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

Abstract

The most recent updated classification of inborn errors of immunity/primary immunodeficiencies, compiled by the International Union of Immunological Societies Expert Committee, was published in January 2020. Within days of completing this report, it was already out of date, evidenced by the frequent publication of genetic variants proposed to cause novel inborn errors of immunity. As the next formal report from the IUIS Expert Committee will not be published until 2022, we felt it important to provide the community with a brief update of recent contributions to the field of inborn errors of immunity. Herein, we highlight studies that have identified 26 additional monogenic gene defects that reach the threshold to represent novel causes of immune defects.

Introduction

Inborn errors of immunity (IEI) are generally considered to result from monogenic germline defects that manifest as increased susceptibility to severe and/or recurrent infectious diseases, autoimmune or autoinflammatory conditions, atopic manifestations, and hematopoietic or solid tissue malignancies [1]. Over the past decade, the discovery of new IEIs has been occurring at an impressive rate. Indeed, the 2011 biennial update published by the IUIS Committee update listed 191 IEIs; this number increased to 430 in the 2019 update [2, 3]. This near-exponential increase in gene discovery is being driven by the accessibility and affordability of next-generation sequencing, and the efficient application of these technologies to elucidate the molecular etiology of unsolved cases of IEIs that are likely to result from single-gene defects [4].

Over the last 12 months, we have witnessed the ongoing rapid identification, and occasionally detailed molecular, biochemical, and cellular characterization, of genetic variants that cause, or are at least associated with, human diseases impacting host defense or immune regulation. Here, we will summarize reports on variants detected in 26 genes which we consider represent novel IEI (Table 1). Many additional genetic variants have been reported recently. However, those listed here have been adjudicated by the IUIS Committee to meet the strict criteria to be considered disease-causing [57]. These criteria include:

• 1. The patient’s candidate genotype is monogenic and must not occur in individuals without the clinical phenotype;

• 2. Experimental studies must indicate the genetic variant impairs, destroys, or alters expression or function of the gene product;

• 3. The causal relationship between the candidate genotype and the clinical phenotype must be confirmed via a relevant cellular phenotype, including—where possible—rescue of a functional defect by reconstitution with the wild-type gene, or via a relevant animal phenotype [57].

Table 1 Newly validated inborn errors of immunity

We also considered (i) the numbers of individuals affected by the novel variants, (ii) sufficient justification for excluding alternative candidate gene variants identified in single cases especially in situations of consanguinity with recessive disease, (iii) the depth of the clinical descriptions of affected individuals, and (iv) the level of immune and mechanistic characterization.

Novel Causes of Inborn Errors of Immunity

Currently, inborn errors of immunity are listed in 10 tables: Immunodeficiencies affecting cellular and humoral immunity (Table I), Combined immunodeficiencies (CID) with syndromic features (Table II), Predominantly antibody deficiencies (Table III), Diseases of immune dysregulation (Table IV), Congenital defects of phagocytes (Table V), Defects in intrinsic and innate immunity (Table VI), Autoinflammatory diseases (Table VII), Complement deficiencies (Table VIII), Bone Marrow failure (Table IX), and Phenocopies of inborn errors of immunity (Table X). Several of these tables are further partitioned into various subtables (e.g., Table I is split into Subtable 1 [T⁻B⁺ Severe Combined Immune Deficiency (SCID)], Subtable 2 [T⁻B⁻ SCID] and Subtable 3 [CID, generally less profound than SCID]) [2, 3].

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 [9,10,11]);

• Predominantly antibody deficiencies (FNIP1 [14, 15], PIK3CG [16, 17], CTNNBL1 [18], TNFSF13 [19]);

• Autoinflammatory diseases (SOCS1 [20,21,22], TET2 [23], CEBPE [24], CDC42 [33,34,35,36,37,38,39], LSM11, RNU7–1 [32], STAT2 [40, 41], RIPK1 [42, 43], NCKAP1L [44,45,46]), 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).

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]. Thus, these findings underscore the importance of appropriately interpreting genetic variants identified by next-generation sequencing, not discarding variants of unknown significance simply because they do not match the expected zygosity or clinical phenotype of previously reported studies, and to rigorously validate the impact of novel variants on the function of the encoded protein.

Joining the Dots with Discoveries of Novel Inborn Errors of Immunity

Many known inborn errors of immunity impact a defined signaling pathway such that mutations in components of these same pathways can represent clinical phenocopies of diseases causes by distinct genetic variants (genetic heterogeneity). In other words, physiological homogeneity can be identified for many genotypes underlying a given phenotype. Classic examples of this are Mendelian susceptibility to mycobacterial disease (MSMD), which results from impaired IFNγ-mediated immunity following exposure to mycobacterial species [58], and herpes simplex virus encephalitis (HSE) resulting from impaired TLR3-mediated anti-HSV1 immunity [59, 60]. Thus, variants in genes affecting the production of IFNγ (e.g., IL12RB1, IL12RB2, IL23R, TYK2, IKBKG, SPPL2A, IRF8) or cellular responses to IFNγ (e.g., IFNGR1, IFNGR2, STAT1, JAK1) result in MSMD in otherwise healthy individuals [58]. Similarly, inactivating mutations in signaling components of the TLR3 signaling pathway (TLR3, UNC93B, TRIF, TRAF3, TBK1, IRF3) underlie HSE due to impaired type 1 IFN-mediated central nervous system (CNS) intrinsic immunity against HSV1 [59, 60].

