Leukocyte subset-derived genomewide expression profiles in pediatric septic shock.
Ontology highlight
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.
SUBMITTER: Wong HR
PROVIDER: S-EPMC2927840 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Rationale: We previously generated genome-wide expression data in children with septic shock, based on whole blood-derive RNA, having the potential to lead the field into novel areas of investigation. Objective: Herein we seek to validate our data through a bioinformatic approach centered on a validation patient cohort. Methods: Microarray- and bioinformatics-centered analyses involving our previous data as a training data set (n = 42) and a new, validation cohort (n = 30) as the test data set. Measurements and Main Results: Class prediction modeling using the training data set and the previously reported genome-wide expression signature of pediatric septic shock correctly identified 93 to 100% of septic shock patients in the test data set, depending on the class prediction algorithm and the gene selection method. Subjecting the test data set to an identical filtering strategy as that used for the training data set, demonstrated 72% concordance between the two gene lists. Subjecting the test data set to a purely statistical filtering strategy, with highly stringent correction for multiple comparisons, demonstrated less than 50% concordance with the previous gene filtering strategy. However, functional analysis of this statistics-based gene list demonstrated similar functional annotations and signaling pathways as that seen in the learning data set. In particular, we validated that pediatric septic shock is characterized by large scale repression of genes related to zinc homeostasis and lymphocyte function. Conclusions: These data demonstrate that the previously reported genome-wide expression signature of pediatric septic shock is applicable to a validation cohort of patients. Keywords: Inflammation; sepsis; innate immunity; T cells; MHC antigen; zinc
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