44 research outputs found
Lymphatic exosomes promote dendritic cell migration along guidance cues
Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified >1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments.Peer reviewe
Proteomic analysis of low quantities of cellular material in the range obtainable from scarce patient samples
The application of proteomics to patient material is increasingly widespread, however, a major shortcoming still are the number of cells or protein material that can be obtained. This study explores the lower limit of cell numbers that can be successfully analysed by liquid chromatography mass spectrometry to determine the protein expression profile that is specific to, and indicative of, the investigated cell type. The aim was to analyse an equivalent quantity of cellular material that can be obtained from, e.g., a fine-needle aspiration biopsy (FNAB). Fifteen thousand and 30,000 cells from adherent (HEK293) and suspension (U937) cell lines were lysed under two different conditions: a ânativeâ and a denaturing buffer. To extend the study to clinical material, human whole PBMCs were also lysed under identical conditions. Proteins from 5,000 and 10,000 cells were analysed by both 1D and 2D-LC-MSMS on an LTQ Orbitrap XL mass spectrometer. In total, 3,219; 1,693 and 659 unique proteins were identified from HEK293, U937 and total PBMCs, respectively. Additionally, an iTRAQ 4-plex experiment was performed to determine the relative quantity of the proteins in the three cell types. In this study, we show that it is feasible to obtain a deep, yet cell-specific protein profile from a very low number of cultured and primary cells. This advancement will enable proteomic-profiling of cellular material from fine needle aspiration biopsies that ultimately can assist cytopathologists in the diagnosis of disease
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Effects of Alanyl-Glutamine Treatment on the Peritoneal Dialysis Effluent Proteome Reveal Pathomechanism-Associated Molecular Signatures*
Peritoneal dialysis (PD) is a modality of renal replacement therapy in which the high volumes of available PD effluent (PDE) represents a rich source of biomarkers for monitoring disease and therapy. Although this information could help guide the management of PD patients, little is known about the potential of PDE to define pathomechanism-associated molecular signatures in PD. We therefore subjected PDE to a high-performance multiplex proteomic analysis after depletion of highly-abundant plasma proteins and enrichment of low-abundance proteins. A combination of label-free and isobaric labeling strategies was applied to PDE samples from PD patients (n = 20) treated in an open-label, randomized, two-period, cross-over clinical trial with standard PD fluid or with a novel PD fluid supplemented with alanyl-glutamine (AlaGln). With this workflow we identified 2506 unique proteins in the PDE proteome, greatly increasing coverage beyond the 171 previously-reported proteins. The proteins identified range from high abundance plasma proteins to low abundance cellular proteins, and are linked to larger numbers of biological processes and pathways, some of which are novel for PDE. Interestingly, proteins linked to membrane remodeling and fibrosis are overrepresented in PDE compared with plasma, whereas the proteins underrepresented in PDE suggest decreases in host defense, immune-competence and response to stress. Treatment with AlaGln-supplemented PD fluid is associated with reduced activity of membrane injury-associated mechanisms and with restoration of biological processes involved in stress responses and host defense. Our study represents the first application of the PDE proteome in a randomized controlled prospective clinical trial of PD. This novel proteomic workflow allowed detection of low abundance biomarkers to define pathomechanism-associated molecular signatures in PD and their alterations by a novel therapeutic intervention
abFASP-MS: Affinity-Based Filter-Aided Sample Preparation Mass Spectrometry for Quantitative Analysis of Chemically Labeled Protein Complexes
Affinity
purification coupled to 1-D gel-free liquid chromatography
mass spectrometry (LCâMS) is a well-established and widespread
approach for the analyses of noncovalently interacting protein complexes.
In this study, two proteins conjugated to a streptavidin-binding peptide
and hemagglutinin double tag were expressed in the respective Flp-In
HEK293 cell lines: green fluorescent protein (SH-GFP) and TANK binding
kinase 1 (SH-TBK1_MOUSE). Fluorescent anti-HA immunoblots revealed
that the expression level of SH-GFP was âŒ50% lower than that
of SH-TBK1_MOUSE. Subsequently, the input material was normalized
to obtain a similar quantity of purified SH-tagged proteins. Optimization
of the release of protein complexes from the <i>anti</i>-HA-agarose with different eluting agents was then assessed. With
respect to the total number of protein groups identified in the purified
complexes, elution with 2% SDS surpassed both 100 mM glycine and 100
mM formic acid. Relative quantitation of the purified protein complexes
using TMT 6-plex reagents confirmed the higher efficiency of the 2%
SDS elution followed by filter-aided sample preparation (FASP). The
data presented in this study provide a new application of FASP to
quantitative MS analysis of affinity-purified protein complexes. We
have termed the approach abFASP-MS, or affinity-based filter-aided
sample preparation mass spectrometry
abFASP-MS: Affinity-Based Filter-Aided Sample Preparation Mass Spectrometry for Quantitative Analysis of Chemically Labeled Protein Complexes
Affinity
purification coupled to 1-D gel-free liquid chromatography
mass spectrometry (LCâMS) is a well-established and widespread
approach for the analyses of noncovalently interacting protein complexes.
