By studying gene expression changes over time in a cohort of trauma patients, Keyur Desai and colleagues identify genes and pathways strongly associated with longer-term complications, which could lead to improved outcome prediction in the first 80 hours after injury., Background Trauma is the number one killer of individuals 1–44 y of age in the United States. The prognosis and treatment of inflammatory complications in critically injured patients continue to be challenging, with a history of failed clinical trials and poorly understood biology. New approaches are therefore needed to improve our ability to diagnose and treat this clinical condition. Methods and Findings We conducted a large-scale study on 168 blunt-force trauma patients over 28 d, measuring ∼400 clinical variables and longitudinally profiling leukocyte gene expression with ∼800 microarrays. Marshall MOF (multiple organ failure) clinical score trajectories were first utilized to organize the patients into five categories of increasingly poor outcomes. We then developed an analysis framework modeling early within-patient expression changes to produce a robust characterization of the genomic response to trauma. A quarter of the genome shows early expression changes associated with longer-term post-injury complications, captured by at least five dynamic co-expression modules of functionally related genes. In particular, early down-regulation of MHC-class II genes and up-regulation of p38 MAPK signaling pathway were found to strongly associate with longer-term post-injury complications, providing discrimination among patient outcomes from expression changes during the 40–80 h window post-injury. Conclusions The genomic characterization provided here substantially expands the scope by which the molecular response to trauma may be characterized and understood. These results may be instrumental in furthering our understanding of the disease process and identifying potential targets for therapeutic intervention. Additionally, the quantitative approach we have introduced is potentially applicable to future genomics studies of rapidly progressing clinical conditions. Trial Registration ClinicalTrials.gov NCT00257231 Please see later in the article for the Editors' Summary, Editors' Summary Background Trauma—a serious injury to the body caused by violence or by an accident—is a major global health problem. Every year, events that include traffic collisions, falls, blows, and fires cause injuries that kill more than 5 million people (9% of annual global deaths). Road traffic accidents alone are responsible for 1.3 million deaths a year and, if current trends continue, will be the fifth leading cause of death worldwide by 2030. Moreover, in many countries, including the US, trauma is the number one killer of individuals aged 1–44 y. Trauma can kill people rapidly through loss of blood or serious physical damage to internal organs, but it can also lead to localized infections and to sepsis, an infection of the bloodstream that is characterized by an amplified, body-wide (systemic) inflammatory response. Inflammation—redness, pain, and swelling—is an immune system response that normally provides protection against infections, but systemic inflammation can result in multiple organ failure (MOF) and death. Why Was This Study Done? Inflammatory complications of trauma are responsible for more than half of late trauma deaths, but at present it is impossible to predict which patients with major injuries will recover and which will spiral down into MOF and death, because the biological processes that underlie post-injury inflammatory complications are poorly understood. If the changes in gene expression (the process that converts the information encoded in genes into functional proteins) that accompany systemic inflammation could be elucidated, it might be possible to improve the diagnosis of MOF and to develop better treatments for post-trauma inflammatory complications. In this prospective, longitudinal clinical genomics study (part of the Inflammation and Host Response to Injury multi-disciplinary research program [IHRI]), the researchers developed an approach to associate early within-patient gene expression changes with later clinical outcomes. A prospective study is one in which patients with a specific condition are enrolled and then followed to see how various factors affect their outcomes; a longitudinal study analyzes multiple samples taken at different times from individual patients; a clinical genomics study investigates how genes and gene expression affect clinical outcomes. What Did the Researchers Do and Find? The researchers followed 168 patients for up to 28 d after they experienced blunt-force trauma (injuries caused when the human body hits or is hit by a large object such as a car). Using a molecular biology tool called a DNA microarray, they determined gene expression patterns in leukocytes (a type of immune system cell) isolated from multiple blood samples collected from each patient during the first few days after injury. Using clinical information collected by trained nurses, they organized the patients into five outcome categories based on a measure of MOF known as the Marshall score. Finally, they developed a statistical method (an analysis framework) to associate the early changes in gene expression with clinical outcomes. A quarter of the patients' genes showed early expression changes that were associated with longer-term post-injury inflammatory complications. Among the associations revealed by this analysis, down-regulation (reduced expression) of MHC-class II genes (which encode proteins involved in antigen presentation, the process by which molecules from foreign invaders are presented to immune cells to initiate an immune response) and up-regulation of genes encoding components of the p38 MAPK signaling pathway (which helps to drive inflammatory responses) between 40 and 80 h post-injury were particularly strongly associated with longer-term post-injury complications and provided the strongest discrimination between patient outcomes. What Do These Findings Mean? The statistical approach used in this study to link the early changes in gene expression that occur after trauma to clinical outcomes provides a detailed picture of genome-wide gene expression responses to trauma. These findings could help scientists understand why some patients develop inflammatory complications of trauma while others do not, and they could help to identify those patients most at risk of developing complications. They could also help to identify targets for therapy, although further studies are needed to confirm and extend these findings. Importantly, the quantitative approach developed by the researchers for analyzing associations between within-patient gene changes over time and clinical outcomes should provide more robust predictions of outcomes than single measurements of gene expression and could be applicable to genomic studies of other rapidly progressing clinical conditions. Additional Information Please access these websites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001093. More details about the Inflammation and Host Response to Injury research program are available; the program's website includes a link to an article that explains how genomics can be used to understand the inflammatory complications of trauma The World Health Organization provides information on injuries and on violence and injury prevention (in several languages) The US National Institutes of Health has a factsheet on burns and traumatic injury in the USA The US Centers for Disease Control and Prevention has information on injury and violence prevention and control MedlinePlus provides links to further resources on injuries