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Discovery of the gene signature for acute lung injury in patients with sepsis.

ABSTRACT: The acute respiratory distress syndrome (ARDS)/acute lung injury (ALI) was described 30 yr ago, yet making a definitive diagnosis remains difficult. The identification of biomarkers obtained from peripheral blood could provide additional noninvasive means for diagnosis. To identify gene expression profiles that may be used to classify patients with ALI, 13 patients with ALI + sepsis and 20 patients with sepsis alone were recruited from the Medical Intensive Care Unit of the University of Pittsburgh Medical Center, and microarrays were performed on peripheral blood samples. Several classification algorithms were used to develop a gene signature for ALI from gene expression profiles. This signature was validated in an independently obtained set of patients with ALI + sepsis (n = 8) and sepsis alone (n = 1). An eight-gene expression profile was found to be associated with ALI. Internal validation found that the gene signature was able to distinguish patients with ALI + sepsis from patients with sepsis alone with 100% accuracy, corresponding to a sensitivity of 100%, a specificity of 100%, a positive predictive value of 100%, and a negative predictive value of 100%. In the independently obtained external validation set, the gene signature was able to distinguish patients with ALI + sepsis from patients with sepsis alone with 88.9% accuracy. The use of classification models to develop a gene signature from gene expression profiles provides a novel and accurate approach for classifying patients with ALI.

SUBMITTER: Howrylak JA

PROVIDER: S-EPMC3774580 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature

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Discovery of the gene signature for acute lung injury in patients with sepsis.

Howrylak Judie A JA Dolinay Tamas T Lucht Lorrie L Wang Zhaoxi Z Christiani David C DC Sethi Jigme M JM Xing Eric P EP Donahoe Michael P MP Choi Augustine M K AM

Physiological genomics 20090127 2

The acute respiratory distress syndrome (ARDS)/acute lung injury (ALI) was described 30 yr ago, yet making a definitive diagnosis remains difficult. The identification of biomarkers obtained from peripheral blood could provide additional noninvasive means for diagnosis. To identify gene expression profiles that may be used to classify patients with ALI, 13 patients with ALI + sepsis and 20 patients with sepsis alone were recruited from the Medical Intensive Care Unit of the University of Pittsbu ...[more]

PMID: 19174476

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Project description:BackgroundAcute kidney injury (AKI) is a common complication in sepsis. However, the trajectories of sepsis-induced AKI and their transcriptional profiles are not well characterized.MethodsSepsis patients admitted to centres participating in Chinese Multi-omics Advances In Sepsis (CMAISE) from November 2020 to December 2021 were enrolled, and gene expression in peripheral blood mononuclear cells was measured on Day 1. The renal function trajectory was measured by the renal component of the SOFA score (SOFArenal) on Days 1 and 3. Transcriptional profiles on Day 1 were compared between these renal function trajectories, and a support vector machine (SVM) was developed to distinguish transient from persistent AKI.ResultsA total of 172 sepsis patients were enrolled during the study period. The renal function trajectory was classified into four types: non-AKI (SOFArenal = 0 on Days 1 and 3, n = 50), persistent AKI (SOFArenal > 0 on Days 1 and 3, n = 62), transient AKI (SOFArenal > 0 on Day 1 and SOFArenal = 0 on Day 3, n = 50) and worsening AKI (SOFArenal = 0 on Days 1 and SOFArenal > 0 on Day 3, n = 10). The persistent AKI group showed severe organ dysfunction and prolonged requirements for organ support. The worsening AKI group showed the least organ dysfunction on day 1 but had higher serum lactate and prolonged use of vasopressors than the non-AKI and transient AKI groups. There were 2091 upregulated and 1,902 downregulated genes (adjusted p < 0.05) between the persistent and transient AKI groups, with enrichment in the plasma membrane complex, receptor complex, and T-cell receptor complex. A 43-gene SVM model was developed using the genetic algorithm, which showed significantly greater performance predicting persistent AKI than the model based on clinical variables in a holdout subset (AUC: 0.948 [0.912, 0.984] vs. 0.739 [0.648, 0.830]; p < 0.01 for Delong's test).ConclusionsOur study identified four subtypes of sepsis-induced AKI based on kidney injury trajectories. The landscape of host response aberrations across these subtypes was characterized. An SVM model based on a gene signature was developed to predict renal function trajectories, and showed better performance than the clinical variable-based model. Future studies are warranted to validate the gene model in distinguishing persistent from transient AKI.

