Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Benchmarking of different methods for obtaining high quality secretomics data

ABSTRACT: The main drawback of secretome analyses are contaminating proteins derived from culture medium or proteins released from dying cells which are hard to distinguish from proteins actively secreted by cells. Therefore, several approaches have been applied allowing to remove contamination from secretome analysis. Here, we will compare these approaches and will evaluate their potential to determine proteins secreted by unconventional secretory pathways.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung, Fibroblast Of Dermis, Cell Culture, Mesenchymal Cell

DISEASE(S): Lung Cancer

SUBMITTER: Gereon Poschmann

LAB HEAD: Gereon Poschmann

PROVIDER: PXD018895 | Pride | 2020-10-19

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	QX03709.raw	Raw
	QX03710.raw	Raw
	QX03711.raw	Raw
	QX03712.raw	Raw
	QX03713.raw	Raw

Items per page:

1 - 5 of 33

Publications

Comparative Secretomics Gives Access to High Confident Secretome Data: Evaluation of Different Methods for the Determination of Bona Fide Secreted Proteins.

Poschmann Gereon G Brenig Katrin K Lenz Thomas T Stühler Kai K

Proteomics 20201117 2

Secretome analysis is broadly applied to understand the interplay between cells and their microenvironment. In particular, the unbiased analysis by mass spectrometry-based proteomics of conditioned medium has been successfully applied. In this context, several approaches have been developed allowing to distinguish proteins actively secreted by cells from proteins derived from culture medium or proteins released from dying cells. Here, three different methods comparing conditioned medium and lysa ...[more]

PMID: 33015975

Similar Datasets

Proteomic analysis of the trypanosomatid Novymonas esmeraldas

Project description:An endosymbiotic event where an archaeon acquired and intracellular protobacteria underpinned the evolution of mitochondria, a key event for the evolution of eukaryotes. Despite is biological importance, the molecular mechanisms driving the early stages of the host-endosymbiont interactions that lead to the evolution of endosymbiont-derived organelles remains poorly understood. Novymonas esmeraldas is a trypanosomatid that recently acquired a -proteobacterial endosymbiont which is compartmentalized into vacuole-like structures called symbiosomes. The life cycle of the host is not synchronized with that of its endosymbiont resulting in heterogeneous numbers of endosymbionts per cell among the population. In order to elucidate the molecular mechanisms mediating this early stage of the host-endosymbiont interactions we isolated the endosymbionts from Novymonas esmeraldas and analyzed the proteome of isolated endosymbionts, holosymbionts (cells containing endosymbionts) and aposymbionts (cells where endosymbionts where removed by treatment with antibiotics). We show that at least one host-encoded protein localizes to the symbiosome and knockout of the corresponding gene leads to an increase of over 2-fold of endosymbionts per cell. This result suggests that controlling the endosymbiont proliferation by the host is an early step for the establishment and posterior evolution of an endosymbiotic event.

2023-05-22 | PXD019306 | Pride

Response of human corneal epithelial cells to the secretomes of wild-type Serratia marcescens and an eepR mutant strain

Project description:The bacterium Serratia marcescens is a common contaminant of contact lens cases and lenses. Serratamolide is one of the secreted hemolytic/cytotoxic factors which contribute to the virulence of this opportunistic pathogen (PMID 22615766). A newly identified transcription factor (eepR) is essential for serratamolide production (PMID 25897029). In the present study, we used immortalized human corneal-limbal epithelial (HCLE) cells (PMID 12766048) as targets for the secreted products of either wild-type (WT) S. marcescens or an isogenic eepR mutant. Microarray data showed that at sub - cytotoxic levels, the secretome of WT bacteria stimulated a > 2-fold response in 712 unique characterized genes. Analysis showed that immune/inflammatory response pathways are significantly enriched in these genes. The scaled response of eepR, ((eepR - control)/(WT â?? control)), was < 0.5 for 418 of these 712 genes (59%). Pathway analysis of these 2-fold attenuated genes confirmed that they too represented immune/inflammatory responses. These data demonstrate that the serratamolide-deficient eepR mutant evokes a much weaker immune/inflammatory response from a clinically relevant cellular target than does the wild-type bacterium. A common batch of HCLE cells was used. Independent preparations of Serratia marcescens secretomes were made for each experiment.

