A Novel Multigenic Immunodeficiency Affecting Interferon Mediated Immunity

Abstract

Primary immunodeficiencies are classically considered monogenic disorders characterized by host susceptibility to specific infectious pathogens. Patients with genetic defects in the IL-12/interferon gamma (IFN-γ) axis have susceptibility to weakly virulent mycobacteria, Mycobacteria tuberculosis, and Salmonella, but are resistant to the majority of other infectious pathogens. Host susceptibility to disseminated cytomegalovirus (CMV) infections typically results from genetic defects in T cell development or function. We studied a patient with disseminated M. tuberculosis and cytomegalovirus viremia. Whole exome sequencing identified two novel homozygous mutations affecting two distinct IFN pathways: the signal transducing chain of the IFN-γ receptor (IFNGR2) and the signaling chain of the IFN-α receptor (IFNAR1). The frameshift deletion in IFNGR2 resulted in a truncated protein with significantly decreased protein expression and absent downstream signaling, as demonstrated by a lack of STAT1 phosphorylation and HLA-DR upregulation in response to IFN-γ stimulation. Human defects in IFNAR1 have not been previously described. The patient’s IFNAR1 mutation replaced the protein’s native stop codon with 46 novel C-terminal amino acids (IFNAR1557Gluext46). The IFNAR1557Gluext46 mutant was expressed in patient fibroblasts at a level comparable to that of wild-type IFNAR1 in control fibroblasts. However, the IFNAR1557Gluext46 mutant led to impaired STAT1/STAT2 phosphorylation and decreased nuclear translocation of STAT1 in response to IFN-α stimulation. Furthermore, the patient had impaired expression of the IFN-α stimulated genes, IFIT1, IFIT2, and IRF7, which are critical for host immunity to CMV. Patient and control fibroblasts were equally susceptible to CMV entry; however, cells expressing IFNAR1557Gluext46 presented impaired expression of the ISG IFIT2, IFN-β and IFI16 after infection with CMV. Moreover, pretreatment with IFN-α did not prevent CMV replication in patient fibroblasts compared to cells expressing the wild type IFNAR1. The patient’s susceptibility to multiple types of infectious pathogens thus resulted from dual defects in Type I and Type II IFN signaling. These findings highlight the utility of whole exome sequencing in the discovery of multigenic primary immunodeficiencies.