Identification of the genes differentially expressed in human dendritic cell subsets by cDNA subtraction and microarray analysis.

Recent studies on dendritic cell (DC)-associated genes have been performed using monocyte-derived DCs (MoDCs) in different maturation stages. In our approach, to uncover the novel DC-associated genes and their expression profiles among the different DC subsets, we constructed a subtracted DC-cDNA library from CD1a(+), CD14(+), and CD11c(-) DCs by subtracting the genes shared with T cells, B cells, and monocytes, and we then screened the libraries with the aid of microarray technique. The genes showing remarkable specificity to DCs in the microarray analysis were selected and confirmed by semiquantitative reverse transcriptase-polymerase chain reaction. Our investigations revealed the following: (1) Genes highly expressed in myeloid DCs are those involved in antigen uptake/processing/presentation, cell metamorphosis, or chemotaxis. (2) Most of the genes previously identified in MoDCs, such as TARC, ferritin L-chain, lysosomal acid lipase, alpha- and beta-tubulin, osteopontin (Eta-1), and others, are not markedly expressed in CD11c(-) DCs regardless of their maturation status. On the other hand, specific transcription factors and MHC class II molecules, such as interferon regulatory factor-4 (IRF4) and HLA-DR, are similarly expressed in both DC subsets. (3) CD14(+) DCs retain unique features of tissue DCs, as evidenced by the gene expression profile of "no CCR7 but more CCR1" and "no TARC but abundant MCP1 and Eta-1." (4) The genes for immunoglobulin (Ig) superfamily Z39Ig, CD20-like precursor, glycoprotein NMB (GPNMB), transforming growth factorbeta (TGF-beta)-induced protein (TGFBI), myeloid DAP12-associated lectin (MDL-1), and 6 novel genes are newly identified as being associated with the phenotypic expression of the DC subsets. These identifications provide important molecular information for further functional studies of the DC subsets.