Pulmonary Alveolar Proteinosis and Multiple Infectious Diseases in a Child with Autosomal Recessive Complete IRF8 Deficiency

Background Autosomal recessive (AR) complete IRF8 deficiency is a rare severe inborn error of immunity underlying an absence of blood myeloid mononuclear cells, intracerebral calcifications, and multiple infections. Only three unrelated patients have been reported. Materials and Methods We studied an Argentinian child with multiple infectious diseases and severe pulmonary alveolar proteinosis (PAP). We performed whole-exome sequencing (WES) and characterized his condition by genetic, immunological, and clinical means. Results The patient was born and lived in Argentina. He had a history of viral pulmonary diseases, disseminated disease due to bacillus Calmette-Guérin (BCG), PAP, and cerebral calcifications. He died at the age of 10 months from refractory PAP. WES identified two compound heterozygous variants in IRF8: c.55del and p.R111*. In an overexpression system, the p.R111* cDNA was loss-of-expression, whereas the c.55del cDNA yielded a protein with a slightly lower molecular weight than the wild-type protein. The mutagenesis of methionine residues downstream from c.55del revealed a re-initiation of translation. However, both variants were loss-of-function in a luciferase assay, suggesting that the patient had AR complete IRF8 deficiency. The patient had no blood monocytes or dendritic cells, associated with neutrophilia, and normal counts of NK and other lymphoid cell subsets. Conclusion We describe the fourth patient with AR complete IRF8 deficiency. This diagnosis should be considered in children with PAP, which is probably due to the defective development or function of alveolar macrophages. Supplementary Information The online version contains supplementary material available at 10.1007/s10875-022-01250-4.


A Patient with Severe Viral and Mycobacterial Diseases, PAP, and Cerebral Calcifications
The patient (II. 2) was a boy born in 2019 to non-consanguineous parents originating from and living in Jujuy, in the North of Argentina (Fig. 1a). His maternal half-sister and his two parents are healthy. He was born at 36 weeks of gestation, with a normal weight and length. Ventriculomegaly was diagnosed on prenatal ultrasound. The patient received BCG and hepatitis B vaccines at birth. He was admitted to the intensive care unit (ICU) at the age of one month, for sepsis and respiratory distress requiring assisted mechanical ventilation. No microorganisms were documented during this first episode, and the patient improved, thanks to empirical broad-spectrum antibiotics. At 4 months of age, he was hospitalized for a second episode of respiratory distress syndrome. Multiplex PCR on nasopharyngeal secretions was positive for a non-SARS-CoV-2 coronavirus but negative for adenovirus, influenza virus, metapneumovirus, Mycoplasma pneumoniae, and Pneumocystis jirovecii. PCR tests on blood for Epstein-Barr virus (EBV), cytomegalovirus (CMV), human herpesvirus 6 (HHV6), and HIV yielded negative results. Acinetobacter baumanii was cultured from bronchoalveolar lavage (BAL). The patient presented one episode of febrile convulsion. A cerebrospinal fluid (CSF) sample collected at the time was found to contain no cells, and normal protein and glucose levels. PCR on CSF for enterovirus, EBV, varicella-zoster virus (VZV), CMV, herpes simplex virus (HSV), and HHV6 yielded negative results. No mycobacterial culture was performed on CSF. The patient was treated with meropenem, vancomycin, colistin, trimethoprim/sulfamethoxazole, and liposomal amphotericin. At the age of 7 months, an axillary adenopathy, 2 × 3 cm in size, was detected at the BCG vaccination site. M. bovis-BCG was isolated from BAL, and the patient was treated with pyrazinamide, ethambutol, rifampicin, and levofloxacin.
A computed tomography (CT) scan of the thorax found mediastinal structures without density alterations, with a thickening of the septal interstitium, overlapping ground glass opacities with a cobblestone pattern and a tendency to consolidate at the base of the lungs (Fig. 1b). These findings were consistent with PAP, which was confirmed by pathological examinations of BAL and of lung biopsy (Fig. 1c). The patient was treated with a bolus of steroids and partial lung washes that were performed weekly at the ICU, with a good response at the start of treatment. The patient also presented facial dysmorphism, with a very wide fontanel, mid facial hypoplasia, bilateral keratoconus, a short nose and neck, retrognathia, and short stature (− 3 SD at the age of one month). Brain CT scan was performed at the age of seven months and showed ventriculomegaly with megacisterna magna, cerebellar hypoplasia, mesencephalic, temporal, ventricular, and ependymal calcifications (Fig. 1d). The patient died at the age of 10 months whilst in palliative care for respiratory failure. Overall, he presented susceptibility to life-threatening mycobacterial (BCG-osis) and viral (coronavirus) infections, associated with severe PAP, and cerebral calcifications.

