title: Proteome Profiling in Lung Injury after Hematopoietic Stem Cell Transplantation.
abstract: Pulmonary complications due to infection and idiopathic pneumonia syndrome (IPS), a noninfectious lung injury in hematopoietic stem cell transplant (HSCT) recipients, are frequent causes of transplantation-related mortality and morbidity. Our objective was to characterize the global bronchoalveolar lavage fluid (BALF) protein expression of IPS to identify proteins and pathways that differentiate IPS from infectious lung injury after HSCT. We studied 30 BALF samples from patients who developed lung injury within 180 days of HSCT or cellular therapy transfusion (natural killer cell transfusion). Adult subjects were classified as having IPS or infectious lung injury by the criteria outlined in the 2011 American Thoracic Society statement. BALF was depleted of hemoglobin and 14 high-abundance proteins, treated with trypsin, and labeled with isobaric tagging for relative and absolute quantification (iTRAQ) 8-plex reagent for two-dimensional capillary liquid chromatography (LC) and data dependent peptide tandem mass spectrometry (MS) on an Orbitrap Velos system in higher-energy collision-induced dissociation activation mode. Protein identification employed a target-decoy strategy using ProteinPilot within Galaxy P. The relative protein abundance was determined with reference to a global internal standard consisting of pooled BALF from patients with respiratory failure and no history of HSCT. A variance weighted t-test controlling for a false discovery rate of ≤5% was used to identify proteins that showed differential expression between IPS and infectious lung injury. The biological relevance of these proteins was determined by using gene ontology enrichment analysis and Ingenuity Pathway Analysis. We characterized 12 IPS and 18 infectious lung injury BALF samples. In the 5 iTRAQ LC-MS/MS experiments 845, 735, 532, 615, and 594 proteins were identified for a total of 1125 unique proteins and 368 common proteins across all 5 LC-MS/MS experiments. When comparing IPS to infectious lung injury, 96 proteins were differentially expressed. Gene ontology enrichment analysis showed that these proteins participate in biological processes involved in the development of lung injury after HSCT. These include acute phase response signaling, complement system, coagulation system, liver X receptor (LXR)/retinoid X receptor (RXR), and farsenoid X receptor (FXR)/RXR modulation. We identified 2 canonical pathways modulated by TNF-α, FXR/RXR activation, and IL2 signaling in macrophages. The proteins also mapped to blood coagulation, fibrinolysis, and wound healing-processes that participate in organ repair. Cell movement was identified as significantly over-represented by proteins with differential expression between IPS and infection. In conclusion, the BALF protein expression in IPS differed significantly from infectious lung injury in HSCT recipients. These differences provide insights into mechanisms that are activated in lung injury in HSCT recipients and suggest potential therapeutic targets to augment lung repair.
authors.affiliation: Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Minnesota Medical School, Minneapolis, Minnesota. Electronic address: bharg005@umn.edu.
authors.forename: Maneesh
authors.initials: M
authors.lastname: Bhargava
authors.affiliation: Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Minnesota Medical School, Minneapolis, Minnesota.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Viken
authors.affiliation: Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.
authors.forename: Sanjoy
authors.initials: S
authors.lastname: Dey
authors.affiliation: Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Steinbach
authors.affiliation: Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota.
authors.forename: Baolin
authors.initials: B
authors.lastname: Wu
authors.affiliation: Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota.
authors.forename: Pratik D
authors.initials: PD
authors.lastname: Jagtap
authors.affiliation: Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota.
authors.forename: LeeAnn
authors.initials: L
authors.lastname: Higgins
authors.affiliation: Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Minnesota Medical School, Minneapolis, Minnesota.
authors.forename: Angela
authors.initials: A
authors.lastname: Panoskaltsis-Mortari
authors.affiliation: Division of Hematology, Oncology and Transplantation, University of Minnesota Medical School, Minneapolis, Minnesota.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Weisdorf
authors.affiliation: Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.
authors.forename: Vipin
authors.initials: V
authors.lastname: Kumar
authors.affiliation: Division of Hematology, Oncology and Transplantation, University of Minnesota Medical School, Minneapolis, Minnesota.
authors.forename: Mukta
authors.initials: M
authors.lastname: Arora
authors.affiliation: Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Minnesota Medical School, Minneapolis, Minnesota.
authors.forename: Peter B
authors.initials: PB
authors.lastname: Bitterman
authors.affiliation: Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Minnesota Medical School, Minneapolis, Minnesota.
authors.forename: David H
authors.initials: DH
authors.lastname: Ingbar
authors.affiliation: Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Minnesota Medical School, Minneapolis, Minnesota; Pulmonary, Critical Care and Sleep Medicine, Minneapolis Veterans Affairs, Minneapolis, Minnesota.
authors.forename: Chris H
authors.initials: CH
authors.lastname: Wendt
mesh_terms: D000328:Adult; D000368:Aged; D001992:Bronchoalveolar Lavage Fluid / Q000737:chemistry; D020869:Gene Expression Profiling; D063990:Gene Ontology; D018380:Hematopoietic Stem Cell Transplantation / Q000009:adverse effects*; D006801:Humans; D055370:Lung Injury / Q000209:etiology*; D008875:Middle Aged; D011014:Pneumonia / Q000209:etiology*; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods
chemical_list: D020543:Proteome
keywords: Bioinformatics; Bronchoalveolar lavage; Idiopathic pneumonia syndrome; Pathways; Proteomics