Background: Group 2 innate lymphoid cells (ILC2s) are major producers of the cytokines driving allergic asthma, and increased ILC2 numbers have been detected in blood and sputum of asthmatic patients. Asthma susceptibility has a strong genetic component, but the underlying mechanisms and whether asthma genetics affect ILC2 biology remain unclear. Objective: We sought to study the ILC2 transcriptome and epigenome during airway inflammation (AI) to couple these to genes and genetic variants associated with asthma pathogenesis. Methods: Mice harboring a reporter for the key ILC2 transcription factor GATA-3 were subjected to IL-33–driven AI, and ILC2s were isolated from bronchoalveolar lavage fluid and mediastinal lymph nodes. Human ILC2s were purified from peripheral blood and activated in vitro. We used RNA sequencing, genome-wide identification of histone-3 lysine-4 dimethylation–marked chromatin, and computational approaches to study the ILC2 transcriptome and epigenome. Results: Activated ILC2s in mice displayed a tissue-specific gene expression signature that emerged from remarkably similar epigenomes. We identified superenhancers implicated in controlling ILC2 identity and asthma-associated genes. More than 300 asthma-associated genetic polymorphisms identified in genome-wide association studies localized to H3K4Me2+ gene regulatory elements in ILC2s. A refined set of candidate causal asthma-associated variants was uniquely enriched in ILC2, but not TH2 cell, regulatory regions. Conclusions: ILC2s in AI use a flexible epigenome that couples adaptation to new microenvironments with functional plasticity. Importantly, we reveal strong correlations between gene regulatory mechanisms in ILC2s and the genetic basis of asthma, supporting a pathogenic role for ILC2s in patients with allergic asthma.

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Keywords airway inflammation, asthma, epigenetics, epigenome, GATA-3, genome-wide association study, Group 2 innate lymphoid cell, superenhancer, TH2 cell, transcription factor
Persistent URL dx.doi.org/10.1016/j.jaci.2017.12.1006, hdl.handle.net/1765/105429
Journal Journal of Allergy and Clinical Immunology
Citation
Stadhouders, R, Li, B.W.S, de Bruijn, M.J.W, Gomez, A. (Antonio), Rao, T.N. (Tata Nageswara), Fehling, H.J. (Hans Jörg), … Hendriks, R.W. (2018). Epigenome analysis links gene regulatory elements in group 2 innate lymphocytes to asthma susceptibility. Journal of Allergy and Clinical Immunology. doi:10.1016/j.jaci.2017.12.1006