Life-threatening influenza pneumonitis in a child with inherited IRF9 deficiency

Hernandez, Nicholas; Melki, Isabelle; Jing, Huie; Habib, Tanwir; Huang, Susie S.Y.; Danielson, Jeffrey; Kula, Tomasz; Drutman, Scott; Belkaya, Serkan; Rattina, Vimel; Lorenzo-Diaz, Lazaro; Boulai, Anais; Rose, Yoann; Kitabayashi, Naoki; Rodero, Mathieu P.; Dumaine, Cecile; Blanche, Stéphane; Lebras, Marie-Noëlle; Leung, Man Chun; Mathew, Lisa Sara; Boisson, Bertrand; Zhang, Shen-Ying; Boisson-Dupuis, Stephanie; Giliani, Silvia; Chaussabel, Damien; Notarangelo, Luigi D.; Elledge, Stephen J.; Ciancanelli, Michael J.; Abel, Laurent; Zhang, Qian; Marr, Nico; Crow, Yanick J.; Su, Helen C.; Casanova, Jean-Laurent

Homozygosity for a splice site mutation in IRF9 We studied a 5-yr-old girl (patient [P]) born to first-cousin Algerian parents and living in France who was hospitalized for severe infection with IAV requiring mechanical ventilation and Tamiflu treatment, and who had a history of recurrent benign bronchiolitis, biliary perforation following measles-mumps-rubella (MMR) vaccination at 1 yr of age, and recurrent fevers without a causative pathogen identified ( Fig. 1 A) . P also was infected with respiratory syncytial virus (RSV) within her first year of life, for which she was hospitalized but not admitted to the intensive care unit (ICU). We characterized P's history of viral infections at age 2 yr, 7 wk before IgG i.v. substitution and after maternal antibodies disappeared, by VirScan (Xu et al., 2015) . We detected significant specific antibodies in P's serum against many other viruses, including HSV-1, human cytomegalovirus, human rhinovirus (HRV), and enterovirus, in addition to confirming infections with RSV and IAV (Fig. S1 ). After her recovery from IAV infection, she experienced adenovirus and parainfluenza virus (PIV) infections, both of which were also confirmed by VirScan. She was admitted to the hospital for these infections, but neither required admission to the ICU. We performed WES on this kindred (trio design) and identified a c.991G>A mutation in IRF9, encoding a critical element of the type I and III IFN signaling pathways (IRF9), which was confirmed by Sanger sequencing (Fig. 1 B; Fu et al., 1990; Veals et al., 1992; Kimura et al., 1996) . P was homozygous for this mutation while both parents and her healthy sister were heterozygous, a familial segregation consistent with an AR pattern of inheritance with complete penetrance (Casanova et al., 2014) . This variation was absent from public databases, including 1,000 genomes, Bravo, and Genome Aggregation Database (GnomAD)-a database that encompasses the exome aggregation consortium (ExAC) database. This mutation occurs in the final nucleotide of exon 7 and is predicted to disrupt the essential splice site at the boundary of exon 7 and intron 7, as well as to produce an aspartic acid to asparagine mutation at amino acid 331 (p.D331N). Because of the different predictions for these mutations on IRF9 protein structure, we will presently refer to this allele by its effect on the cDNA, c.991G>A. The combined annotation-dependent depletion (CADD) score of this variant was high, above the mutation significance cutoff ( Fig. 1 C) , Figure 1 . A private IRF9 variant alters mRNA splicing in a child with severe influenza pneumonitis. (A) Pedigrees of the IRF9-deficient family. The double lines connecting the parents indicate consanguinity. The proband is indicated by an arrow. Filled shapes indicate affected individuals while open shapes identify unaffected individuals. (B) Chromatograms demonstrating c.991G>A mutation in patient PBMC-derived DNA (red arrow). (C) Population genetics of homozygous coding missense and predicted loss-of-function IRF9 mutations taken from GnomAD and in-house cohorts. The patient's variant is private and shown in red, while two other variants, shown in blue, were also identified in our cohort. (D) Schematic illustration of the IRF9 gene. The exons are numbered 1-9, and regions corresponding to functionally significant domains are colored brown (for the DNA-binding domain, DBD), gray (nuclear localization sequence, NLS), or purple (IAD). Patient mutation