2015-12-31 | E-GEOD-71320 | biostudies-arrayexpress

DsbA plays a critical and multi-faceted role in the production of secreted virulence factors by Erwinia carotovora

Project description:Erwinia carotovora subsp. atroseptica (Eca) is an enterobacterial phytopathogen causing economically-significant soft rot disease. Pathogenesis is mediated by multiple secreted virulence factors, many of which are secreted by the Type II (Out) secretion system. DsbA catalyses the introduction of disulphide bonds into periplasmic and secreted proteins. In this study, the extracellular proteome (secretome) of wild type Eca SCRI1043 and dsbA and out mutants was analysed by spectral counting mass spectrometry. This revealed that dsbA inactivation had a huge impact on the secretome and identified diverse DsbA- and Out-dependent secreted proteins, representing known, predicted and novel candidate virulence factors. Further characterisation of the dsbA mutant showed that secreted enzyme activities, motility, production of the quorum sensing signal and virulence were absent or greatly reduced. The impact of DsbA on secreted virulence factor production was mediated at multiple levels, including impacting on the Out secretion system and the virulence gene regulatory network. Transcriptome analyses revealed that the abundance of a broad, but defined, set of transcripts, including many virulence factors, was altered in the dsbA mutant, identifying a new virulence regulon responsive to extracytoplasmic conditions. In conclusion, DsbA plays a crucial, multi-faceted role in the pathogenesis of Eca. Keywords: Mutant comparison RNA samples used for genome-wide transcriptional profiling using microarrays: RNA was hybridised to four Eca genomic arrays, with each array hybridising one wild type and one dsbA mutant sample (from four independent cultures of each strain) and incorporating a dye-swap (i.e. wild type labelled with Cy3 in 2/4 and with Cy5 in 2/4).

2010-06-20 | E-GEOD-10647 | biostudies-arrayexpress

Control of secreted protein gene expression and the mammalian secretome by the metabolic regulator PGC-1a

Project description:Secreted proteins serve pivotal roles in the development of multicellular organisms, acting as structural matrix, extracellular enzymes and signal molecules. In this study we demonstrate, unexpectedly, that PGC-1α, a critical transcriptional co-activator of metabolic gene expression, functions to down-regulate expression of diverse genes encoding secreted molecules and extracellular matrix (ECM) components to modulate the secretome. We show that both endogenous and exogenous PGC-1α down-regulate expression of numerous genes encoding secreted molecules. Mechanistically, results obtained using mRNA stability measurements as well as intronic RNA expression analysis are consistent with a transcriptional effect of PGC-1α on expression of genes encoding secreted proteins. Interestingly, PGC-1α requires the central heat shock response regulator HSF1 to affect some of its targets, and both factors co-reside on several target genes encoding secreted molecules in cells. Finally, using a mass spectrometric analysis of secreted proteins, we demonstrate that PGC-1α modulates the secretome of mouse embryonic fibroblasts (MEFs).

2016-12-01 | GSE87100 | GEO

Locally advanced rectal cancer transcriptomic-based secretome analysis according to neoadjuvant chemoradiotherapy response

Project description:Most patients with locally advanced rectal cancer (LARC) present incomplete pathological response (pIR) to neoadjuvant chemoradiotherapy (nCRT). Despite the efforts to predict treatment response using tumor-molecular features, as differentially expressed genes, no molecule has proved to be a strong biomarker. The tumor secretome analysis is a promising strategy for biomarkers identification, which can be assessed using transcriptomic data. Here, we performed transcriptomic-based secretome analysis to select potentially secreted proteins using an in silico approach. The tumor expression profile of 28 LARC biopsies carefully selected and collected before nCRT was compared with normal rectal tissues (NT). The expression profile showed no significant differences between cases with complete (pCR) and incomplete response to nCRT. Genes with increased expression (pCR = 106 and pIR = 357) were used for secretome analysis based on public databases (Vesiclepedia, Human Cancer Secretome Database and Plasma and Proteome Database). Seventeen potentially secreted candidates (pCR=1, pIR=13 and 3 in both groups) were further investigated in two independent datasets (TCGA and GSE68204) confirming their over-expression in LARC. The potential secreted biomarkers were also confirmed as associated with the nCRT response (GSE68204). These putative proteins are candidates to be assessed in liquid biopsies aiming a personalized treatment in LARC patients.

