Genome-wide analysis of human peripheral leukocyte gene expression

Human peripheral leukocytes are the key operatives in the human immune network, mediating immune responses through both innate and acquired immunity. While much progress has been made to elucidate the mechanisms of leukocyte functions, our understanding of the genetic blueprint of leukocytes and the molecular basis of their functioning is far from complete. This project was started in 1997 and aimed to profile gene expression of human peripheral leukocytes and to identify novel leukocyte-specific genes. More than 15,000 ESTs were generated from an adult leukocyte cDNA library, representing over 7,000 unique genes—or approximately one-third to one-half of the total number of genes expressed in leukocytes. During this project, we identified a novel EST showing sequence similarity to members of the C-type lectin superfamily. Further characterization revealed that this gene, CLEC-6, was a leukocyte-specific gene located in the C-type lectin superfamily cluster at chromosome 12q13, and generated a saccharide-modified polymer that showed no mannose-affinity. In order to identify genes differentially expressed in leukocytes during the immune system maturation, we generated over 5,000 umbilical cord blood ESTs. Northern in silico revealed that genes involved in the synthesis and functioning of MHC I molecules, including four MHC I molecules and beta-microglobulin, were down-regulated in the umbilical cord blood. To expand the utility of our leukocyte-derived ESTs, we developed a “LeukoChip” containing nearly 6,000 unique genes. With cDNA microarray, we explored the differential expression profile of coronary artery disease leukocytes, identified the up-regulated expression of three leukocyte-secreted proteins, and suggested the potential role of peripheral leukocyte in systemic inflammation during atherogenesis. In summary, the present leukocyte gene-profiling project combines genomic, computational and conventional molecular biology approaches to provide a basic molecular foundation that will be important for understanding gene expression and regulation in leukocyte function, development and pathogenesis.