nu/+ mice, with a trend toward normalization over time. Overall, these data indicate that FOXN1 gene dosage is most critical during embryonic and early post-natal life so that FOXN1 haploinsufficiency causes low TRECs and T-cell lymphopenia at birth that progressively improves with age. This aspect is of fundamental importance when interpreting results of newborn screening for SCID. However, the observation that a few babies with heterozygous LoF FOXN1 variants developed serious infections suggests careful clinical monitoring and adoption of preventive measures. Finally, HSCT is not a curative treatment for individuals with FOXN1 haploinsufficiency, consistent with the thymus-intrinsic role of the molecule.

4 |. NOS2 DEFICIENCY

Drutman et al described a previously healthy 51-year-old man from Iran who, after acute CMV infection, had an onset of progressive CMV disease that led to his death 29 months later.⁹ Immunologic tests performed during CMV infection revealed a decreased number of CD4⁺ T cells with a normal CD8⁺ T-cell count, and a decreased number of B cells and natural killer (NK) cells. Whole-exome sequencing (WES) revealed a homozygous frameshift mutation in nitric oxide synthase 2 (NOS2, c.1436_1437insT), which was predicted to lead to a premature stop codon in the oxygenase domain p.Ile391IlefsTer26 (herein called I391fs). NOS2 catalyzes the formation of nitric oxide from arginine. The analysis of function associated with NOS2 I391fs variant confirmed that this homozygous mutation encodes a truncated NOS2 protein that cannot produce nitric oxide. The mechanistic connection between NOS2 deficiency and the patient’s CMV phenotype will need further investigation. Possible explanations include the following: (I) NOS2 expression in CMV-infected epithelial cells is required to control the infection, (II) NOS2 expression in myeloid cells is required in order to limit CMV, and (III) NOS2 mediates a T-cell signaling program that is essential for long-term T-cell homeostasis in humans.

5 |. ITPKB DEFICIENCY

Inositol phosphate 3-kinases (ITPKs) control inositol phosphate signaling downstream of TCR activation.¹⁰ Antigen receptor engagement activates ITPKs, which in turn phosphorylate the phosphatidylinositol (4,5) bisphosphate to generate phosphatidylinositol (3,4,5) trisphosphate (PIP3), resulting in membrane recruitment and activation of the pleckstrin homology domains of PDK1-, ITK/TEC-, and AKT-family kinases. Moreover, ITPKs are essential to convert inositol 1,4,5- trisphosphate (IP3) into inositol 1,3,4,5-tetrakisphosphate (IP4).¹⁰ Three ITPK isoforms have been described: ITPKA is exclusively expressed in neurons, whereas ITPKB and ITPKC are ubiquitously expressed.¹⁰ Although they share highly homologous kinase domains at their C-terminus, these ITPK proteins differ in their N-terminus domains. Recently, Almutairi et al reported the first patient with ITPKB deficiency.¹¹ The patient, born of consanguineous Egyptian parents, developed failure to thrive, persistent thrush shortly after birth, recurrent pneumonia beginning at age two months, and Klebsiella pneumoniae skin abscesses at age 6 and 10 months. Laboratory tests revealed anemia, leukopenia, neutropenia, thrombocytopenia, and profound CD3⁺ CD4⁺ and CD8⁺ cell lymphopenia with normal CD19⁺ and CD56⁺ natural killer (NK)-cell numbers. The patient died at age 11 months with severe pneumonia and Staphylococcus aureus sepsis. Overall, the clinical and laboratory findings were consistent with T⁻B⁺NK⁺SCID. After the exclusion of potentially deleterious mutations in any known primary immunodeficiency genes, WES identified a homozygous frameshift variant in ITPKB (c.2583delT, p.Arg862Glufs*4). Immunoblotting revealed reduced expression and lower molecular weight of the mutant protein compared with wild-type ITPKB. Moreover, the ITPKB^{Arg862Glufs*4} mutant completely lacked kinase activity. Interestingly, Itpkb^−/− mice are characterized by a cell-intrinsic, severe block in thymocyte differentiation from the CD4⁺ CD8⁺ stage to the single positive with a profound reduction of CD4⁺ and CD8⁺ cells in thymus and spleen. Taken together, the similarities between the patient and the Itpbk^−/− mice, in conjunction with the absence of ITPKB^{Arg862Glufs*4} kinase activity, strongly support a pathogenic role of ITPKB mutation in causing the patient’s clinical and immunologic phenotype.

6 |. CONCLUSIONS

IEI represent experiments of nature in which gene defects compromise immune function, thereby providing important insights into the mechanisms of how the immune system works in vivo. Thanks to the increased availability of high-throughput DNA sequencing and the improvement in genomic data interpretation, the number of newly identified genes associated with IEI has exponentially increased over the last decade. Interestingly, the improved ability to define IEI pathophysiology at the molecular level has set the basis for the development of targeted therapeutic interventions (the “precision medicine” approach), based on the use of small molecules and biologics to target a specific cell function.

TABLE 1.

Key findings regarding the four analyzed inborn errors of immunity

Disease	Genetic defect	Inheritance	Main Features	Reference
PAX1 deficiency	PAX1	AR	OTFCS2 (facial dysmorphism, external ear anomalies with preauricular pits and hearing impairment, branchial cysts or fistulas, anomalies of the vertebrae and the shoulder girdle, and mild intellectual disability), severe T-cell immunodeficiency (T−B+NK+ SCID/Omenn syndrome)	Yamazaki et al4
FOXN1 haploinsufficiency	FOXN1	AD	At birth and during infancy: low TRECs, increased susceptibility to infections and persistent lymphopenia. In adulthood: normal T-cell counts (aside from CD8+ T-cell lymphopenia) and isolated nail dystrophy	Bosticardo et al8
NOS2 deficiency	NOS2	AR	Fatal CMV infection in a previously healthy 51-year-old man; T and B lymphopenia, reduced NK cells	Drutman et al9
ITPKB deficiency	ITPKB	AR	Failure to thrive, oral thrush, recurrent pneumonia, skin abscesses, dead at 11 months; T−B+NK+ SCID	Almutairi et al11

Abbreviations: AD, autosomal dominant; and ITPKB, inositol-trisphosphate 3-kinase B; AR, autosomal recessive; CMV, cytomegalovirus; FOXN1, forkhead box N1; NOS2, nitric oxide synthase 2; OTFCS2, otofaciocervical syndrome type 2; PAX1, paired box 1; SCID, severe combined immunodeficiency; TRECs, T-cell receptor excision circles.

Key Messages.

The number of newly identified genes associated with IEI has exponentially increased over the last decade. In addition to identifying novel genes, it is now clear that distinct clinical phenotypes may be sustained by gain-of-function (GoF) or loss-of-function (LoF) mutations in the same gene. Different activity degrees of mutant proteins due to hypomorphic and hypermorphic mutations may also cause EIE phenotypic variability. Key findings regarding the four analyzed IEI are described in Table 1.