Pathogenic ILC1 and NKp46+ ILC3 Are Defined by Core and Tissue-Specific Transcriptional Signatures in Autoimmune Neuroinflammation

Abstract

Abstract During multiple sclerosis, myelin-specific CD4+T cells invade the central nervous system (CNS) where they initiate a chronic inflammatory disease, leading to demyelination and neurodegeneration. Therefore, it is crucial to identify immunological factors allowing disease-inducing T cells to enter the CNS. Our previous study revealed a novel function of T-bet-expressing NKp46+ innate lymphocytes (ILC) as CNS gatekeepers, which control functional stability and access of autoreactive Th17 cells to the CNS. However, the identity of NKp46+ ILC subset(s) that regulate neuroinflammation and their mechanism of action are still poorly characterized. T-bet-expressing NKp46+ ILC encompass three subsets – conventional natural killer (NK) cells, ILC1 and NKp46+ ILC3. Here, we demonstrate that the pathogenic role of T-bet-expressing NKp46+ ILC maps to ILC1 and NKp46+ ILC3 but not NK cells. Single cell RNA-Seq analysis revealed that meninges-infiltrating NK cells exhibit undifferentiated phenotype devoid of expression of effector molecules and reminiscent of blood NK cells, explaining the functional redundancy of NK cells in the disease process. By contrast, NKp46+ ILC1/3, which directly interact with myelin-specific CD4+ T cells, were defined by the core set of 13 genes, which was not shared by splenic or meningeal NK cells. A subset of the ILC-specific genes was highly expressed by meningeal, but not splenic, ILCs, suggesting their importance in disease pathology. Thus, our transcriptional analysis identified modules of gene expression that coordinate functional polarization of ILCs in meningeal microenvironment and provides a blueprint for the discovery of ILC-specific targeted therapy for the treatment of CNS autoimmune disorder.