2019-07-01 | GSE123390 | GEO

Defining the adult hippocampal neural stem cell secretome: in vivo versus in vitro transcriptomic differences and their correlation to secreted protein levels.

Project description:Recent evidence shows that adult hippocampal neural stem and progenitor cells (NSPCs) secrete a variety of proteins that affect tissue function. Though several individual NSPC-derived proteins have been shown to impact cellular processes like neuronal maturation and stem cell maintenance, a broad characterization of NSPC-secreted factors is lacking. Secretome profiling of low abundance stem cell populations is typically achieved via proteomic characterization of in vitro, isolated cells. Here, we analyzed the in vitro NSPC secretome using conditioned media from cultured adult mouse hippocampal NSPCs and detected over 200 different bioactive proteins with an antibody array. We next assessed the NSPC secretome on a transcriptional level with RNA sequencing (RNAseq) of cultured NSPCs. This comparison revealed that quantification of gene expression did not accurately predict relative protein abundance for several factors. Furthermore, comparing our transcriptional data with previously published single cell RNA sequencing datasets of freshly isolated hippocampal NSPCs, we found key differences in gene expression of secreted proteins between cultured and acutely isolated NSPCs. Understanding the components and functions of the NSPC secretome is essential to understanding how these cells may modulate the hippocampal neurogenic niche, as well as how they can be applied therapeutically. Cumulatively, our data emphasize the importance of using proteomic analysis in conjunction with transcriptomic studies and highlights the need for better methods of global unbiased secretome profiling.

2020-02-13 | GSE138381 | GEO

The Golgi stacking protein GRASP55 represents an effector protein of the natural compound Prodigiosin

Project description:The bacterial secondary metabolite prodigiosin has been shown to exert anticancer, antimalarial, antibacterial and immunomodulatory properties. With regard to cancer, it has been reported that it affects tumor cells but not non-malignant cells, making it a promising lead compound for anticancer drug discovery. However, a direct protein target has not yet been experimentally identified. Here, we identify the Golgi stacking protein GRASP55 as effector target protein of prodigiosin and found evidence that GRASP55 knockout cells show an altered pattern on secreted proteins upon prodigionsin treatment.

2023-10-24 | PXD042909 | Pride

A secretome CRISPR screen identifies SFRP1 as a regulator of epidermal self-renewal [RNA-seq]

Project description:Secreted epidermal proteins play pivotal roles in cell-cell communication, extracellular matrix remodeling, and antimicrobial defense. However, the complete spectrum of secreted proteins in the epidermis has not been experimentally defined. In this study, we performed mass spectrometry on conditioned media from primary human keratinocytes, identifying 406 proteins that constitute the keratinocyte secretome. To assess functional impacts of uncharacterized secreted proteins on epidermal stem cell behavior, we devised a colony formation assay-based CRISPR screen. The screen identified six candidate proteins that promoted proliferation of epidermal progenitors and two proteins that inhibited it. Secreted frizzled related protein-1 (SFRP1), an inhibitor of Wnt signaling, was the most potent inhibitor of progenitor proliferation in the screen. We discovered that in addition to regulating Wnt activity, SFRP1 restrained epidermal stem cell proliferation by inhibiting ectopic expression of leukemia inhibitory factor (LIF). Collectively, our study defines the keratinocyte secretome, demonstrates the application of a CRISPR screen to assess the function of non-cell autonomous factors, and highlights SFRP1’s role in regulating epidermal balance.

2025-04-30 | GSE269627 | GEO