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Series GSE136156 Query DataSets for GSE136156
Status Public on Aug 22, 2019
Title Unconventional ST2- and CD127-negative lung ILC2 populations are induced by Alternaria
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Background: Alternaria exposure is associated with severe asthma in humans. Alternaria exposure in mice potently activates group 2 innate lymphoid cells (ILC2s) via the IL-33/ST2 axis and causes ILC2s to robustly secrete type 2 cytokines.  Objective: Our aim was to determine whether conventionally used ILC2 markers, ST2 (IL-33R) and CD127 (IL-7Ra), were sufficient to identify all Th2-cytokine producing ILCs after Alternaria exposure. Methods: Mice received intranasal Alternaria for three days prior to analysis. Lung ILCs were identified by flow cytometry as CD45+Lineage−Thy1.2+ lymphocyte-sized cells, divided into four subsets based on ST2 and CD127 expression, and stained for intracellular cytokines and transcription factors. Sort-purified ILC subpopulations were also analyzed by RNA sequencing and qPCR. Results: Alternaria exposure led to accumulation of all ILC populations regardless of ST2 or CD127 expression. Nearly half of the GATA-3+, IL-5+, and IL-13+ ILCs were “unconventional” as they were either single or double negative for ST2/CD127. Further, these populations upregulated CD25, KLRG1, and ICOS after Alternaria challenge. Some activated unconventional IL-5+ ILC2s also produced IFNγ and IL-17A. In addition to shared ILC2 transcripts (Gata3, Il5, Il13) in all populations, RNA-seq further identified novel transcripts enriched in each subset. Finally, transcripts from all populations that correlated best with IL-5 and IL-13 production included Tnfrsf18, Ffar2, and Pde4b. Conclusions: Unconventional ST2- and CD127-negative mouse lung ILC2 populations are induced by Alternaria. Thus, commonly used lung ILC2 identification methods based on ST2 and CD127 do not accurately account for the total ILC2 burden and may exclude nearly half of these cells.
Overall design Using a Alternaria (fungi) extract allergic mouse model of allergy, 4 different subsets of murine lung Innate Lymphoid Cells (ILC) were sorted based on immunophenotypic markers from dispersed lung tissue. Tot RNA was extracted from each samples and library preparation made in technical duplicates using the Smart-Seq2 protocol (Picelli et al. 2013 and Rosales et al. 2018). Sequencing libraries were sequenced on Illumina Platform. Standard differential gene expression analysis were performed and specific gene signature for each ILC subset were identified.
Contributor(s) Cavagnero KJ, Badrani JH, Wang A, Seumois G, Doherty TA
Citation(s) 33679760
Submission date Aug 21, 2019
Last update date Mar 11, 2021
Contact name Taylor Doherty
Organization name La Jolla Institute for Immunology
Street address 9420 Athena Cir
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (8)
GSM4041790 ILC_ST2_pos_CD127_pos_Rep1
GSM4041791 ILC_ST2_pos_CD127_neg_Rep1
GSM4041792 ILC_ST2_neg_CD127_pos_Rep1
BioProject PRJNA561402
SRA SRP219038

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Supplementary file Size Download File type/resource
GSE136156_All_htseqCounts.txt.gz 231.6 Kb (ftp)(http) TXT
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