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

(E) Shown are Δ log2 fold change values of a subset of ISGs that were found to be induced ≥1.5-fold (linear scale) in B-LCL cells (upper panels) or primary fibroblasts (lower panels) of the IRF9-deficient patient upon in vitro stimulation with IFN-α. To select this subset of ISGs, the IFN-α2b-induced genes in the healthy controls identified in the mRNA-seq analysis were used. In the IRF9-deficient patient, these genes were first passed through a filter by querying the gene identifiers against the interferome database and by retaining genes that were responsive to in vitro IFN stimulation. ISGs that failed to be induced at least 1.5-fold (linear scale) in patient cells were excluded. The retained ISGs were stratified in three groups of less (Δ less than −0.585), similar (−0.585 < Δ < 0.585), and higher (Δ > 0.585) induced genes relative to the average responses in the healthy control subjects. The numbers of genes in each group are shown in brackets. ***, significant differences at P < 0.0001 by the Kruskal-Wallis test. (F) Log2 FC of induced ISGs in IRF9-deficient B-LCLs (upper panels) or primary fibroblasts (lower panels) and their corresponding values in healthy donors. (G) Network analysis of a subset of highly inducible (> fivefold linear scale) ISGs among control subjects' B-LCLs and their responsiveness in the IRF9-deficient patient. Biological pathway and physical interactions are depicted as blue and red lines, respectively. 1.5 FC was used as the cut-off to distinguish responsive (red circle) and nonresponsive (blue circle) ISGs. The highly inducible ISGs that were used for query are shaded in yellow. healthy individuals using siRNA, or transfected these cells with a nontargeting siRNA (siNeg) instead (Fig. 6 A) . Knockdown of either IRF9 or MAVS resulted in increased viral transcripts compared with siNeg cells upon infection with HRV, suggesting that IRF9 is nonredundant for immunity to positive-sense RNA viruses in addition to the negative-sense viruses already tested. Similarly, knockdown of IRF9 increased the number of infected cells and the relative number of viral transcripts produced to a similar extent as did MAVS knockdown when compared with siNeg cells, for both RSV and PIV (Fig. 6 , C-F). Collectively, these data indicate that IRF9 deficiency leads to a broad defect in cell-intrinsic immunity to viruses in vitro. Altogether, these data strongly suggest that inherited IRF9 deficiency underlies P's impaired immunity to influenza infection and her subsequent hospitalization for ARDS.