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Series GSE90641 Query DataSets for GSE90641
Status Public on May 03, 2021
Title Epigenome analyses implicate ILC2s as key mediators of allergic airway inflammation
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Group 2 innate lymphoid (ILC2) cells are major producers of the cytokines that drive allergic asthma and elevated levels of ILC2s have been detected in the blood and sputum of asthma patients. Asthma susceptibility has strong (epi)genetic components, but the underlying mechanisms and whether they are linked to ILC2 biology remain unclear. To reveal the molecular basis of ILC2 function in allergic airway inflammation (AAI) and assess its relevance for understanding how genetic variation affects asthma susceptibility. Gata3-IRES-YFP reporter mice were used to isolate ILC2s from bronchoalveolar lavage fluid and lymph nodes. Human naive ILC2s were purified from peripheral blood and activated in vitro. We employed RNA-Seq, ChIPm-Seq and computational approaches to study the transcriptome and epigenome in the context of ILC2 activation, tissue-specific functions and genetic susceptibility to asthma. Activated ILC2s displayed a tissue-specific gene expression signature that emerged from a highly similar epigenome. We identify superenhancers - a class of regulatory regions susceptible to epigenetic drugs - controlling ILC2 identity and asthma-associated genes. The majority of genes implicated in asthma by genome-wide association studies resided in an active or primed state in ILC2s. A substantial number of asthma-associated genetic variants were found in ILC2 gene regulatory elements. Our genome-wide analyses reveal new potential functions for ILC2s in AAI, which possess a plastic and flexible epigenome. Importantly, we reveal a strong link between gene regulatory mechanisms in ILC2s and the (epi)genetic basis of asthma susceptibility, supporting a pathogenic role for ILC2s in human asthma.

Overall design Biological replicate (n=2-4) ChIP-Seq and RNA-Seq
Contributor(s) Stadhouders R, Hendriks RW
Citation(s) 29486229
Submission date Nov 29, 2016
Last update date Aug 02, 2021
Contact name Ralph Stadhouders
Organization name Erasmus Medical Center
Department Pulmonary Medicine
Street address Dr. Molewaterplein 50
City Rotterdam
ZIP/Postal code 3015 GE
Country Netherlands
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (10)
GSM2409792 k4me2_naiveT_1
GSM2409793 k4me2_naiveT_2
GSM2409794 k4me2_Th2_1
BioProject PRJNA355272
SRA SRP094050

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE90641_RAW.tar 3.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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