The Molecular and Epigenetic Mechanisms of Innate Lymphoid Cell (ILC) Memory and its Relevance for Asthma

Repetitive exposure of Rag1-/- mice to the Alternaria allergen extract generated a form of memory that elicited an asthma-like response upon a subthreshold recall challenge 3-15 weeks later. This memory was associated with lung ICOS+ST2+ILC2s. Genetic, pharmacologic and antibody-mediated inhibition, and adoptive transfer established an essential role for ILC2s in memory-driven asthma. ATAC-seq demonstrated a distinct epigenetic landscape of memory ILC2s, and identified Bach2 and AP1 (JunD and Fosl2) motifs as major drivers of altered gene accessibility. scRNA-seq, gene knockout and signaling studies suggest that repetitive allergenic stress induces a gene repression program involving Nr4a2, Zeb1, Bach2, and JunD, and a preparedness program involving Fhl2, FosB, Stat6, Srebf2 and MPP7 in memory ILC2s. A mutually regulated balance between these two programs establishes and maintains memory. The preparedness program (e.g. Fhl2) can be activated with a subthreshold cognate stimulation, which downregulates repressors and activates effector pathways to elicit the memory-driven phenotype. Overall design: Total 17 samples. 11 samples from Rag1 KO mice and 6 samples from wild-type C57B/6 mice. Study groups: 1) Alt/Alt: mice senstized with the Alternaria allergen (Alt) and underwent recall challenge with Alt; 2) Alt/-:mice sensitized with Alt and underwent no (-) recall challenge; 3) Sal/Alt: mice senitized with saline (Sal) and underwent recall challenge with Alt. 4) Sal/-: mice sensitized with Sal and underwent no (-) recall challenge. Each groups had three replicates except Alt-; which had two biological replicates. 6 samples were from wild type C57BL/6 mice. This study had two groups Alt/Alt and Sal/Alt,each groups had three bilogical replicates.