Leukocyte subset-derived genomewide expression profiles in pediatric septic shock

Abstract

Objective: To directly assess whether genomewide expression profiles derived from leukocyte subsets are comparable to that of whole blood as measured by enrichment for genes corresponding to metabolic and signaling pathways.

Design: Prospective observational study involving microarray-based bioinformatics based on RNA individually derived from whole blood, neutrophils, monocytes, and lymphocytes, respectively.

Setting: Three pediatric intensive care units in the United States.

Patients: Children < or =10 yrs of age: five normal control subjects and 13 meeting criteria for septic shock on day 1 of presentation to the pediatric intensive care unit.

Interventions: None other than standard care.

Measurements and main results: Baseline analyses using whole blood-derived RNA demonstrated increased expression of genes corresponding to signaling pathways involving innate immunity, redox balance, and protein ubiquitination and decreased expression of genes corresponding to the adaptive immune system. Subsequent analyses using leukocyte-specific RNA were congruent with the gene expression profiles demonstrated using whole blood-derived RNA as measured by enrichment for genes corresponding to metabolic and signaling pathways. Gene network analysis, derived from a composite gene list involving the individual gene expression profiles of neutrophils, monocytes, and lymphocytes, respectively, revealed a gene network corresponding to antigen presentation, cell-mediated immunity, and humoral-mediated immunity. Finally, a subanalysis focused on network gene nodes localized to the nuclear compartment revealed functional annotations related to transcriptional repression and epigenetic regulation.

Conclusions: These data demonstrate that genome-level repression of adaptive immunity gene programs early in the course of pediatric septic shock remained evident when analyses were conducted using leukocyte subset-specific RNA.

Figure 1

Venn analysis comparing the genes differentially upregulated between patients with septic shock and controls for each leukocyte subset.

Figure 2

Venn analysis comparing the genes differentially downregulated between patients with septic shock and controls for each leukocyte subset.

Figure 3

Gene network derived from a merged list of genes common to all gene lists represented by the Venn diagrams in Figure 1 and Figure 2. Red intensity within in a gene node corresponds to increased expression in the patients with septic shock, relative to controls, and green intensity within a gene node corresponds to decreased expression in the patients with septic shock, relative to controls. This network has a score of 28, which is equivalent to a p value of 1.0E-28. The p value provides an estimate of the probability that the network genes are present in the uploaded gene list by chance alone. A network legend and a complete list of the network genes are provided in the Supplementary Data.