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Series GSE96530 Query DataSets for GSE96530
Status Public on Sep 12, 2023
Title LPS binding protein and activation signatures are upregulated during asthma exacerbations in children
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Asthma exacerbations in children are associated with respiratory viral infection and atopy, resulting in systemic immune activation and infiltration of immune cells into the airways. The gene networks driving the immune activation and subsequent migration of immune cells into the airways remains incompletely understood. Cellular and molecular profiling of PBMC was employed on paired samples obtained from atopic asthmatic children (n = 19) during acute virus-associated exacerbations and later during convalescence. Systems level analyses were employed to identify coexpression networks and infer the drivers of these networks, and validation was subsequently obtained via independent samples from asthmatic children. During exacerbations, PBMC exhibited significant changes in immune cell abundance and upregulation of complex interlinked networks of coexpressed genes. These were associated with priming of innate immunity, inflammatory and remodelling functions. We identified activation signatures downstream of bacterial LPS, glucocorticoids and TGFB1. We also confirmed that LPS binding protein was upregulated at the protein-level in plasma. Multiple gene networks known to be involved positively or negatively in asthma pathogenesis, are upregulated in circulating PBMC during acute exacerbations, supporting the hypothesis that systemic pre-programming of potentially pathogenic as well as protective functions of circulating immune cells preceeds migration into the airways. Enhanced sensitivity to LPS is likely to modulate the severity of acute asthma exacerbations through exposure to environmental LPS.
 
Overall design The study design consisted of 19 paired samples from acute exacerbation of asthma (acute visit =AV) and following recovering at convalescence (CV). RNA-Seq profiles were generated by sequencing llumina HiSeq2500, 50bp single-end reads, v4 chemistry. Each sample was sequenced across two lanes.
 
Contributor(s) Jones AC, Leffler J, Laing IA, Bizzintino J, Khoo S, LeSoeuf PN, Sly PD, Strickland DH, Holt PG, Bosco A
Citation(s) 37438758
Submission date Mar 13, 2017
Last update date Sep 12, 2023
Contact name Anya Jones
E-mail(s) Anya.Jones@telethonkids.org.au
Organization name Telethon Kids Institute, The University of Western Australia
Lab Systems Immunology
Street address Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue
City Nedlands
State/province Western Australia
ZIP/Postal code 6009
Country Australia
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (76)
GSM2534995 AAS_01_Atopic asthmatic_acute_visit_L004
GSM2534996 AAS_01_Atopic asthmatic_acute_visit_L005
GSM2534997 AAS_02_Atopic asthmatic_convalescent_visit_L004
Relations
BioProject PRJNA378936
SRA SRP101776

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

Supplementary file Size Download File type/resource
GSE96530_AAS_VST_transformed_counts.txt.gz 5.3 Mb (ftp)(http) TXT
GSE96530_AAS_VST_transformed_counts_collapsed.txt.gz 2.7 Mb (ftp)(http) TXT
GSE96530_AAS_raw_counts.txt.gz 1.9 Mb (ftp)(http) TXT
GSE96530_AAS_raw_counts_collapsed.txt.gz 1.1 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
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