FIGURE 1.

In vivo cigarette smoke exposure alters miRNA profiles in alveolar macrophages. A, differentially expressed miRNAs in smokers' alveolar macrophages are down-regulated and link to up-regulated mRNAs. Alveolar macrophages were isolated from four active smokers (>10 pack years) and four never smokers. An analysis of mRNA expression was performed using Human Exon Array 1.0 ST arrays from Affymetrix. miRNA expression was analyzed using TaqMan Low Density Arrays version 2.0 (ABI). Altered miRNAs (>2-fold change) were analyzed for potential mRNA targets using TargetScan and TarBase. The miRNA target information was compared with significantly altered mRNAs (q ≤ 0.10). The q value (false discovery rate) for the mRNAs was calculated using the Partek GS implementation of the step-up method. Gene IDs common to both lists (miRNA targets and mRNAs) were plotted. Each dot represents a gene/miRNA pair as predicted by Target Scan and/or TarBase. The top right quadrant is of particular interest because it identifies down-regulated miRNAs that link to up-regulated mRNAs. B, miRNAs that are down-regulated in smokers' alveolar macrophages have intact transcriptional profiles. A panel of down-regulated miRNAs (miR-708, miR-200a, miR-210, miR-187, miR-149, miR-429, miR-146b-3p, and miR-200c) was tested in RNA isolated from smoker and never smoker alveolar macrophages. Each miRNA was tested using primers specific for the mature miRNA and primers specific for the primary miRNA transcript (the stem loop structure with accompanying 5′- and 3′-ends). The data are a composite of results from four smokers and four never smokers with significance determined by Student's t test. Error bars, S.E.