Molecular phenotyping of the immune system by microarray analysis

Gene Expression Alterations in Immune System Pathways following Exposure to Immunosuppressive Chemicals

Exposure to environmental agents can affect a number of adverse immunological outcomes, including changes in the incidence of infectious disease. Diethylstilbestrol (DES), dexamethasone (DEX), cyclophosphamide, and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) are immunosuppressive chemicals that can induce similar pathophysiological end points in the thymus; however, the mechanism of toxicity is different for each compound. We examined differential gene expression in the spleen and thymus following chemical exposure and correlated these changes with alterations in functional immune end points and our knowledge of the known mechanisms of action. RNA from the spleen and thymus has been analyzed using Illumina Sentrix arrays and BeadStudio software. Preliminary data suggest that DES induced the greatest number of gene changes in the spleen, while DEX induced the most changes in the thymus. In both spleen and thymus, genomic analysis revealed gene expression changes that were common to multiple chemicals and that may be associated with xenobiotic-induced immune system perturbations, including alterations in genes associated with apoptosis, antigen processing and presentation, and response to biotic stimulus. This was particularly evident in the thymus, where there were many similarities in the expression profiles, as well as gene alterations unique to a single compound. In contrast, expression profiles in spleen were more distinct. The category of genes most profoundly affected by all four chemicals was response to biotic stimulus: there were both clusters of genes modulated by multiple chemicals and genes altered by a single chemical. The distinct gene profiles may specifically relate to cellular targets and mechanism of action.

Tracking gene expression in primary immunodeficiencies

PURPOSE OF REVIEW

Extensive research on molecular genetics in recent decades has provided a wealth of information about the mechanisms of primary immunodeficiency diseases. Microarray technology enables the survey of the expression of thousands of genes simultaneously. This review focuses on the commonly used arrays and initial applications in the study of primary immunodeficiency diseases. The application of this technology has been found to accelerate the discovery rate of gene expression disturbances in primary immunodeficiency diseases and provide potential molecular diagnostic tools.

RECENT FINDINGS

The important role of microarray technology in functional genomic study has been demonstrated by the exponential growth in the number of scientific publications in the last few years. Microarray analysis has been used to study gene expression in several immunodeficiency diseases with known gene mutations as well as those with unknown causes. It has provided snapshots of gene expression and has presented the molecular phenotypes in the cells at defined times and under certain stimulation conditions. Studies comparing differential gene expression in patients and normal controls have allowed us to better understand the immunodeficiencies at the molecular level.

SUMMARY

Application of microarray technology in immunodeficiency study has facilitated tracking the expression of thousands of genes simultaneously. The molecular phenotypes obtained from microarray results can be used in diagnosis of diseases, supplemental to clinical phenotypes. It is a powerful survey tool that can detect disturbed gene expression in immunodeficiency diseases, which will provide clues for disease gene discovery and potential targets for drug development.