Identification of Compound Heterozygous IRF8 Variants
Whole-exome sequencing (WES) was performed for this patient. The homozygosity rate inferred from WES was low (0.37%), consistent with the absence of consanguinity between the two parents. Principal component analysis (PCA) confirmed that the patient was of Latino American descent (Fig. 1e). An analysis of rare variants with a minor allele frequency (MAF) < 10 −3 , predicted to be deleterious, for genes with a low gene damage index, identified 95 variants (Fig. 1f). Only two of these variants concerned a gene known to be involved in IEI, IRF8. One of these heterozygous variants was a single-base pair deletion (c.55del) predicted to create a frameshift (p.D19Tfs*8), and the other was a single-base pair substitution (c.331C > T) that was predicted to result in a nonsense variant (p.R111*) (Supplementary Fig. 1a). Both variants were confirmed by Sanger sequencing (Fig. 1g). The c.55del variant was inherited from the patient's mother, whereas the c.331C > T variant was inherited from the patient's father; the patient was therefore compound heterozygous ( Fig. 1a and g). Both variants showing the origins of the patient plotted on the main ethnic origins extracted from the 1000 Genomes database and our own WES database. f Analyses of WES data and identification of two heterozygous coding variants in IRF8. g Electropherogram of exons 2 and 3 showing the variants (c.55del and p.R111*) found in the patient (II.2) relative to healthy controls and his parents (I.2 and I.3). h Minor allele frequency (MAF) and combined annotation-dependent depletion (CADD) score of the heterozygous IRF8 variants found in the patient (red symbols) and of all variants found in patients with AR complete IRF8 deficiency (brown symbols). The dotted line corresponds to the mutation significance cutoff (MSC), with its 99% confidence interval. i Diagram of the human IRF8 protein, showing the DNAbinding domain (DBD) and IRF-associated domain 1 (IAD). Coding exons are indicated by Roman numerals (II to IX). The new reported variants are indicated in red, and the variants previously identified as responsible for AR complete IRF8 deficiency are shown in brown. All methionine residues are indicated in green ◂ 1 3 were predicted to be deleterious, with combined annotationdependent depletion (CADD) scores of 33 for c.55del and 37 for p.R111*. These values are above the 99% mutation significance cutoff (MSC) of 8.2 for IRF8 [2] (Fig. 1h). The p.R111* variant was previously reported in a Chinese patient with AR IRF8 deficiency [11]. However, neither of these variants has ever been reported in database of germline variants such as the public databases ExAC, gno-mAD v2.1.1 or v3.1.1 [4], BRAVO/TOPmed freeze 8 [5], and ATAV [6] containing WES or whole-genome sequencing (WGS) data for more than 150,000 individuals, or in the WES data of our in-house cohort of more than 15,000 patients with severe infectious diseases (Fig. 1h). We also screened for copy number variants (CNV), in particular for homozygous or hemizygous large deletions [13]. Using WES data, targeted screening for heterozygous large deletions encompassing TBX1 locus was negative. No CGH or SNP microarray was performed due to the lack of material. No relevant rare or private variants in other genes for which mutations are known to be associated with PAP [14][15][16] (namely, ADA, ABCA3, CSF2RA, CSF2RB, GATA2, MARS, NKX21, RAB5B, SFTPB, SFTPC, and SLC7A7), or susceptibility to mycobacterial disease [17] were identified by WES. However, biallelic mutations of IRF8 are known to underlie syndromic MSMD [1,[8][9][10]. These results suggest that this patient had AR IRF8 deficiency.

