Antigen-specific gene expression profiles of peripheral blood mononuclear cells do not reflect those of T-lymphocyte subsets

Abstract

Advances in microarray technology have allowed for the monitoring of thousands of genes simultaneously. This technology is of particular interest to immunologists studying infectious diseases, because it provides tremendous potential for investigating host-pathogen interactions at the level of immune gene expression. To date, many studies have focused either on cell lines, where the physiological relevance is questionable, or on mixed cell populations, where the contributions of individual subpopulations are unknown. In the present study, we perform an intrasubject comparison of antigen-stimulated immune gene expression profiles between a mixed population of peripheral blood mononuclear cells (PBMC) and the two predominant cell types found in PBMC, CD4+ and CD8+ T lymphocytes. We show that the microarray profiles of CD4+ and CD8+ T lymphocytes differ from each other as well as from that of the mixed cell population. The independence of the gene expression profiles of different cell types is demonstrated with a ubiquitous antigen (Candida albicans) as well as with a disease-specific antigen (human immunodeficiency virus p24). This study has important implications for microarray studies of host immunity and underscores the importance of profiling the expression of specific cell types.

Figures

FIG. 1.

Venn diagrams of changed genes in single and mixed cell populations. The number of genes showing expression changes at the twofold level is given for each subset. (a and b) HIV-negative sample responses to C. albicans; (c and d) HIV-positive sample responses to C. albicans; (e and f) HIV-positive sample responses to p24. Diagrams a, c, and e represent gene up-regulations, while diagrams b, d, and f represent gene down-regulations. Red, green, and blue sections represent genes changed only in the CD4+, CD8+, and PBMC populations, respectively. Sections in yellow, purple, and light blue represent genes sharing trends in two cell populations as shown. Sections in white represent genes showing the same trend in all cell populations.

FIG. 2.

Fold change in gene expression in response to antigenic stimulation in single and mixed cell populations. Shown are ratios for selected genes with differing values in each cell population. Genes shown to have changed expression in one cell population do not meet the twofold criteria in the other two populations. (a) HIV-negative sample responses to C. albicans stimulation with respect to expression of MIF, TNFRSF5, and MCP-1. (b) Effects of p24 stimulation on expression of IL-6, TRAP-1, and IGF2 in the HIV-positive sample.

FIG. 3.

Comparison of responses to different recall antigens in an HIV-positive sample. Responses to different recall antigens show similarity within the same individual. Shaded or solid bars, numbers of genes changed in response to C. albicans or p24, respectively. Open bars, numbers of genes similarly changed in response to both antigens in individual cell types.