Immune cell transcriptome datasets reveal novel leukocyte subset-specific genes and genes associated with allergic processes.

Sue M. Liu, Ramnik Xavier, Kim L. Good, Tatyana Chtanova, Rebecca Newton, Mary Sisavanh, Sabine Zimmer, Chaoyang Deng, Diego G. Silva, Melinda J. Frost, Stuart Tangye, Michael Rolph, Charles R. Mackay

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

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. Conclusion 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. Clinical implications A comprehensive dataset of gene expression profiles of human leukocytes should provide new targets or biomarkers for human inflammatory diseases.
Original languageEnglish
Pages (from-to)496-503
Number of pages8
JournalJournal of Allergy and Clinical Immunology
Volume118
DOIs
Publication statusPublished - 2006
Externally publishedYes

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Transcriptome
Leukocytes
Genes
Basophils
Mast Cells
Datasets
Toll-Like Receptors
Plasma Cells
Computational Biology
Eosinophils
Innate Immunity
Hypersensitivity
Biomarkers
Inflammation

Cite this

Liu, Sue M. ; Xavier, Ramnik ; Good, Kim L. ; Chtanova, Tatyana ; Newton, Rebecca ; Sisavanh, Mary ; Zimmer, Sabine ; Deng, Chaoyang ; Silva, Diego G. ; Frost, Melinda J. ; Tangye, Stuart ; Rolph, Michael ; Mackay, Charles R. / Immune cell transcriptome datasets reveal novel leukocyte subset-specific genes and genes associated with allergic processes. In: Journal of Allergy and Clinical Immunology. 2006 ; Vol. 118. pp. 496-503.
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title = "Immune cell transcriptome datasets reveal novel leukocyte subset-specific genes and genes associated with allergic processes.",
abstract = "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. Conclusion 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. Clinical implications A comprehensive dataset of gene expression profiles of human leukocytes should provide new targets or biomarkers for human inflammatory diseases.",
author = "Liu, {Sue M.} and Ramnik Xavier and Good, {Kim L.} and Tatyana Chtanova and Rebecca Newton and Mary Sisavanh and Sabine Zimmer and Chaoyang Deng and Silva, {Diego G.} and Frost, {Melinda J.} and Stuart Tangye and Michael Rolph and Mackay, {Charles R.}",
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Liu, SM, Xavier, R, Good, KL, Chtanova, T, Newton, R, Sisavanh, M, Zimmer, S, Deng, C, Silva, DG, Frost, MJ, Tangye, S, Rolph, M & Mackay, CR 2006, 'Immune cell transcriptome datasets reveal novel leukocyte subset-specific genes and genes associated with allergic processes.', Journal of Allergy and Clinical Immunology, vol. 118, pp. 496-503. https://doi.org/10.1016/j.jaci.2006.04.040

Immune cell transcriptome datasets reveal novel leukocyte subset-specific genes and genes associated with allergic processes. / Liu, Sue M.; Xavier, Ramnik; Good, Kim L.; Chtanova, Tatyana; Newton, Rebecca; Sisavanh, Mary; Zimmer, Sabine; Deng, Chaoyang; Silva, Diego G.; Frost, Melinda J.; Tangye, Stuart; Rolph, Michael; Mackay, Charles R.

In: Journal of Allergy and Clinical Immunology, Vol. 118, 2006, p. 496-503.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Immune cell transcriptome datasets reveal novel leukocyte subset-specific genes and genes associated with allergic processes.

AU - Liu, Sue M.

AU - Xavier, Ramnik

AU - Good, Kim L.

AU - Chtanova, Tatyana

AU - Newton, Rebecca

AU - Sisavanh, Mary

AU - Zimmer, Sabine

AU - Deng, Chaoyang

AU - Silva, Diego G.

AU - Frost, Melinda J.

AU - Tangye, Stuart

AU - Rolph, Michael

AU - Mackay, Charles R.

PY - 2006

Y1 - 2006

N2 - 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. Conclusion 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. Clinical implications A comprehensive dataset of gene expression profiles of human leukocytes should provide new targets or biomarkers for human inflammatory diseases.

AB - 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. Conclusion 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. Clinical implications A comprehensive dataset of gene expression profiles of human leukocytes should provide new targets or biomarkers for human inflammatory diseases.

U2 - 10.1016/j.jaci.2006.04.040

DO - 10.1016/j.jaci.2006.04.040

M3 - Article

VL - 118

SP - 496

EP - 503

JO - The Journal of allergy

JF - The Journal of allergy

SN - 0091-6749

ER -