The IRF8 Variants of the Patient Are Loss-of-Function
Both variants of the patient were located in the DNAbinding domain of the IRF8 protein (Fig. 1i). We studied their impact by transiently transfecting human embryonic kidney (HEK)293 T cells with the wild-type IRF8 (WT; NM_002198. 2), or mutant c.55del or p.R111* cDNAs, and with the three previously described LOF mutants as controls (p.K108E [8,9], p.R83C [10], p.R291Q [10]). Constructs were epitope-tagged at the carboxy-terminus (V5). Transfection was efficient, as shown by qPCR, with similar levels of IRF8 cDNA detected in HEK293T cells transfected with the WT and mutant alleles ( Supplementary Fig. 1b). Immunoblotting of cell extracts with either the monoclonal IRF8 antibody recognizing p.G85 at the amino-terminus or an antibody recognizing the carboxyterminal V5 tag showed that the WT form, and the p.K108E, p.R83C, and p.R291Q variants were produced at the expected molecular weight (MW) (Fig. 2a). Surprisingly, a band was detected at a molecular weight slightly lower than expected for the c.55del variant, whereas no protein was detected at all for the p.R111* variant (Fig. 2a). Two ATG codons downstream from c.55del and upstream from p.R111* were identified and predicted in silico to lead to a re-initiation of translation (encoding p.M22 and p.M35, respectively) [11]. We tested this hypothesis, by mutating the corresponding methionine codons (p.M22 and p.M35) to create a methionine-to-alanine (ATG > GCG) substitution. In the WT-IRF8 cDNA, the mutation of p.M22 (WT/M22A), p.M35 (WT/M35A), or both (WT/M22A/M35A) had no effect on the MW of the protein produced (Fig. 2a). Conversely, in c.55del cDNA, the mutation of p.M22 (c.55del/M22A) resulted in protein with a slightly lower MW, whereas the mutation of p.M35 (c.55del/M35A) resulted in protein of similar MW to the c.55del protein (Fig. 2a). The substitution of both methionine residues (c.55del/M22A/M35A) completely abolished protein production (Fig. 2a). Thus, in overexpression systems, the c.55del mutation leads to a re-initiation of translation at the downstream ATG encoding p.M22. The resulting protein is truncated by 21 amino acids and has a lower MW (p.M1_S21del). The c.55del variant displayed impaired accumulation in the nucleus, like the previously described p.K108E mutant [9] as shown by analysis of cytoplasmic and nuclear extracts from HEK293T cells ( Supplementary  Fig. 1c) and by confocal microscopy on HeLa cells (Fig. 2b). In luciferase assays on HEK293T cells, the c.55del and p.R111* proteins, like the three previously reported mutants (p.K108E [8,9], p.R83C [10], p.R291Q [10]), were completely unable to inhibit IRF1-driven ISRE-transcriptional activity (Fig. 2c). These results indicate that both the variants from the patient are LOF and suggest that the patient displayed AR complete IRF8 deficiency.

