ABSTRACT: The project aimed at investigating the impact of chronic low grade inflammation on plasma functions and plasma proteomes in healthy individuals.
Project description:The project examines the mechanisms of neutrophil dysfunction during sepsis. Our work uncovered the central role of cell free circulating histones in eliminating mature neutrophil in favour of immature cells and characterized the mechanisms that regulate their release following systemic infection. Mature and immature neutrophil Ly6Ghigh and Ly6Glow populations isolated from the spleens of WT and TCRα-deficient mice either naïve or infected with C. albicans were characterized. In addition, these populations were compared to neutrophils isolated from WT mice receiving Clodronate-liposomes and recombinant G-CSF. These studies demonstrated that T-cell derived histones drive the release of G-CSF in the spleen and progressively eliminate mature neutrophils by shortening their lifespan. Finally, we conducted proteomic analysis of plasmas isolated from patients with microbial sepsis to correlate markers of neutrophil death to plasma cytokine and histone levels, confirming the pathogenic role these molecules play during sepsis in humans.
Project description:Analysis of plasma proteomes from 8 week old C57BL/6J WT or TCRα-/- (Tcratm1Phi) either naïve or infected by intravenous injection of 5x105 yeast (clinical isolate SC5314), and collected 72 hrs post-infection
Project description:The project examines the mechanisms of neutrophil dysfunction during sepsis. Our work uncovered the central role of cell free circulating histones in eliminating mature neutrophil in favour of immature cells and characterized the mechanisms that regulate their release following systemic infection. Mature and immature neutrophil Ly6Ghigh and Ly6Glow populations isolated from the spleens of WT and TCRα-deficient mice either naïve or infected with C. albicans were characterized. In addition, these populations were compared to neutrophils isolated from WT mice receiving Clodronate-liposomes and recombinant G-CSF. These studies demonstrated that T-cell derived histones drive the release of G-CSF in the spleen and progressively eliminate mature neutrophils by shortening their lifespan. Finally, we conducted proteomic analysis of plasmas isolated from patients with microbial sepsis to correlate markers of neutrophil death to plasma cytokine and histone levels, confirming the pathogenic role these molecules play during sepsis in humans.
Project description:We performed quantitative proteomic profiling of 786 plasma samples from COVID-19 inpatients, treated at two different hospitals (Charité – Universitätsmedizin Berlin and University Hospital of Innsbruck). Sampling was performed at multiple time points throughout the course of the disease, to create a time-resolved map of COVID-19 progression. Full DIA-NN analysis reports are provided, as well as raw files for the QC runs.
Project description:Clinical proteomics holds the promise to accelerate the discovery of disease biomarkers, as well as to predict disease trajectories. Here we present a new platform for high-throughput plasma and serum proteomics, which combines an automated sample preparation workflow, robust high-flow liquid chromatography, and an optimized SWATH-MS acquisition scheme as well as data processing workflow. The process requires as little as 5uL serum or plasma and makes use of fast 5-minute chromatographic gradients. The dataset shows the robustness and precision of the workflow and consists of commercial plasma and serum samples that were distributed in 4 different 96 well plates and injected within a sample series of 417 serum injections. Further, the dataset includes of injections of a single sample (pooled from 32 prepared commercial serum samples) every 10 injections.
Project description:Global healthcare systems are challenged by the COVID-19 pandemic. There is a need to optimize allocation of treatment and resources in intensive care, as clinically established risk assessments such as SOFA and APACHE II scores show only limited performance for predicting the survival of severely ill COVID-19 patients. Comprehensively capturing the host physiology, we speculated that proteomics in combination with new data-driven analysis strategies could produce a new generation of prognostic discriminators. We studied two independent cohorts of patients with severe COVID-19 who required intensive care and invasive mechanical ventilation. SOFA score, Charlson comorbidity index and APACHE II score were poor predictors of survival. Instead, using plasma proteomes quantifying 302 plasma protein groups at 387 timepoints in 57 critically ill patients on invasive mechanical ventilation, we found 14 proteins that showed trajectories different between survivors and non-survivors. A proteomic predictor trained on single samples obtained at the first time point at maximum treatment level (i.e. WHO grade 7) and weeks before the outcome, achieved accurate classification of survivors (AUROC 0.81, n=49). We tested the established predictor on an independent validation cohort (AUROC of 1.0, n=24). The majority of proteins with high relevance in the prediction model belong to the coagulation system and complement cascade. Our study demonstrates that predictors derived from plasma protein levels have the potential to substantially outperform current prognostic markers in intensive care.
Project description:This study compared the therapeutic effects of medium cut-off (MCO) and high flux (HF) dialyzers using metabolomics and proteomics. This was a single-center prospective trial of 20 patients receiving maintenance hemodialysis (HD). A consecutive dialyzer membrane was used for 15-week study periods as follows: 1st HF dialyzer, MCO dialyzer, 2nd HF dialyzer, for 5 weeks respectively. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis was used to identify proteins.
Project description:The Ely study, established in 1990, is a prospective study of the aetiology of type 2 diabetes and was described in detail elsewhere. The Ely study comprises individuals of European ancestry aged 50–79 years, registered at a single medical practice in Ely, Cambridgeshire, UK and evaluated in three phases. All participants of the Ely study gave their written informed consent and the study was approved by the local ethics committee. Two hundred participants from Ely phase 3 with complete fasting and OGTT sample availability were selected for measurement (105 women / 95 men).
Project description:Yeast (Saccharomyces cerevisiae) cooperating metabolic communities (SeMeCos) were chronologically aged in minimal media (no amino acid supplementation). Samples were collected during exponential, early stationary and stationary phases for proteomic analysis. Comparison was performed between wild-type (knock-in, "kin"), 4p-SeMeCo ("4p") and MET15-3p-SeMeCo ("3p") cultures. Four independent biological replicates were acquired for each timepoint measured.