Inherited IRF9 deficiency: a novel genetic etiology of severe influenza

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Project Summary Influenza A virus (IAV) is a zoonotic pathogen that causes seasonal epidemics annually and has the potential to cause worldwide pandemics. Life-threatening pneumonia occurs in only a small minority of infected individuals (0.04-0.4% of cases). Pre-existing pulmonary disease and acquired immunodeficiencies are well- known risk factors. The vast majority of severe influenza cases, however, remain unexplained, especially in children. Intriguingly, classical primary immunodeficiencies do not predispose to severe influenza. We recently reported an otherwise healthy child with severe influenza due to inherited autosomal recessive (AR) IRF7 deficiency resulting in impaired interferon (IFN)-α/β production in both plasmacytoid dendritic cells (pDCs) and induced pluripotent stem cell (iPSC)-derived pulmonary epithelial cells (PECs). This was the first demonstration that influenza susceptibility could be heritable. We hypothesize that additional cases of severe influenza in children and young adults may result from single-gene inborn errors of immunity, not necessarily displaying complete penetrance. We recently performed whole-exome sequencing (WES) in a cohort of 25 patients and their parents (trio design) with life-threatening influenza without secondary bacterial pneumonia. We discovered a homozygous IRF9 mutation in a child with life-threatening influenza and a history of adverse reaction to MMR vaccination. IRF9, with STAT1 and STAT2, is one of the three subunits of ISGF3, the main transcriptional complex that drives antiviral type I IFN responses. The mutation is private to this kindred and affects an essential nucleotide at a splice site. We intend to test whether the mutation is deleterious, in terms of expression and function. We will also test the patient's cells for response to type I IFN and their control of influenza virus in the presence of type I IFNs. Finally, we will compare the genome-wide transcriptome responses to type I IFNs in the patient's cells with those from other patients with autosomal recessive, complete defects in IFNAR1, IFNAR2, STAT1, and STAT2. Our preliminary data are convincing and strong, as we showed that the splice mutation is not leaky and the encoded protein is loss of ISGF3 expression and function. Moreover, the patient's cells seem to control influenza virus poorly even in the presence of exogenous type I IFNs. Finally, we have collected cells from patients with all types of inborn errors of the type I IFN responsive pathway. Our project is thus highly innovative, yet supported by strong preliminary evidence. Collectively, our project will characterize, in depth, the molecular and cellular basis of a new primary immunodeficiency, autosomal recessive IRF9 deficiency, thereby documenting a second genetic and immunological etiology of severe influenza of childhood. This study will give weight to the emerging notion that severe influenza of childhood can be caused by single-gene inborn errors of immunity. Our study will also have new and important biological implications, providing the first analysis of IRF9-dependent and -independent responses to type I IFNs in humans. Overall, our discovery will have both biological and clinical implications.