A novel form of cell type-specific partial IFN-γR1 deficiency caused by a germ line mutation of the IFNGR1 initiation codon

Xiao-Fei Kong Guillaume Vogt Ariane Chapgier Christophe Lamaze Jacinta Bustamante Carolina Prando Anny Fortin Anne Puel Jacqueline Feinberg Xin-Xin Zhang Pauline Gonnord Ulla M. Pihkala-Saarinen Mikko Arola Petra Moilanen Laurent Abel Matti Korppi Ste phanie Boisson-Dupuis Jean-Laurent Casanova IFN-gR1 deficiency is a genetic etiology of Mendelian susceptibility to mycobacterial diseases, and includes two forms of complete recessive deficiency, with or without cell surface expression, and two forms of partial deficiency, dominant or recessive. We report here a novel form of partial and recessive Interferon g receptor 1 (IFN-gR1) deficiency, which is almost as severe as complete deficiency. The patient is homozygous for a mutation of the initiation codon (M1K). No detectable expression and function of IFN-gR1 were found in the patient's fibroblasts. However, IFN-gR1 expression was found to be impaired, but not abolished, on the EBV-transformed B cells, which could respond weakly to IFN-g. The mechanism underlying this weak expression involves leaky translation initiation at both non-AUG codons and the third AUG codon at position 19. It results in the residual expression of IFN-gR1 protein of normal molecular weight and function. The residual IFN-g signaling documented in this novel form of partial IFN-gR1 deficiency was not ubiquitous and was milder than that seen in other forms of partial IFN-gR1 deficiency, accounting for the more severe clinical phenotype of the patient, which was almost as severe as that of patients with complete deficiency. - INTRODUCTION Mendelian susceptibility to mycobacterial diseases (MSMD, MIM 209950) is a rare congenital syndrome that confers predisposition to poorly virulent mycobacterial species, such as Bacillus Calmette Guerin (BCG) and environmental mycobacteria, in otherwise healthy children (1 4). Until now, five MSMD-causing autosomal genes have been identified, including IFNGR1, which encodes the IFN-g receptor ligandbinding chain (3 7); IFNGR2, which encodes the accessory chain of the IFN-g receptor (8 12); IL12B, which encodes the p40 subunit shared by IL-12 and IL-23 (13,14); IL12RB1, which encodes the b1 chain shared by the receptors for IL-12 and IL-23 (15 17); signal transducer and activator of transcription 1 (STAT1) (18 21) and one X-linked gene, NF-kB essential modulator (NEMO), which mediates signaling in the NF-kB pathway (22). Interferon g receptor 1 (IFN-gR1) deficiency was the first identified and is second most common etiology of MSMD. Until now, IFN-gR1 deficiency has been identified worldwide in 118 patients from 32 countries with 33 different mutations (Fig. 1A and unpublished data). Two major forms of IFN-gR1 deficiency have been described: complete and partial (23,24). Two forms of complete IFN-gR1 deficiency have been defined on the basis cell surface expression of the receptor or not. Both forms show an abolished response to IFN-g with regards to receptor binding, STAT1 homodimers known as gamma-activating factors (GAF) activation and HLA-DR induction. Mutations causing complete IFN-gR1 deficiencies without cell surface expression have often been found to be nonsense mutations, deletions or insertions in the coding regions for extracellular domain of IFN-gR1, which result in frameshift and a subsequent premature stop codon. The IFN-gR1 protein was not detectable on the cell surface, probably due to the degradation of the corresponding mRNA by the nonsense mediated surveillance system (3,4,25 33). The mutations identified in complete IFN-gR1 deficiency with cell surface expression were missense mutations or inframe deletions. IFNGR1 mRNA is translated to mature protein that can be transported to the cell surface but is unable to bind with IFN-g (7,34). Patients with complete IFN-gR1 deficiency have severe clinical phenotypes, generally presenting with disseminated BCG or non-virulent mycobacterial infection early in life. High plasma concentrations of IFN-g have frequently been observed in these patients (35). Bone marrow transplantation is currently the only curative treatment available for patients with complete IFN-gR1 deficiency (36 42). This solution remains difficult, however, due to a high rate of graft rejection resulting largely from the high concentrations of circulating IFN-g (38). Partial, as opposed to complete, IFN-gR1 deficiency is characterized by impaired but not abolished IFN-g responses. Two forms of partial IFN-gR1 deficiency have been defined on the basis of differences in their characteristics and the recessive or dominant nature of defects. The recessive form is caused by a single mutation which changes from isoleucine to threonine at amino acid 87 (I87T). This single amino acid substitution decreases IFN-gR1 expression on the cell surface and results in an impaired response to IFN-g (5,50). Dominant IFN-gR1 mutations principally affect exon 6 and include one hotspot mutation (818del4) (6,43 46). The dominant mutations give rise to a premature stop codon in the proximal intracellular domain, resulting in the production of a truncated protein lacking the intra-cellular receptor trafficking sites (6,47 49). The truncated proteins therefore accumulate on the cell surface and impede the normal signal transduction by exerting dominant-negative effects on the normal IFN-gR1 molecules. Patients with partial IFN-gR1 deficiencies generally have mild susceptibility to environmental mycobacterial disease or BCG-osis that were treatable with IFN-g and antibiotics (36). We report here the characterization of a novel form of partial recessive IFN-gR1 deficiency, more severe than the partial forms described in previous studies. Identification and segregation of the M1K mutation We investigated a patient (P) presenting severe BCG and Mycobacterium avium infections in childhood, born to consanguineous parents in Finland (Fig. 1B). We assessed the response of whole blood from the patient to BCG and BCG IFN-g/ IL-12, as previously described (51). We found that levels of IL-12p40 and IL-12p70 production in response to stimulation with BCG plus IFN-g were no higher than those after BCG alone. In contrast, IFN-g production in response to BCG plus IL-12 was normal (Supplementary Material, Fig. S1 and data not shown). Plasma IFN-g concentration was very high (370 ng/ml, undetectable in controls, data not shown), as reported in patients with complete IFN-gR1 or IFN-gR2 deficiency (35). The IFNGR1 gene was considered the most likely candidate gene on the basis of the patients clinical phenotype. Sequencing of the coding regions of IFNGR1 revealed a homozygous nucleotide substitution resulting in the replacement of the first methionine-encoding codon by a lysine-encoding codon (M1K) (Fig. 1C). Both parents were found to be heterozygous for this mutation and the patients sibling carried only the wild-type allele. All of family members were healthy, with no clinical signs of mycobacterial diseases. Th (...truncated)