Immune cell transcriptome datasets reveal novel leukocyte subset-specific genes and genes associated with allergic processes.
BACKGROUND
The precise function of various resting and activated leukocyte subsets remains unclear. For instance, mast cells, basophils, and eosinophils play important roles in allergic inflammation but also participate in other immunologic responses. One strategy to understand leukocyte subset function is to define the expression and function of subset-restricted molecules.


OBJECTIVE
To use a microarray dataset and bioinformatics strategies to identify novel leukocyte markers as well as genes associated with allergic or innate responses.


METHODS
By using Affymetrix microarrays, we generated an immune transcriptome dataset composed of gene profiles from all of the major leukocyte subsets, including rare enigmatic subsets such as mast cells, basophils, and plasma cells. We also assessed whether analysis of genes expressed commonly by certain groups of leukocytes, such as allergic leukocytes, might identify genes associated with particular responses.


RESULTS
Transcripts highly restricted to a single leukocyte subset were readily identified (>2000 subset-specific transcripts), many of which have not been associated previously with leukocyte functions. Transcripts expressed exclusively by allergy-related leukocytes revealed well known as well as novel molecules, many of which presumably contribute to allergic responses. Likewise, Nearest Neighbor Analysis of genes coexpressed with Toll-like receptors identified genes of potential relevance for innate immunity.


CONCLUSIONS
Gene profiles from all of the major human leukocyte subsets provide a powerful means to identify genes associated with single leukocyte subsets, or different types of immune response.


CONCLUSIONS
A comprehensive dataset of gene expression profiles of human leukocytes should provide new targets or biomarkers for human inflammatory diseases.
Liu
Sue M
SM
Immunology and Inflammation Research Program, Garvan Institute of Medical Research, 384 Victoria Street, Sydney 2010, Australia.
Xavier
Ramnik
R
Good
Kim L
KL
Chtanova
Tatyana
T
Newton
Rebecca
R
Sisavanh
Mary
M
Zimmer
Sabine
S
Deng
Chaoyang
C
Silva
Diego G
DG
Frost
Melinda J
MJ
Tangye
Stuart G
SG
Rolph
Michael S
MS
Mackay
Charles R
CR
D020869:Gene Expression Profiling; D006801:Humans; D006967:Hypersensitivity / Q000235:genetics*; D007962:Leukocytes / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D051193:Toll-Like Receptors / Q000235:genetics
D051193:Toll-Like Receptors