Recent discoveries have further linked common clinical phenotypes with unique genotypes that converge in a shared pathway. Thus, the non-redundant role of IFNγ-mediated immunity in host defense against mycobacterial infection [58] has been definitively established by the identification of individuals with inactivating bi-allelic mutations in not only IFNG itself [26] but also TBX21 [25], the transcription factor that regulates expression and production of IFNγ.

Interestingly, variants in the small nucleolar RNA SNORA31 predispose affected individuals to HSE. Mechanistically, patient’s iPSC-derived cortical neurons were found to be highly susceptible to HSV-1 infection in vitro, and this could be restored by exogenous IFNβ [29, 60]. However, responses of these cells to TLR3 and IFNβ, but not HSV1, are intact, revealing that SNORA31 functions to regulate cell-intrinsic immunity to HSV-1 by a mechanism independent of TLR3 signaling [29, 60]. The discovery of individuals with SNORA31 variants will facilitate further understanding of CNS-intrinsic host defense.

The discoveries of individuals with complete gp130-deficiency due to null/nonsense bi-allelic mutations of IL6ST [11], or pathogenic dominant-negative heterozygous variants of IL6ST [9], and a phenotype of eczema, hyper-IgE, and eosinophilia, likely explain these features of autosomal dominant hyper-IgE syndrome due to STAT3 negative dominance [61] and further highlight the role of IL-6 signaling in restraining atopic and allergic responses. Furthermore, the lack of mucocutaneous candidiasis in patients with impaired signaling via receptors for IL-6 (IL6R, IL6ST mutations [9, 11, 50, 62, 63]; anti-IL-6 autoantibodies [64]), IL-23 (biallelic IL23R variants) [65] or IL-21 (biallelic IL21 or IL21R variants) [66] argues that individually these cytokines are not required for the STAT3-mediated generation of human Th17 cells and host defense against fungal infections. Rather, the combinatorial defect of impaired STAT3 signaling downstream of these receptors explains chronic mucocutaneous candidiasis in an individual with dominant-negative STAT3 mutations. These findings again reveal the capacity for inborn errors of immunity to provide convincing evidence for basic immunological concepts. Indeed, this is further exemplified by the discovery that variants of ATG4A or MAP1LC3B2 cause recurrent HSV2 infection of the CNS, thereby establishing hitherto non-redundant functions of the autophagy pathway in non-hematopoietic cell-mediated intrinsic anti-viral immune responses [30].

SARS-CoV2 and Inborn Errors of Immunity

The COVID19 pandemic of 2020 has clearly changed the world in many ways. It has also yielded opportunities to understand host requirements for immunity against SARS-CoV2 infection. A recent study of ~ 650 individuals who developed severe COVID-19 found that ~ 3.5% of patients harbored germline loss-of-function variants in genes previously found to be important for host defense against influenza or other viral infections (e.g., bi-allelic loss of function mutations of IRF7 or IFNAR1, heterozygous mutations in TLR3, TICAM1, TBK1, or IRF3) [67] due to the key role of these genes in the type 1 IFN signaling pathway [59, 68]. An accompanying study found that, strikingly, ~ 10% of patients with severe COVID-19 have high levels of neutralizing autoantibodies (autoAbs) against type 1 IFNs in their serum [48]. The impact of these autoAbs was evidenced by the inability to detect IFN in serum from these patients, and their capacity to prevent anti-viral immune responses in vitro [48] (Table 1). These studies defined a crucial and non-redundant role for type 1 IFNs in immune control of SARS-CoV2 infection, and thus prevention of severe COVID-19. Furthermore, they also established that autoAbs against type 1 IFN phenocopy an inborn error of immunity, as previously determined for autoAbs against IFNγ and susceptibility to mycobacterial disease, anti-Th17 cytokine (IL-17A, IL-17F, IL-22) autoAbs in individuals with chronic mucocutaneous candidiasis, or pyogenic infections due to anti-IL-6 autoAbs [64, 69].

Conclusions

Discoveries over the past 12 months in the field of inborn errors of immunity have further identified non-redundant functions of key genes in human immune cell development, host defense, and immune regulation. In some cases, these functions go well beyond what may have been expected or anticipated based on animal models (e.g., TBX21 [25]). They have also already highlighted the heterogenous phenotypes that can result from variants in the same gene (e.g., CDC42 [33,34,35,36,37,38,39, 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.