Childhood herpes simplex virus 1 (HSV-1) encephalitis (HSE) is a devastating viral illness of unclear pathogenesis. HSE is the most frequent form of sporadic viral encephalitis in developed countries and affects otherwise healthy children with no relevant family history, unlike infectious conditions observed in classical primary immune deficiencies. Therefore, HSE was not suspected to have a genetic etiology. Partner 1 of the project recently showed, thanks to the support of the ANR, that the disease does result in some children, from single-gene mutations impairing TLR3- and IFN-a/ß-mediated immunity to HSV-1 in the central nervous system (CNS). We previously reported 13 patients, each carrying homozygous or heterozygous mutations in one of five different TLR3 pathway genes (TLR3, TRIF, UNC93B1, TRAF3, TBK1). We also demonstrated that patient-specific induced pluripotent stem cell (iPSC)-derived TLR3-deficient neurons and oligodendrocytes were highly susceptible to HSV-1 infection, suggesting that impaired TLR3- and IFN-mediated CNS-intrinsic anti-HSV-1 immunity underlies the pathogenesis of HSE in those patients. However, no genetic etiology has yet been identified for most HSE patients investigated in the laboratory (237 of 250).
In the present project, we aim to test the hypothesis that childhood HSE is not only a viral disease, but also the consequence of a collection of CNS-intrinsic inborn errors of immunity to HSV-1 infection, which is possibly, but not necessarily, related to the TLR3-IFN circuit. The principal objective is to identify novel HSE-causing genes and to dissect the related CNS-specific cellular basis of HSE pathogenesis, by means of powerful next-generation sequencing approaches, and cutting-edge iPSC and CNS cell differentiation technologies. We will perform whole-exome sequencing (WES) in all patients to search for novel HSE-predisposing mutations, through: 1) a hypothesis-based approach, searching for mutations in known TLR3- and IFN- pathway genes; 2) an unbiased genome-wide (GW) approach, searching for mutations in novel genes by combining WES data with GW linkage analysis in informative families, and our recently developed human gene connectome analysis. Whole genome sequencing (WGS) will be considered in patients without mutations found by WES. In addition, population genetic analyses will be performed on all candidate genes identified to assess the intensity of natural selection acting on then and prioritize their exploration. Finally, we will use iPSC-derived CNS-specific cells to investigate the impact of each of the new genetic etiologies identified on CNS-intrinsic anti-HSV-1 immunity.
Partner 1 has built a unique cohort of 250 HSE patients. Fibroblast cell lines are available from200 patients, facilitating the investigation of the TLR3-IFN pathway and HSV-1 infection in patients-specific cells. A hypothesis-based analysis of the WES data in a first subset of 170 HSE patients has revealed nonsynonymous mutations of 18 important genes of the TLR3 and IFN pathways, in a group of 52 patients. The unbiased GW analysis of these WES data has identified nonsynonymous mutations in novel genes related to the host pre-mRNA decay and sncRNA generation pathway, including DBR1 and SNORA31, in eight patients. Moreover, we have simplified our protocol to obtain patient-specific CNS cells from iPSCs. Partner 2 has provided proof of concept, in the specific context of immunity-related genes, of the highly complementary value of population genetics in unmasking essential determinants of host immune responsiveness. This project is thus highly innovative, but supported by strong preliminary evidence. Our research will provide unique insight into the role of CNS-intrinsic immunity in host defense against HSV-1 infection in the CNS, and shed light on the pathogenesis of this devastating pediatric illness, paving the way for new therapeutic approaches, such as the use of IFN-a in addition to acyclovir.
Madame Shen-Ying Zhang (Laboratoire de Génétique Humaine des Maladies Infectieuses - INSERM U1163 (exU980))
The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.
IP-GEH Unité de Génétique Evolutive Humaine
GHMI-INSERM U1163 (exU980) Laboratoire de Génétique Humaine des Maladies Infectieuses - INSERM U1163 (exU980)
Help of the ANR 468,000 euros
Beginning and duration of the scientific project: December 2014 - 48 Months