In this study, two proteins conjugated to a streptavidin-binding peptide
and hemagglutinin double tag were expressed in the respective Flp-In
HEK293 cell lines: green fluorescent protein (SH-GFP) and TANK binding
kinase 1 (SH-TBK1_MOUSE). Fluorescent anti-HA immunoblots revealed
that the expression level of SH-GFP was âŒ50% lower than that
of SH-TBK1_MOUSE. Subsequently, the input material was normalized
to obtain a similar quantity of purified SH-tagged proteins. Optimization
of the release of protein complexes from the <i>anti</i>-HA-agarose with different eluting agents was then assessed. With
respect to the total number of protein groups identified in the purified
complexes, elution with 2% SDS surpassed both 100 mM glycine and 100
mM formic acid. Relative quantitation of the purified protein complexes
using TMT 6-plex reagents confirmed the higher efficiency of the 2%
SDS elution followed by filter-aided sample preparation (FASP). The
data presented in this study provide a new application of FASP to
quantitative MS analysis of affinity-purified protein complexes. We
have termed the approach abFASP-MS, or affinity-based filter-aided
sample preparation mass spectrometry
Identification of Kinase Inhibitor Targets in the Lung Cancer Microenvironment by Chemical and Phosphoproteomics
abFASP-MS: Affinity-Based Filter-Aided Sample Preparation Mass Spectrometry for Quantitative Analysis of Chemically Labeled Protein Complexes
Affinity
purification coupled to 1-D gel-free liquid chromatography
mass spectrometry (LCâMS) is a well-established and widespread
approach for the analyses of noncovalently interacting protein complexes.
In this study, two proteins conjugated to a streptavidin-binding peptide
and hemagglutinin double tag were expressed in the respective Flp-In
HEK293 cell lines: green fluorescent protein (SH-GFP) and TANK binding
kinase 1 (SH-TBK1_MOUSE). Fluorescent anti-HA immunoblots revealed
that the expression level of SH-GFP was âŒ50% lower than that
of SH-TBK1_MOUSE. Subsequently, the input material was normalized
to obtain a similar quantity of purified SH-tagged proteins. Optimization
of the release of protein complexes from the <i>anti</i>-HA-agarose with different eluting agents was then assessed. With
respect to the total number of protein groups identified in the purified
complexes, elution with 2% SDS surpassed both 100 mM glycine and 100
mM formic acid. Relative quantitation of the purified protein complexes
using TMT 6-plex reagents confirmed the higher efficiency of the 2%
SDS elution followed by filter-aided sample preparation (FASP). The
data presented in this study provide a new application of FASP to
quantitative MS analysis of affinity-purified protein complexes. We
have termed the approach abFASP-MS, or affinity-based filter-aided
sample preparation mass spectrometry
TMBIM5 is the Ca 2+ /H + antiporter of mammalian mitochondria
Mitochondrial Ca(2+) ions are crucial regulators of bioenergetics and cell death pathways. Mitochondrial Ca(2+) content and cytosolic Ca(2+) homeostasis strictly depend on Ca(2+) transporters. In recent decades, the major players responsible for mitochondrial Ca(2+) uptake and release have been identified, except the mitochondrial Ca(2+)/H(+) exchanger (CHE). Originally identified as the mitochondrial K(+)/H(+) exchanger, LETM1 was also considered as a candidate for the mitochondrial CHE. Defining the mitochondrial interactome of LETM1, we identify TMBIM5/MICS1, the only mitochondrial member of the TMBIM family, and validate the physical interaction of TMBIM5 and LETM1. Cellâbased and cellâfree biochemical assays demonstrate the absence or greatly reduced Na(+)âindependent mitochondrial Ca(2+) release in TMBIM5 knockout or pHâsensing site mutants, respectively, and pHâdependent Ca(2+) transport by recombinant TMBIM5. Taken together, we demonstrate that TMBIM5, but not LETM1, is the longâsought mitochondrial CHE, involved in setting and regulating the mitochondrial proton gradient. This finding provides the final piece of the puzzle of mitochondrial Ca(2+) transporters and opens the door to exploring its importance in health and disease, and to developing drugs modulating Ca(2+) exchange
A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma
<div><p>We performed a pilot proteogenomic study to compare lung adenocarcinoma to lung squamous cell carcinoma using quantitative proteomics (6-plex TMT) combined with a customized Affymetrix GeneChip. Using MaxQuant software, we identified 51,001 unique peptides that mapped to 7,241 unique proteins and from these identified 6,373 genes with matching protein expression for further analysis. We found a minor correlation between gene expression and protein expression; both datasets were able to independently recapitulate known differences between the adenocarcinoma and squamous cell carcinoma subtypes. We found 565 proteins and 629 genes to be differentially expressed between adenocarcinoma and squamous cell carcinoma, with 113 of these consistently differentially expressed at both the gene and protein levels. We then compared our results to published adenocarcinoma versus squamous cell carcinoma proteomic data that we also processed with MaxQuant. We selected two proteins consistently overexpressed in squamous cell carcinoma in all studies, MCT1 (SLC16A1) and GLUT1 (SLC2A1), for further investigation. We found differential expression of these same proteins at the gene level in our study as well as in other public gene expression datasets. These findings combined with survival analysis of public datasets suggest that MCT1 and GLUT1 may be potential prognostic markers in adenocarcinoma and druggable targets in squamous cell carcinoma. Data are available via ProteomeXchange with identifier PXD002622.</p></div
Kvalitet inom universitets och högskolebibliotek - redovisning av enkÀt 2008
Ett övergripande problem med utvĂ€rdering av informations/biblioteksverksamhet Ă€r att det fortfarande nĂ€stan enbart Ă€r traditionella uppgifter som utvĂ€rderas. En annan aspekt Ă€r att mĂ€ta kvalitet och nytta i andra Ă€n ekonomiska termer â d.v.s. kvalitativa indikatorer och mĂ„tt. Denna rapport innehĂ„ller en inventering (ej bedömning) vilka metoder, ansatser och initiativ som idag finns eller hĂ„ller pĂ„ att utvecklas pĂ„ lĂ€rosĂ€tena/biblioteken för att mĂ€ta kvalitet pĂ„ icke-kvantitativa sĂ€tt