Human plasma BOS iTRAQ
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap Elite
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: Sophie Paczesny
PROVIDER: MSV000079451 | MassIVE | Mon Jan 11 14:44:00 GMT 2016
REPOSITORIES: MassIVE
Similar Datasets
Project description:We compared 4 pools of plasma in the same iTRAQ proteomics experiment. The pool 1 contained plasma from twelve patients with strict BOS and with plasma sample available at onset of the clinical symptoms (named BOS), pool 2 contained plasma from sixteen patients with pulmonary infections (infection), pool 3 contained plasma from fifteen patients with chronic GVHD without pulmonary involvement (CGVHD no lung), and pool 4 contained plasma from fifteen patients after transplant with no chronic complications (at similar time point as BOS samples) (no complications).
2016-02-03 | MSV000079490 | MassIVE
Project description:We compared 4 pools of plasma in the same iTRAQ proteomic experiment. The pool 1 contained plasma from twelve patients with strict BOS criteria and with plasma sample available at onset of the clinical symptoms (named BOS), pool 2 contained plasma from sixteen patients with pulmonary infections (infection), pool 3 contained plasma from fifteen patients with chronic GVHD without pulmonary involvement (CGVHD no lung), and pool 4 contained plasma from fifteen patients after transplant with no chronic complications (at similar time point as BOS samples) (no complications). Each pool contained 25 μl of plasma.
The four pooled plasmas were then individually immunodepleted of the twenty common hyper-abundant proteins with a ProteoPrep®20 plasma immunodepletion kit (Sigma-Aldrich) according to manufacturer?s procedure. The cysteine residues were alkylated and all samples were trypsinized. Each pool was labeled with a different tag allowing for differential quantification. The samples were labeled in the following order: 1) BOS with 114, 2) Infection with 115, 3) cGVHD with 116, and 4) No complication with 117. The four pooled plasma samples were dissolved in buffer A (7mM potassium phosphate, 30% acetonitrile, pH 2.65) and combined right before fractionation with a SCX column (Zorbax 300-SCX 5µm, 2.1 x 150 mm, Agilent). The fractions were collected every minute at 200 µL/min flow rate from 1% solvent B (7mM potassium phosphate, 500 mM KCl, 30% acetonitrile, pH 2.65) to 60% over 40 minutes (1% B for 7 minutes, 6 to 15% B for 18 minutes, 15 to 34% B for 10 minutes, and 34 to 60% B for 5 minutes) as well as during column washing at 98% solvent B for 10 minutes. These fractions were consolidated into 11 fractions using the UV trace to distribute the peptide quantities to be similar.
LC-MS/MS analysis was performed with an Easy-nLC 1000 (Thermo Scientific) coupled to an Orbitrap Elite mass spectrometer (Thermo Scientific). The peptide sample was diluted in 30 µL of 2% acetonitrile and 0.1% formic acid in water and 8-4 µL was loaded onto the column in triplicates and separated using a two-mobile-phase system consisting of 0.1% formic acid in water (A) and 0.1% formic acid in acetonitrile (B). A 90 minute gradient from 7% to 35% B at a flow rate of 400 nL/min was used for chromatographic separations. The mass spectrometer was operated in a data-dependent MS/MS mode over the m/z range of 400-1800. The mass resolution was set at 60,000. For each cycle, the 10 most abundant ions from the scan were selected for MS/MS analysis using 40% normalized HCD collision energy and analyzed with an orbitrap with the resolution set to 15000.
