Inborn errors of immunity underlying severe viral infection of the brainstem – CNSVIRGEN

It has long remained elusive how the central nervous system (CNS) fends off a variety of viral infections. We demonstrated that forebrain HSV1 encephalitis of childhood can result from monogenic deficiencies of TLR3-IFN-mediated CNS-intrinsic immunity. We recently discovered autosomal recessive deficiency of human RNA debranching enzyme 1 (DBR1) in 5 children from 3 unrelated families, who all suffered from brainstem viral encephalitis (BVE) due to HSV1, Influenza B virus, or Norovirus. This discovery provided proof-of-principle that devastating BVE in otherwise healthy children could develop due to inborn errors of brainstem-specific, cell-intrinsic immunity to viruses. However, the fine molecular and cellular mechanisms through which DBR1 governs antiviral immunity in the human brainstem remains unknown. Also, it remains unclear whether other inborn errors of immunity, DBR1 related or not, underlie BVE pathogenesis in most or only some patients with BVE due to various virus infections. In this project, we will search for key molecules controlling antiviral immunity in the human brainstem following two specific aims: 1) The dissection of the fine molecular and cellular mechanisms by which DBR1 controls tissue- and cell-intrinsic antiviral immunity in the brainstem. 2) The search and in-depth characterization of new inborn errors of immunity, DBR1-related or not, in otherwise children suffering from BVE due to diverse viruses.
More specifically, we will dissect the molecular and cellular basis of the pathogenesis of BVE, in patients with BVE genetic etiologies, using patient-specific dermal fibroblasts, and, more importantly, patient induced pluripotent stem cell (iPSC)-derived CNS-specific cells. High throughput RNA sequencing (RNA-Seq) technologies will be used to dissect the precise immune pathway(s) and component(s) essential for antiviral responses against brainstem viral infection, in cells from healthy controls in comparison with those from human patients with BVE-causing genetic defects, or with other infectious diseases. We have already obtained very strong preliminary results, in particular with the analysis of total RNA-Seq data in DBR1-deficient fibroblasts and the differentiation of brainstem neurons from DBR1-deficient patient-specific iPSCs. We will use NGS, including WES in particular (and WGS at a later stage), to search for new genetic etiologies of BVE. This project capitalizes on a unique cohort of children suffering from BVE, with 110 recruited patients so far. We will analyze the WES data at the population and individual patient levels, following a candidate gene-based approach and an unbiased genome-wide approach. All newly discovered genetic etiologies of BVE will be characterized in depth using the established fibroblasts and iPSC-mediated cellular models.
The major added value of human studies is that they enable us to define the function of host defense genes in natura, in particular in the CNS. This unique study takes advantage of the synergic partnership of three laboratories, with expertise in human genetics and immunology, human evolutionary genetics, and RNA biology, to search for key molecules and cells controlling antiviral immunity in the human brainstem. The findings of this study will have major immunological and clinical implications, in particular to guide future treatment of patients with devastating BVE.