Profiling changes in gene expression during differentiation and maturationof monocyte-derived dendritic cells using both oligonucleotide microarraysand proteomics

Dendritic cells (DCs) are antigen-presenting cells that play major role in initiating primary immune responses. We have utilized two independent appro aches, DNA microarrays and proteomics, to analyze the expression profile of human CD14(+) blood monocytes and their derived DCs. Analysis of gene expr ession changes at the RNA level using oligonucleotide microarrays complemen tary to 6300 human genes showed that similar to 40% of the genes were expre ssed in DCs, A total of 255 genes (4%) were found to be regulated during DC differentiation or maturation. Most of these genes were not previously ass ociated with DCs and included genes encoding secreted proteins as well as g enes involved in cell adhesion, signaling, and lipid metabolism. Protein an alysis of the same cell populations was done using two-dimensional gel elec trophoresis. A total of 900 distinct protein spots were included, and 4% of them exhibited quantitative changes during DC differentiation and maturati on. Differentially expressed proteins were identified by mass spectrometry and found to represent proteins with Ca2+ binding, fatty acid binding, or c haperone activities as well as proteins involved in cell motility, In addit ion, proteomic analysis provided an assessment of post-translational modifi cations. The chaperone protein, calreticulin, was found to undergo cleavage , yielding a novel form. The combined oligonucleotide microarray and proteo mic approaches have uncovered novel genes associated with DC differentiatio n and maturation and has allowed analysis of post-translational modificatio ns of specific proteins as part of these processes.