2015-07-30 | MSV000079203 | MassIVE
Project description:Graft-versus-host disease (GvHD) is still one of the major complications following allogeneic stem cell transplantation (SCT) triggered by alloreactive donor T cells. Whereas murine data have clearly shown the beneficial effects of regulatory T cells (Tregs) on the development of GvHD, data from the human system are rare mainly due to low cell numbers of circulating or organ-infiltrating Tregs in lymphopenic patients. Here, we present a comparative analysis of Tregs from patients with and without acute/ chronic GvHD designed as a dynamical approach studying the whole genome profile over the first 6 months after SCT. For this purpose, blood samples were collected monthly for FACS-based isolation of CD4+CD25highCD127low/- Tregs. The Treg transcriptome showed a high stability in the first half year representing the most sensitive time window for tolerance induction. However, the comparison of the Treg transcriptome from patients with and without GvHD uncovered regulated gene transcripts that point to a reduced suppressive function of Tregs with diminished migration capacity to the target organs likely contributing to the development of GvHD. These findings highlight the critical role of human Tregs in the pathophysiology of GvHD and identify novel targets for the manipulation of Tregs to optimize cellular immune intervention strategies. Keywords: cell type comparison Relative gene expressions were determined by normalized intensity values. GeneSpring analysis was performed using the Treg transcriptome data with following comparisons: no GvHD d90 versus no GvHD d150, no GvHD d90 versus acute GvHD, no GvHD d150 versus chronic GvHD, acute GvHD versus chronic GvHD, acute GvHD versus GvHD d90 and chronic GvHD versus GvHD d150 (Figure 2). Cut-off was a transcript fold change of 2 or -2 in at least one comparison. Student´s t-test was used to identify significant expression changes.
2010-12-31 | E-GEOD-23332 | biostudies-arrayexpress
Project description:Haploidentical hematopoietic cell transplantation (haplo-HCT) is an increasingly used treatment for hematologic malignancies. Although post-transplant cyclophosphamide (PtCy) has improved graft vs. host disease (GvHD) prophylaxis in haplo-HCT, patients continue to experience life-threatening complications. IFN-γ and IL-6 are central in the pathophysiology of GvHD and cytokine release syndrome (CRS), and both cytokines signal through Janus kinase (JAK)-1. We tested the effect of adding the JAK-1 selective inhibitor, itacitinib, to PtCy-haplo-HCT to mitigate these complications and improve overall survival. This open-label, single-arm study evaluated the safety and efficacy of itacitinib combined with standard GvHD prophylaxis after haplo-HCT. A total of 42 patients were treated with itacitinib 200 mg daily from day -3 through +100 or +180, followed by a taper. Itacitinib resulted in low CRS grades, all patients had grade 0 (22%) or grade 1 (78%) CRS and there were no cases of grade 2-5 CRS. There were no cases of primary graft failure. No patients developed grade 3-4 aGvHD through day +180. The cumulative incidence of grade 2 aGvHD at day +100 was 21.9%. The 1-year cumulative incidence of moderate or severe chronic GvHD was 5%. The cumulative incidence of relapse at 2 years was 14%. Overall survival (OS) at 1 year was 80%. The cumulative incidence of nonrelapse mortality at day 180 was 8%. Itacitinib, when added to standard GvHD prophylaxis, was well tolerated and resulted in low rates of CRS, acute and chronic GvHD, NRM and encouraging rates of GvHD-free relapse-free survival (GRFS) and OS after haplo-HCT.
2024-11-15 | GSE282021 | GEO
Project description:Bronchiolitis obliterans syndrome (BOS) is the main reason for poor outcomes after lung transplantation (LTx). We and others have recently identified B cells as major contributors to BOS after LTx. The extent of B cell heterogeneity and the relative contributions of B cell subpopulations to BOS, however, remain entirely unclear. Here, we provide a comprehensive analysis of cell population changes and their gene expression patterns during chronic rejection after orthotopic LTx in mice. Out of a total of 11 major cell types, Mzb1-expressing plasma cells (PCs) were the most prominently increased population in BOS lungs. These findings were validated in two different cohorts of human BOS after LTx. A Bhlhe41, Cxcr3, Itgb1-triple positive-B cell subset, also expressing classical markers of the innate-like B-1 B cell population, served as the progenitor pool for Mzb1+ PCs. This subset accounted for the increase in IgG2c production within BOS lung grafts. A genetic lack of immunoglobulins decreased BOS severity after LTx. In summary, we provide a detailed analysis of cell population changes during BOS. IgG-positive PCs and their progenitors – an innate B cell subpopulation – are the major source of local antibody production and a significant contributor to BOS after LTx.