Impairment of Leukocyte Development and Function in the Patient
The patient displayed constant marked leukocytosis due to the proliferation of polymorphonuclear neutrophils (Fig. 3a). Monocytes were not identified with any certainty on conventional hemograms (probably confused with large lymphocytes) (Fig. 3a), and the complete absence of these cells was demonstrated by flow cytometry (Fig. 3b). Bone marrow aspiration was performed, and no signs of lymphoma or leukemia were detected. The patient had slightly high plasma FTL3 ligand levels ( Supplementary Fig. 1d). Circulating pDC and cDC1 were also found to be absent by flow cytometry (Fig. 3b). The number of NK cells was within the normal range (Fig. 3c), and the distribution of CD56 br and CD56 dim cells was normal (Fig. 3d). The patient displayed mild CD4 + T lymphopenia (Fig. 3c), with a normal percentage of naïve CD4 + T cells (Table 1). T H 17, T H 1, and Treg CD4 + T cells were present at their usual percentages, whereas the percentage of T H F cells was slightly lower than normal (Table 1). CD8 + T cells were present within the normal range (Fig. 3c). The patient presented B-cell lymphopenia (Fig. 3c) and had low levels of memory B-cell subsets (CD27 + , CD27 + IgD + , and CD27 + IgD − ) for his age (Table 1). Platelet levels were either low or in the low end of the normal range (Fig. 3a).
Despite an absence of pDCs, plasma IFN-α levels were at upper range of controls in the patient ( Supplementary  Fig. 1d). Following stimulation with IL-12, phytohemagglutinin (PHA)-activated peripheral blood mononuclear cells (PBMCs) or PHA-blasts from the patient displayed normal levels of intracellular IFN-γ production by CD8 + and CD8 − T cells (Supplementary Fig. 1e). Whole-blood activation with LPS + IL-12 resulted in an impaired IFN-γ production (data not shown). Consistent with a complete absence of circulating myeloid mononuclear cells, following activation with LPS and IFN-γ, whole blood from the patient was completely unable to produce IL-1β, IL-10, IL-12p70, and IL-23, and TNF levels were low (Fig. 1e). Screening for anti-GM-CSF and anti-type I IFN autoantibodies, which can underlie PAP and severe COVID-19 pneumonia [18], respectively, was negative in a plasma sample of the patient collected at the age of nine months ( Supplementary Fig. 1f  and 1g).

Discussion
The newly identified patient with AR complete IRF8 deficiency described here presented clinical and immunological features common to the other three patients reported [8][9][10][11]: susceptibility to severe infectious disease (including BCG-osis following exposure to BCG vaccine and viral infections), intracerebral calcifications [8][9][10], and absence of circulating monocytes [8][9][10][11] and DCs [8][9][10], with massive neutrophilia [8][9][10][11]. FTL3 ligand levels were slightly elevated, as previously described in another patient with AR complete IRF8 deficiency [8]. This is seen in patients with bone marrow failure [19,20]. The other three patients described had normal [11] or increased [8][9][10] NK cell counts, while the patient reported here had a normal count of NK cells, and a normal distribution of CD56 dim and CD56 br NK cells. IRF8 is expressed by microglial cells [1], which has led to the suggestion that its complete deficiency is a microgliopathy [21,22] resembling other conditions caused by mutations of genes expressed by microglia, variants of which have been shown to lead to intracerebral calcification [21,22]. Follow-up of patients with AR complete IRF8 deficiency, including patients undergoing HCST, would be required to determine whether the cerebral calcifications observed underlie any neurological phenotype. In addition to intracerebral calcifications, the patient described here also had other brain lesions and signs of developmental features (including mid facial hypoplasia and keratoconus) that had not been described in other patients with AR complete IRF8 deficiency. Heterozygous CNVs or complex rearrangements were not ruled out by GCH array due to lack of material. A description of more patients is needed to conclude if these features are related to AR complete IRF8 deficiency. The patient reported here also presented severe refractory PAP, as demonstrated by pathological examinations of BAL and a lung biopsy. PAP was not reported in any of the other three patients with AR complete IRF8 deficiency, despite respiratory distress [8][9][10][11] and in-depth respiratory evaluations in one of these patients [10], including BAL [10]. PAP is mostly caused by inborn errors of surfactant homeostasis or the GM-CSF pathway in children, or by autoantibodies against GM-CSF in adults [14]. Interestingly, PAP has been reported in patients with autosomal dominant GATA2 deficiency who also display impaired monocytes and DC counts [20,23,24]. The impaired development or function of intra-alveolar macrophages is probably the cellular basis of PAP in these patients.