Project description:Acute lung injury (ALI) is a severe inflammatory process of the lung. The only proven life-saving support is mechanical ventilation (MV) using low tidal volumes (LVT) plus moderate to high levels of positive end-expiratory pressure (PEEP). However, it is currently unknown how they exert the protective effects. To identify the molecular mechanisms modulated by protective MV, this study reports transcriptomic analyses based on microarray and microRNA sequencing in lung tissues from a clinically relevant animal model of sepsis-induced ALI. Sepsis was induced by cecal ligation and puncture (CLP) in male Sprague-Dawley rats. At 24 hours post-CLP, septic animals were randomized to three ventilatory strategies: spontaneous breathing, LVT (6 ml/kg) plus 10 cmH2O PEEP and high tidal volume (HVT, 20 ml/kg) plus 2 cmH2O PEEP. Healthy, non-septic, non-ventilated animals served as controls. After 4 hours of ventilation, lung samples were obtained for histological examination and gene expression analysis using microarray and microRNA sequencing. Validations were assessed using parallel analyses on existing publicly available genome-wide association study findings and transcriptomic human data. The catalogue of deregulated processes differed among experimental groups. The 'response to microorganisms' was the most prominent biological process in septic, non-ventilated and in HVT animals. Unexpectedly, the 'neuron projection morphogenesis' process was one of the most significantly deregulated in LVT. Further support for the key role of the latter process was obtained by microRNA studies, as four species targeting many of its genes (Mir-27a, Mir-103, Mir-17-5p and Mir-130a) were found deregulated. Additional analyses revealed 'VEGF signaling' as a central underlying response mechanism to all the septic groups (spontaneously breathing or mechanically ventilated). Based on this data, we conclude that a co-deregulation of 'VEGF signaling' along with 'neuron projection morphogenesis', which have been never anticipated in ALI pathogenesis, promotes lung-protective effects of LVT with high levels of PEEP.

Project description:IntroductionIn this study, we sought to determine the association between red blood cell (RBC) transfusion and outcomes in patients with acute lung injury (ALI), sepsis and shock.MethodsWe performed a secondary analysis of new-onset ALI patients enrolled in the Acute Respiratory Distress Syndrome Network Fluid and Catheter Treatment Trial (2000 to 2005) who had a documented ALI risk factor of sepsis or pneumonia and met shock criteria (mean arterial pressure (MAP) < 60 mmHg or vasopressor use) within 24 hours of randomization. Using multivariable logistic regression, we examined the association between RBC transfusion and 28-day mortality after adjustment for age, sex, race, randomization arm and Acute Physiology and Chronic Health Evaluation III score. Secondary end points included 90-day mortality and ventilator-free days (VFDs). Finally, we examined these end points among the subset of subjects meeting prespecified transfusion criteria defined by five simultaneous indicators: hemoglobin < 10.2 g/dL, central or mixed venous oxygen saturation < 70%, central venous pressure ? 8 mmHg, MAP ? 65 mmHg, and vasopressor use.ResultsWe identified 285 subjects with ALI, sepsis, shock and transfusion data. Of these, 85 also met the above prespecified transfusion criteria. Fifty-three (19%) of the two hundred eighty-five subjects with shock and twenty (24%) of the subset meeting the transfusion criteria received RBC transfusion within twenty-four hours of randomization. We found no independent association between RBC transfusion and 28-day mortality (odds ratio = 1.49, 95% CI (95% confidence interval) = 0.77 to 2.90; P = 0.23) or VFDs (mean difference = -0.35, 95% CI = -4.03 to 3.32; P = 0.85). Likewise, 90-day mortality and VFDs did not differ by transfusion status. Among the subset of patients meeting the transfusion criteria, we found no independent association between transfusion and mortality or VFDs.ConclusionsIn patients with new-onset ALI, sepsis and shock, we found no independent association between RBC transfusion and mortality or VFDs. The physiological criteria did not identify patients more likely to be transfused or to benefit from transfusion.

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Discovery of the gene signature for acute lung injury in patients with sepsis.

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Discovery of the gene signature for acute lung injury in patients with sepsis.

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