4 research outputs found
An integrated transcriptome and expressed variant analysis of sepsis survival and death
BackgroundSepsis, a leading cause of morbidity and mortality, is not a homogeneous disease but rather a syndrome encompassing many heterogeneous pathophysiologies. Patient factors including genetics predispose to poor outcomes, though current clinical characterizations fail to identify those at greatest risk of progression and mortality.MethodsThe Community Acquired Pneumonia and Sepsis Outcome Diagnostic study enrolled 1,152 subjects with suspected sepsis. We sequenced peripheral blood RNA of 129 representative subjects with systemic inflammatory response syndrome (SIRS) or sepsis (SIRS due to infection), including 78 sepsis survivors and 28 sepsis non-survivors who had previously undergone plasma proteomic and metabolomic profiling. Gene expression differences were identified between sepsis survivors, sepsis non-survivors, and SIRS followed by gene enrichment pathway analysis. Expressed sequence variants were identified followed by testing for association with sepsis outcomes.ResultsThe expression of 338 genes differed between subjects with SIRS and those with sepsis, primarily reflecting immune activation in sepsis. Expression of 1,238 genes differed with sepsis outcome: non-survivors had lower expression of many immune function-related genes. Functional genetic variants associated with sepsis mortality were sought based on a common disease-rare variant hypothesis. VPS9D1, whose expression was increased in sepsis survivors, had a higher burden of missense variants in sepsis survivors. The presence of variants was associated with altered expression of 3,799 genes, primarily reflecting Golgi and endosome biology.ConclusionsThe activation of immune response-related genes seen in sepsis survivors was muted in sepsis non-survivors. The association of sepsis survival with a robust immune response and the presence of missense variants in VPS9D1 warrants replication and further functional studies.Trial registrationClinicalTrials.gov NCT00258869. Registered on 23 November 2005.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-014-0111-5) contains supplementary material, which is available to authorized users
Proteomic Analysis of Primary Human Airway Epithelial Cells Exposed to the Respiratory Toxicant Diacetyl
Occupational
exposures
to the diketone flavoring agent, diacetyl,
have been associated with bronchiolitis obliterans, a rare condition
of airway fibrosis. Model studies in rodents have suggested that the
airway epithelium is a major site of diacetyl toxicity, but the effects
of diacetyl exposure upon the human airway epithelium are poorly characterized.
Here we performed quantitative LC–MS/MS-based proteomics to
study the effects of repeated diacetyl vapor exposures on 3D organotypic
cultures of human primary tracheobronchial epithelial cells. Using
a label-free approach, we quantified approximately 3400 proteins and
5700 phosphopeptides in cell lysates across four independent donors.
Altered expression of proteins and phosphopeptides were suggestive
of loss of cilia and increased squamous differentiation in diacetyl-exposed
cells. These phenomena were confirmed by immunofluorescence staining
of culture cross sections. Hyperphosphorylation and cross-linking
of basal cell keratins were also observed in diacetyl-treated cells,
and we used parallel reaction monitoring to confidently localize and
quantify previously uncharacterized sites of phosphorylation in keratin
6. Collectively, these data identify numerous molecular changes in
the epithelium that may be important to the pathogenesis of flavoring-induced
bronchiolitis obliterans. More generally, this study highlights the
utility of quantitative proteomics for the study of in vitro models
of airway injury and disease
Proteomic Analysis of Primary Human Airway Epithelial Cells Exposed to the Respiratory Toxicant Diacetyl
Occupational
exposures
to the diketone flavoring agent, diacetyl,
have been associated with bronchiolitis obliterans, a rare condition
of airway fibrosis. Model studies in rodents have suggested that the
airway epithelium is a major site of diacetyl toxicity, but the effects
of diacetyl exposure upon the human airway epithelium are poorly characterized.
Here we performed quantitative LC–MS/MS-based proteomics to
study the effects of repeated diacetyl vapor exposures on 3D organotypic
cultures of human primary tracheobronchial epithelial cells. Using
a label-free approach, we quantified approximately 3400 proteins and
5700 phosphopeptides in cell lysates across four independent donors.
Altered expression of proteins and phosphopeptides were suggestive
of loss of cilia and increased squamous differentiation in diacetyl-exposed
cells. These phenomena were confirmed by immunofluorescence staining
of culture cross sections. Hyperphosphorylation and cross-linking
of basal cell keratins were also observed in diacetyl-treated cells,
and we used parallel reaction monitoring to confidently localize and
quantify previously uncharacterized sites of phosphorylation in keratin
6. Collectively, these data identify numerous molecular changes in
the epithelium that may be important to the pathogenesis of flavoring-induced
bronchiolitis obliterans. More generally, this study highlights the
utility of quantitative proteomics for the study of in vitro models
of airway injury and disease