DNA Extraction, WES, and Sanger Sequencing
Genomic DNA was extracted from whole-blood samples with the QIAamp DNA Mini Kit (QIAGEN). Exons were captured with the Agilent SureSelect Human All Exon V5 kit and sequenced on an Illumina platform with a read length of 100 base pairs and a main depth coverage of 100 × . Paired-end reads were mapped onto the human reference genome GRCh37 with the Burrows-Wheeler aligner (BWA), and the following analysis was performed as recommended by the Broad Institute guidelines, with the Genome Analysis Toolkit (GATK). Duplicate reads were marked with PICARD, and variants were called with "Haplotype Caller" from GATK (100,341 variants were obtained). We annotated the final VCF file with SnpEff/ SnpSift. The following databases were included: dbSNP, ExAC, 1000 Genomes, ClinVar, and the prediction tools Polyphen2, SIFT, and Mutation Taster. Variant prioritization was performed with the web-based server B_Platform (Bitgenia, www. bitgenia. com). Candidate variants were analyzed for presence in the set of candidate genes, population frequency, possible impact on the protein sequence, and previous clinical reports in databases. Exons 2 and 3 of IRF8 were amplified from genomic DNA with the primers 5′-GCC AGC ACC TTT GCT GCA AAC CTC -3′ and 5′-GAT GTC ACT CAA CAT CTC CACT-3′, and 5′-GAT GTG TGG GGT CCT GGT CAT GGT G-3′ and 5′-ACT ATG TGC CCC AGA CCC TGT GTC T-3′ primers, respectively, at a Tm of 60 °C, with GoTaq DNA Polymerase (#M3005, Promega). They were then sequenced by the Sanger sequencing method with Big Dye Terminator v3. 1 (Thermo Fisher Scientific), and subjected to capillary electrophoresis (#A30469, Applied Biosystems 3500xL system, Thermo Fisher Scientific).

Plasmid Cloning and Mutagenesis
Empty vector or plasmid (EV) pcDNA3.1 was obtained from Thermo Fisher Scientific, and pCMV6 EV and IRF1-WT-DDK tagged plasmid (#RCPS100001 and #RC203500, respectively) were obtained from Origene. IRF8-WT-V5-tagged (NM_002163) was inserted not the vector by cloning. Constructs carrying single-nucleotide mutant alleles were generated from this plasmid by mutagenesis with the appropriate primers, with the Pfu Ultra II Fusion HS DNA (#600,674, Agilent) polymerase or CloneAmpHiFi PCR Premix (#639,298, Takara) followed by digestion with DpnI (#R0176L, New England Biolab). Plasmids were amplified in competent cells of E. Fig. 3 Counts and function of peripheral leukocytes, hemoglobin, and platelets. a Monitoring of the levels of leukocytes, neutrophils, eosinophils, lymphocytes, monocytes, hemoglobin, and platelets in the patient. b Flow cytometry study of monocytes, mDC, cDC1, and pDC. c Monitoring of the levels of CD4 + and CD8 + T cells, B cells, and NK cells in the patient (black line). d Dot plot of CD16 + and CD56 + expression for NK cells. e Induction of cytokines, measured in the supernatant of two controls, and of the patient, after stimulation with LPS ± IFN-γ. The results are expressed as a ratio relative to nonstimulated cells

Western Blotting
Total protein extracts were prepared by mixing cells with modified radioimmunoprecipitation assay buffer supplemented with protease inhibitors (Complete, Roche) and phosphatase inhibitor cocktail (PhosphoStop, Roche), 0.1 mM dithiothreitol (DTT; Life Technologies), 10 −3 mM Na 3 VO 4 , and 1 mM PMSF, and incubating for 40 min on ice. The cytoplasmic and nuclear contents of the cells were separated with NE-PER nuclear and cytoplasmic extraction reagents (#78,835, Thermo Fisher Scientific

Luciferase Assay
We used the ISRE3 reporter plasmid (pGL4. 10[luc2] backbone, Promega #E6651), as previously described [25]. HEK293T cells in 96-well plates were transiently transfected with the (ISRE) reporter plasmid (100 ng/well and 100 µL of DMEM-10% FBS medium) and the pRL-SV40 plasmid (Promega, #E2231, 40 ng/well), with or without the IRF1 WT p.CMV6 plasmid (50 ng/well), with or without IRF8-WT or mutant forms, in the presence of the Lipofectamine LTX kit (Thermo Fisher Scientific, #15,338-100) and with or without EV, to ensure that the same amount of plasmid was present in each well, in accordance with the manufacturer's instructions. Cells were used for the ISRE assay with the Dual-Luciferase system kit (Promega #E1980), according to the manufacturer's protocol, 24 h after transfection. Signal intensity was determined with a Victor X4 plate reader (Perkin Elmer). Experiments were performed in triplicate, and results are expressed as dual reporter activity.

