A genomic storm in critically injured humans

Wenzhong Xiao, Michael N Mindrinos, Junhee Seok, Joseph Cuschieri, Alex G Cuenca, Hong Gao, Douglas L Hayden, Laura Hennessy, Ernest E Moore, Joseph P Minei, Paul E Bankey, Jeffrey L Johnson, Jason Sperry, Avery B Nathens, Timothy R Billiar, Michael A West, Bernard H Brownstein, Philip H Mason, Henry V Baker, Celeste C Finnerty, Marc G Jeschke, M Cecilia López, Matthew B Klein, Richard L Gamelli, Nicole S Gibran, Brett Arnoldo, Weihong Xu, Yuping Zhang, Steven E Calvano, Grace P McDonald-Smith, David A Schoenfeld, John D Storey, J Perren Cobb, H Shaw Warren, Lyle L Moldawer, David N Herndon, Stephen F Lowry, Ronald V Maier, Ronald W Davis, Ronald G Tompkins, Inflammation and Host Response to Injury Large-Scale Collaborative Research Program, Lily Altstein, Ulysses G J Balis, David G Camp 2nd, Asit K De, Brian G Harbrecht, Shari E Honari, Bruce A McKinley, Carol L Miller-Graziano, Frederick A Moore, Grant E O'Keefe, Laurence G Rahme, Daniel G Remick, Michael B Shapiro, Richard D Smith, Robert Tibshirani, Mehmet Toner, Bram Wispelwey, Wing H Wong, Wenzhong Xiao, Michael N Mindrinos, Junhee Seok, Joseph Cuschieri, Alex G Cuenca, Hong Gao, Douglas L Hayden, Laura Hennessy, Ernest E Moore, Joseph P Minei, Paul E Bankey, Jeffrey L Johnson, Jason Sperry, Avery B Nathens, Timothy R Billiar, Michael A West, Bernard H Brownstein, Philip H Mason, Henry V Baker, Celeste C Finnerty, Marc G Jeschke, M Cecilia López, Matthew B Klein, Richard L Gamelli, Nicole S Gibran, Brett Arnoldo, Weihong Xu, Yuping Zhang, Steven E Calvano, Grace P McDonald-Smith, David A Schoenfeld, John D Storey, J Perren Cobb, H Shaw Warren, Lyle L Moldawer, David N Herndon, Stephen F Lowry, Ronald V Maier, Ronald W Davis, Ronald G Tompkins, Inflammation and Host Response to Injury Large-Scale Collaborative Research Program, Lily Altstein, Ulysses G J Balis, David G Camp 2nd, Asit K De, Brian G Harbrecht, Shari E Honari, Bruce A McKinley, Carol L Miller-Graziano, Frederick A Moore, Grant E O'Keefe, Laurence G Rahme, Daniel G Remick, Michael B Shapiro, Richard D Smith, Robert Tibshirani, Mehmet Toner, Bram Wispelwey, Wing H Wong

Abstract

Human survival from injury requires an appropriate inflammatory and immune response. We describe the circulating leukocyte transcriptome after severe trauma and burn injury, as well as in healthy subjects receiving low-dose bacterial endotoxin, and show that these severe stresses produce a global reprioritization affecting >80% of the cellular functions and pathways, a truly unexpected "genomic storm." In severe blunt trauma, the early leukocyte genomic response is consistent with simultaneously increased expression of genes involved in the systemic inflammatory, innate immune, and compensatory antiinflammatory responses, as well as in the suppression of genes involved in adaptive immunity. Furthermore, complications like nosocomial infections and organ failure are not associated with any genomic evidence of a second hit and differ only in the magnitude and duration of this genomic reprioritization. The similarities in gene expression patterns between different injuries reveal an apparently fundamental human response to severe inflammatory stress, with genomic signatures that are surprisingly far more common than different. Based on these transcriptional data, we propose a new paradigm for the human immunological response to severe injury.

Trial registration: ClinicalTrials.gov NCT00257231.

Figures

Figure 1.
Figure 1.
Organ injury and genomic changes associated with severe blunt trauma. (A) Whole blood was taken from severe blunt trauma patients, leukocytes were isolated, and total cellular RNA was extracted and hybridized onto an HU133 Plus 2.0 GeneChip. The continuum of clinical responses to severe blunt trauma in the 1,637 total patients from which the 167 sampling trauma patients were drawn is shown graphically. Each row represents an individual patient ordered by time to recovery (TTR), and the x axis represents time from injury in days. Patients are sorted from least to most severe organ injury and mortality. The presence and severity of organ injury is represented by colors from blue (least severe) to red (most severe). Black indicates death. (B) K-means clustering of the genes into 30 clusters based on patterns of expression over time. Red indicates increased and blue indicates decreased expression relative to the mean (white). 5,136 genes were differentially expressed between patients and controls (ctrl; FDR <0.001 and at least twofold change). (C and D) Summary of the canonical pathways most affected by trauma. The graph shows the −log10 (p value) of the enrichment of the pathway.
Figure 2.
Figure 2.
Validation of the genomic response to trauma in burn patients and healthy adults challenged with low-dose bacterial endotoxin. (A and B) Comparison of direction of changes among the genes identified in Fig. 1 B, between trauma and burns (A) and trauma and endotoxemia (B). (C) Scatter plots of log2 fold changes (x and y axes) of 5,855 genes (FDR <0.001 and at least twofold change) in trauma, burns, or endotoxemia (bottom left) and corresponding Pearson correlation coefficient (r). The axes in C represent fold changes.
Figure 3.
Figure 3.
Differences in gene expression patterns between patients with a complicated and uncomplicated clinical recovery. Heat map of 1,201 genes whose expression was at least twofold different at any time point when compared with controls (CTRL) for patients with a complicated (Comp) or uncomplicated recovery (Uncomp). (A) Cluster analysis of the two cohorts. The brackets to the right of the cluster indicate cluster 2 and 8 shown in B and C, respectively. (B) One cluster of genes whose expression was up-regulated in patients with a complicated recovery. (C) One cluster of genes whose expression was down-regulated in patients with a complicated recovery.
Figure 4.
Figure 4.
A genomic storm: Refining the immune, inflammatory paradigm in trauma. (A) The current paradigm explains complications of severe injury as a result of excessive proinflammatory responses (SIRS) followed temporally by compensatory antiinflammatory responses (CARS) and suppression of adaptive immunity. A second-hit phenomenon results from sequential insults, which leads to more severe, recurrent SIRS and organ dysfunction. (B) The proposed new paradigm involves simultaneous and rapid induction of innate (both pro- and antiinflammatory genes) and suppression of adaptive immunity genes. Complicated recoveries are delayed, resulting in a prolonged, dysregulated immune–inflammatory state.

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