Proteomic Profiles in Acute Respiratory Distress Syndrome Differentiates Survivors from Non-Survivors Maneesh Bhargava 1 *, Trisha L. Becker 1 , Kevin J. Viken 1 , Pratik D. Jagtap 2 , Sanjoy Dey 3 , Michael S. Steinbach 3 , Baolin Wu 4 , Vipin Kumar 3 , Peter B. Bitterman 1 , David H. Ingbar 1 , Christine H. Wendt 1,5 1 Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America, 2 Minnesota Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota, United States of America, 3 Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America, 4 School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America, 5 Minneapolis VA Medical Center, University of Minnesota, Minneapolis, Minnesota, United States of America Abstract Acute Respiratory Distress Syndrome (ARDS) continues to have a high mortality. Currently, there are no biomarkers that provide reliable prognostic information to guide clinical management or stratify risk among clinical trial participants. The objective of this study was to probe the bronchoalveolar lavage fluid (BALF) proteome to identify proteins that differentiate survivors from non-survivors of ARDS. Patients were divided into early-phase (1 to 7 days) and late-phase (8 to 35 days) groups based on time after initiation of mechanical ventilation for ARDS (Day 1). Isobaric tags for absolute and relative quantitation (iTRAQ) with LC MS/MS was performed on pooled BALF enriched for medium and low abundance proteins from early-phase survivors (n = 7), early-phase non-survivors (n = 8), and late-phase survivors (n = 7). Of the 724 proteins identified at a global false discovery rate of 1%, quantitative information was available for 499. In early-phase ARDS, proteins more abundant in survivors mapped to ontologies indicating a coordinated compensatory response to injury and stress. These included coagulation and fibrinolysis; immune system activation; and cation and iron homeostasis. Proteins more abundant in early-phase non-survivors participate in carbohydrate catabolism and collagen synthesis, with no activation of compensatory responses. The compensatory immune activation and ion homeostatic response seen in early-phase survivors transitioned to cell migration and actin filament based processes in late-phase survivors, revealing dynamic changes in the BALF proteome as the lung heals. Early phase proteins differentiating survivors from non-survivors are candidate biomarkers for predicting survival in ARDS. Citation: Bhargava M, Becker TL, Viken KJ, Jagtap PD, Dey S, et al. (2014) Proteomic Profiles in Acute Respiratory Distress Syndrome Differentiates Survivors from Non-Survivors. PLoS ONE 9(10): e109713. doi:10.1371/journal.pone.0109713 Editor: Nades Palaniyar, The Hospital for Sick Children and The University of Toronto, Canada Received March 20, 2014; Accepted September 11, 2014; Published October 7, 2014 This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Data Availability: The authors confirm that all data underlying the findings are fully available without restriction. The data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD001095. Funding: 12SDG8160000 American Heart Association Scientist Development Grant (MB PI). 1UL1RR033183-01 and 8UL1TR000114-02 UMN KL2 Scholars Award (MB, Blarzar-PI). MFN MED FDN/3899-9238-09 Minnesota Medical Foundation Research Grant (MB PI). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * Email: bharg005@umn.edu Introduction Acute Respiratory Distress Syndrome (ARDS) is characterized by the abrupt onset of tachypnea, hypoxia, and loss of lung compliance in response to infectious or inflammatory triggers [1]. Extensive research has improved our understanding of ARDS pathophysiology [2], epidemiology [3,4], treatment options [5–7], and outcomes [3,8], yet ARDS patients continue to have a high mortality rate. There is strong interest in identifying biomarkers to predict the development of ARDS in at-risk subjects [9–11], assist in diagnosis [12–15], and inform prognosis [13,16–20]. Biomark- ers enabling risk stratification would not only be useful in the clinical care setting, but also in clinical trials of new therapeutic interventions to phenotype clinical trial subjects and serve as surrogate endpoints. Development of ARDS is associated with the activation of a large number of inflammatory mediators that damage the alveolar epithelium, endothelium, and basement membrane. Biomarkers based on the tissue of origin have been studied in both single center studies [11,21,22] and in NHLBI ARDS network cohorts [13,16,21]. Most studies have focused on investigating an individual biomarker in blood, bronchoalveolar lavage fluid (BALF), or urine. Markers of inflammation such as interleukin- 1b [23], interleukin 6 [7], and soluble TNF receptor I and II [24] are associated with poor prognosis in ARDS. Markers of endothelial damage including ICAM-1 [7,21], Angiopoeitin (Ang) [13], and Von Willibrand Factor (vWF) [25] correlate with higher mortality from ARDS. Poorer outcomes are also associated with higher plasma levels of SP-D (but not SP-A), a marker of type 2 alveolar epithelial cell damage [19], and receptor of advance glycation end products (RAGE), a marker of type 1 alveolar epithelial cell damage. Several other molecules, such as those involved in coagulation [26], damage to extracellular matrix [20], and oxidative stress (urine NO) [20], correlate with ARDS outcomes. A combination of biomarkers and clinical predictors PLOS ONE | www.plosone.org 1 October 2014 | Volume 9 | Issue 10 | e109713