2022-07-25 | GSE166386 | GEO
Project description:The aim of the study was to identify the miRNA expression profile of CD4+CD25high Tregs in SCT patients with and without GvHD early and late after transplantation compared to healthy donors. pool of n = 3 patients without GvHD early (< d100) and late (> d100) after SCT, n=3 patients with GvHD early (< d100) and late (> d100) after SCT and n = 3 sex- and age matched healthy donors for every timepoint
2011-12-01 | E-GEOD-26769 | biostudies-arrayexpress
Project description:Graft-versus-host disease (GvHD) is still one of the major complications following allogeneic stem cell transplantation (SCT) triggered by alloreactive donor T cells. Whereas murine data have clearly shown the beneficial effects of regulatory T cells (Tregs) on the development of GvHD, data from the human system are rare mainly due to low cell numbers of circulating or organ-infiltrating Tregs in lymphopenic patients. Here, we present a comparative analysis of Tregs from patients with and without acute/ chronic GvHD designed as a dynamical approach studying the whole genome profile over the first 6 months after SCT. For this purpose, blood samples were collected monthly for FACS-based isolation of CD4+CD25highCD127low/- Tregs. The Treg transcriptome showed a high stability in the first half year representing the most sensitive time window for tolerance induction. However, the comparison of the Treg transcriptome from patients with and without GvHD uncovered regulated gene transcripts that point to a reduced suppressive function of Tregs with diminished migration capacity to the target organs likely contributing to the development of GvHD. These findings highlight the critical role of human Tregs in the pathophysiology of GvHD and identify novel targets for the manipulation of Tregs to optimize cellular immune intervention strategies. Keywords: cell type comparison
2010-12-31 | GSE23332 | GEO
Project description:Novel biomarkers to identify infectious patients transmitting Mycobacterium tuberculosis are urgently needed to control the global tuberculosis (TB) pandemic. We hypothesized that proteins released into the plasma in active pulmonary TB are clinically useful biomarkers to distinguish TB cases from healthy individuals and patients with other respiratory infections. We applied a highly sensitive non-depletion tandem mass spectrometry discovery approach to investigate plasma protein expression in pulmonary TB cases compared to healthy controls in South African and Peruvian cohorts. . Plasma samples were analysed from 11 untreated male patients with active pulmonary TB and 10 male healthy control samples. Each plasma sample was initially separated into four segments by size exclusion chromatography, and each segment was processed individually. Analyses of plasma segments were performed in twelve iTRAQ (isobaric tags for relative and absolute quantification) 8-plex experimental sets in a block randomised design comprising three experimental sets. Each iTRAQ experiment contained a bridging master-pool plasma sample run in every experiment. Healthy controls were matched to TB samples by age, ethnicity, and smoking status within each iTRAQ set. Protein abundances from the plasma segments and multi-consensus reports were combined and adjusted for experimental batch effects. Protein abundances from the remaining combined plasma segment proteomes between experimental sets and the combined multi-consensus proteomes were analysed by complementary bioinformatic approaches to identify candidate diagnostic protein biomarkers. In total, 4,696 protein identifications were made across all iTRAQ experiments, at 5% FDR (false discovery rate). This comprised 2,332 unique host-derived proteins and 22 Mtb-derived proteins. Of these, 594 host proteins had a quantification result for every sample analysed and therefore comprised the complete quantified proteome. Subsequent bioinformatic analysis identified 118 differentially expressed proteins by three complementary bioinformatic pipelines and were taken forward in subsequent validation work as strong candidate biomarkers of pulmonary TB.
2024-06-22 | PXD051070 | Pride
Project description:Single cell analysis of gene expression in blood B cells from allogeneic hematopoietic stem cell transpant (HCT) patients that either developed chronic GVHD, or never developed chronic GVHD.
2023-05-02 | GSE161343 | GEO
Project description:A non-invasive diagnostic test does not exist for acute graft versus host disease (aGVHD). We therefore sought to identify biomarkers for aGVHD using antibody microarrays (Schleicher and Schuell Serum Biomarker Chips, Whatman) that simultaneously assayed 120 plasma proteins. We measured these proteins in a set of 42 patient plasma samples following an allogeneic bone marrow transplant (BMT): 21 patients with a diagnosis of aGVHD grade II-IV (+GVHD) and 21 patients without aGVHD (–GVHD) at similar times after transplant. We excluded data from 2 hybridizations that had very bright dots and appeared as outliers in preliminary principal components analysis, so that we finally compared 20 +GVHD to 20 -GVHD samples. Keywords: disease state analysis, antibody microarray
2008-10-31 | GSE9791 | GEO