Profiling dendritic cell maturation with dedicated microarrays

Abstract: Dendritic cell (DC) maturation is the process by which immature DC in the periphery differentiate into fully competent antigen-present-ing cells that initiate the T cell response. However, DC respond to many distinct maturation stimuli, and different types of mature DC induce qualita-tively different T cell responses. As DC maturation involves the coordinated regulation of hundreds of genes, comprehensive assessment of DC matura-tion status would ideally involve monitoring the expression of all of these transcripts. However, whole-genome microarrays are not well-suited for routine phenotyping of DC, as the vast majority of genes represented on such chips are not relevant to DC biology, and their cost limits their use for most laboratories. We therefore developed a DC-dedi-cated microarray, or “DC Chip”, incorporating probes for 121 genes up-regulated during DC mat-uration, 93 genes down-regulated during matura-tion, 14 DC-specific genes, and 90 other genes with known or probable immune functions. These microarrays were used to study the kinetics of DC maturation and the differences in maturation pro-files among five healthy donors after stimulation with tumor necrosis factor- polyI:C. Results obtained with the DC Chip were consistent with flow cytometry, enzyme-linked immunosorbent as-say, and real-time polymerase chain reaction, as well as previously published data. Furthermore, the coordinated regulation of a cluster of genes (indoleamine dioxygenase, kynureninase, kynure-nine monoxygenase, tryptophanyl tRNA syn-thetase, and 3-hydroxyanthranilate 3,4-dioxygen-ase) involved in tryptophan metabolism was ob-served. These data demonstrate the use of the DC Chip for monitoring the molecular processes in-volved in the orientation of the immune respons