title: Analysis of CD4+ T-cell gene expression in allergic subjects using two different microarray platforms.
abstract: BACKGROUND
  Allergic diseases are thought to involve dysregulated activation of T cells including CD4+ lymphocytes. T-cell activation results in changes in gene expression, but the optimal method to study gene expression profiles in T cells, and how this changes over time, are not known.
  
  
  METHODS
  Circulating CD4+ T cells were obtained from subjects with atopic asthma, nonatopic asthma or nonallergic controls, and total mRNA was rapidly isolated. Atopy was defined as positive skin prick test to one of nine allergens. Gene expression was analyzed using hybridization and Affymetrix oligonucleotide arrays (Hu133A and Hu133B chips, n = 84), or by reverse transcription-polymerase chain reaction (RT-PCR) with a pathway-targeted array (Human Th1-Th2-Th3 RT(2) Profiler PCR Array, Superarray, n = 16).
  
  
  RESULTS
  Using Affymetrix arrays, it was difficult to discern a dominant allergy-associated profile because of heterogeneity in gene expression profiles. In contrast, a Th2-like signature was evident using RT-PCR arrays with increased expression of expected genes (e.g. IL-4, 5, 9, and 13, all P < 0.05) as well as unexpected gene transcripts (e.g. osteopontin). Gene expression profiles were relatively stable over time in circulating CD4+ T cells from two subjects using both platforms.
  
  
  CONCLUSIONS
  Unstimulated CD4+ T cells isolated from allergic subjects express a characteristic profile of genes when analyzed using RT-PCR based microarrays.
authors.affiliation: Division Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA.
authors.forename: N N
authors.initials: NN
authors.lastname: Hansel
authors.forename: C
authors.initials: C
authors.lastname: Cheadle
authors.forename: G B
authors.initials: GB
authors.lastname: Diette
authors.forename: J
authors.initials: J
authors.lastname: Wright
authors.forename: K M
authors.initials: KM
authors.lastname: Thompson
authors.forename: K C
authors.initials: KC
authors.lastname: Barnes
authors.forename: S N
authors.initials: SN
authors.lastname: Georas
mesh_terms: D000328:Adult; D015704:CD4 Antigens / Q000235:genetics*; D015496:CD4-Positive T-Lymphocytes / Q000276:immunology*; D016022:Case-Control Studies; D005260:Female; D015870:Gene Expression; D005819:Genetic Markers; D006801:Humans; D006967:Hypersensitivity / Q000175:diagnosis* / Q000235:genetics; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D011237:Predictive Value of Tests; D011379:Prognosis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D012720:Severity of Illness Index; D014481:United States
chemical_list: D015704:CD4 Antigens; D005819:Genetic Markers