Peripheral blood gene expression changes during allergen inhalation challenge in atopic asthmatic individuals.
OBJECTIVE
(1) To investigate the effects of globin mRNA depletion in detecting differential gene expression in peripheral blood and (2) to investigate changes in peripheral blood gene expression in atopic asthmatic individuals undergoing allergen inhalation challenge.


METHODS
Asthmatic subjects (20-60 years of age, with stable, mild allergic asthma, n = 9) underwent allergen inhalation challenges. All had an early asthmatic response of ≥20% fall in forced expiratory volume in 1 second. Blood was collected immediately prior to and 2 hours after allergen challenge using PAXgene tubes (n = 4) and EDTA tubes (n = 5). Aliquots of the PAXgene blood samples were subjected to globin reduction (PAX-GR). Transcriptome analysis was performed using Affymetrix GeneChip(®) Human Gene 1.0 ST arrays. Data were preprocessed using factor analysis for robust microarray summarization and analyzed using linear models for microarrays. Pathway analyses were performed using Ingenuity Pathway Analysis.


RESULTS
Globin reduction uncovered probe sets of lower abundance. However, it significantly reduced the ability to detect differentially expressed genes (DEGs) when compared to non-globin-reduced PAXgene samples (PAX-NGR). Combined transcriptional analysis of four PAX-NGR and five EDTA sample pairs identified 1595 DEGs associated with allergen inhalation challenge (false discovery rate ≤ 5%), with the top-ranked network of perturbed biological functions consisting of inflammatory response, cellular movement, and immune cell trafficking.


CONCLUSIONS
While we have demonstrated a diminished ability to detect DEGs after globin reduction, we have nevertheless identified significant changes in the peripheral blood transcriptome of people with mild asthma 2 hours after allergen inhalation challenge.
James Hogg Research Centre, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.
Sarah H Y
SH
Kam
Amrit
A
Singh
Jian-Qing
JQ
He
Jian
J
Ruan
Gail M
GM
Gauvreau
Paul M
PM
O'Byrne
J Mark
JM
Fitzgerald
Scott J
SJ
Tebbutt
D000328:Adult; D000485:Allergens / Q000008:administration & dosage / Q000276:immunology; D001249:Asthma / Q000097:blood* / Q000276:immunology / Q000503:physiopathology; D001769:Blood / Q000378:metabolism*; D001985:Bronchial Provocation Tests; D002465:Cell Movement / Q000235:genetics; D015536:Down-Regulation / Q000235:genetics; D015852:Eukaryotic Initiation Factor-2 / Q000235:genetics; D005260:Female; D005541:Forced Expiratory Volume / Q000502:physiology; D020869:Gene Expression Profiling / Q000379:methods*; D005914:Globins / Q000235:genetics; D006454:Hemoglobins / Q000235:genetics; D006801:Humans; D007249:Inflammation / Q000235:genetics; D007372:Interferons / Q000235:genetics; D008297:Male; D016210:Methacholine Chloride / Q000008:administration & dosage; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D019869:Phosphatidylinositol 3-Kinases / Q000235:genetics; D051057:Proto-Oncogene Proteins c-akt / Q000235:genetics; D012313:RNA / Q000235:genetics / Q000302:isolation & purification; D015398:Signal Transduction / Q000235:genetics; D015854:Up-Regulation / Q000235:genetics; D055815:Young Adult
D000485:Allergens; D015852:Eukaryotic Initiation Factor-2; D006454:Hemoglobins; D016210:Methacholine Chloride; D012313:RNA; D005914:Globins; D007372:Interferons; D019869:Phosphatidylinositol 3-Kinases; D051057:Proto-Oncogene Proteins c-akt