Confocal Microscopy
HeLa cells were plated on chambered coverslip (#80,826, iBidi) and were left untransfected or were transiently transfected with IRF8-WT or mutant cDNA constructs or with EV. Twenty-four hours later, cells were fixed 15 min in 4% formaldehyde in phosphate-buffered saline (PBS), pH 7.4 at 37 °C. The cells were then incubated overnight at 4 °C with primary antibody (unconjugated IRF8, clone D20D8, #5628, Cell Signaling). They were washed three times in PBS, stained by incubation with secondary antibodies for

Whole-Blood Cell Stimulation and ELISA on Supernatants and Plasma
Whole-blood samples were diluted 1/2 with RPMI 1640 (GIBCO BRL) and stimulated with lipopolysaccharide (LPS) from Salmonella Minnesota (100 ng/mL, Sigma-Aldrich), PMA (10 −7 M; Sigma-Aldrich) with ionomycin (I) (10 −5 M; Sigma-Aldrich), IL-12 (GIBCO BRL), and IFN-γ (Imukin). Patient samples and samples from two agematched healthy controls were run in parallel. Supernatants were recovered after 48 h and were used for enzyme-linked immunosorbent assays (ELISA) for human TNF and human IFN-γ (Thermo Fischer Scientific). ELISA was performed on plasma from the patient, GATA2-deficient patients [20] and healthy donors, for human Flt-3 ligand (FLT3L) (R&D Systems, DFK00) in accordance with the kit manufacturer's instructions. Similarly, plasma IFN-α levels were measured by SIMOA on patient, and healthy donors, in accordance with the kit manufacturer's instructions (Quanterix). SIMOA was also performed on plasma from the patient, and healthy donors, in accordance with the kit manufacturer's instructions. The production of myeloid cytokines was assessed after 24 h of stimulation with LPS, with or without IFNγ, with LEGENDplex™ Human Inflammation Panel 1 (#740,809, BioLegend).

Study of IFN-γ Induction in PHA-Blasts
PHA blasts from the patient and an age matched control were generated stimulating 1 × 10 6 PBMC with PHA (Gibco, diluted 1/50 in RPMI 20% ABS Penicillin/Streptomycin/ Glutamine) plus recombinant IL2 (Roche, 50 IU) during 48 h. After two washes with RPMI, mediumcells were divided in two aliquots and incubated either with RPMI 2% FCS (basal tube) or 0.1 µg/ml recombinant IL12 R&D (stimulated tube) for another 24 h. Then, both basal and stimulated tubes were re-stimulated with PMA 100 ng/ml and ionomycin (1 µg/ml) in RPMI 20% ABS P/S/G for 5 h in the presence of 10 µg/ml Brefeldin A (Sigma). Cells from basal and simulated tubes were then washed twice, lysed with Becton Dickinson (BD) FACS lysing, and permeabilized with BD FACS permeabilizing solution 2. Permeabilized cells were stained with IFN-γ FITC, CD3 PerCP, and CD8 PE (BD) for 30 min; washed twice with PBS /BSA; and acquired in a FACS Canto II. Percentages of IFN-γ positive cells from basal and IL12 stimulated blast cells were analyzed on gated CD3 + CD8 + and CD3 + CD8-populations on FlowJo.

Screening of Autoantibodies to GM-CSF and Type I IFNs
Recombinant E. coli-derived human (rh)GM-CSF (#215-GMP, R&D Systems) was first biotinylated with EZ-Link Sulfo-NHS-LC-Biotin (#A39257, Thermo Fisher Scientific), according to the manufacturer's instructions, with a biotin-to-protein molar ratio of 1:12. The detection reagent contained a secondary antibody (Alexa Fluor 647 goat antihuman IgG (#A21445, Thermo Fisher Scientific)) diluted in Rexxip F (#P0004825, Gyros Protein Technologies; 1:500 dilution of the 2 mg/ml stock to yield a final concentration of