Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Assessment of the epithelial/mesenchymal phenotype of pancreatic cancer cells based on data-independent acquisition – mass spectrometry.

ABSTRACT: Based on data-independent acquisition (DIA)-mass spectrometry (MS), we assessed the epithelial/mesenchymal phenotype of three pancreatic cancer cell lines: CAPAN-1, PANC-1 and MIA PaCa-2 in 2D cell culture.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Malignant Cell, Cell Culture

DISEASE(S): Pancreatic Ductal Carcinoma

SUBMITTER: Lode Denolf

LAB HEAD: Kris Gevaert

PROVIDER: PXD057259 | Pride | 2025-11-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	AllSamp_report.tsv	Tabular
	B2037_Bp_Neo7_CMB-1197_KRGEV_NeleVandenbussche_SG_DIA-P1.raw	Raw
	B2039_Bp_Neo7_CMB-1197_KRGEV_NeleVandenbussche_SG_DIA-P2.raw	Raw
	B2041_Bp_Neo7_CMB-1197_KRGEV_NeleVandenbussche_SG_DIA-P3.raw	Raw
	B2043_Bp_Neo7_CMB-1197_KRGEV_NeleVandenbussche_SG_DIA-P4.raw	Raw

Items per page:

1 - 5 of 15

Publications

EMT-associated bias in the Parsortix® system observed with pancreatic cancer cell lines.

Vandenbussche Nele N Imschoot Renske R Lintermans Béatrice B Denolf Lode L Taminau Joachim J Fieuws Charlotte C Berx Geert G Gevaert Kris K Claes Kathleen B M KBM

Molecular oncology 20250618 11

Pancreatic cancer has a 5-year survival rate of 12%, highlighting the need for reliable biomarkers for early detection and disease monitoring. Circulating tumor cells (CTCs) have emerged as a promising biomarker, yet their detection remains challenging. This study evaluates the Parsortix® system, a microfluidic device that enriches CTCs based on size and deformability, using pancreatic cancer cell lines. As increasing evidence indicates that during epithelial-to-mesenchymal transition (EMT) a ce ...[more]

PMID: 40531655

Similar Datasets

ascTAM Prostacylin MRE269

Project description:Tumor associated macrophages from high grade serous ovarian cancer ascites were treated with 1 μM of the Prostacyclin analoga MRE and DMSO (as solvent control). The aim of this experiment is to see which effect the Prostacyclin analoga has on RNA expression (activation of signaling pathways). Background: Prostacyclin receptor expression is elevated in TAMs. Prostacyclinsynthase expression was detected mainly in CAFs.

2023-08-31 | E-MTAB-12441 | biostudies-arrayexpress

Proteome of injured spinal cord isolated from SD rats with cryoapplication and compression SCI models

Project description:Here we utilized LS-MS/MS proteomics to elucidate global changings in proteostasis and signaling pathways, which are activated at the injury site, after spinal cord injury (SCI) in SD rats accomplished by copper cryo-conductor supercooled by liquid nitrogen in comparison with compression impact.

2025-10-30 | PXD067635 | Pride

Proteomics of tau repeat domain interactome via split TurboID proximity labeling in neuronal cells

Project description:In Alzheimer's disease (AD) and other tauopathies, tau dissociates from microtubules and forms toxic aggregates that contribute to neurodegeneration. Although some of the pathological interactions of tau have been identified from postmortem brain tissue, these studies are limited by their inability to capture transient interactions. To investigate the interactome of aggregate-prone fragments of tau, we applied an in vitro proximity labeling technique using split TurboID fused with the tau microtubule repeat domain (TauRD), a core region implicated in tau aggregation. We characterized this split TurboID TauRD displaying the requirement for both ligase fragment co-expression for robust enzyme activity and nuclear and cytoplasmic localization of the recombinant proteins. Following enrichment of biotinylated proteins and mass spectrometry, we identified over 700 TauRD interactors. Gene ontology analysis of enriched TauRD interactors highlighted processes often dysregulated in tauopathies, including spliceosome complexes, RNA-binding proteins (RBPs), and nuclear speckles. These in vitro results were further supported by integrating the TauRD interactome data with human AD tau interactome datasets and protein co-expression networks from human AD and related tauopathies. This revealed an overlap with the in vitro TauRD interactome and several modules enriched with RBPs and increased in AD and PSP. These findings emphasize the importance of nuclear pathways in tau pathology, such as RNA splicing and nuclear-cytoplasmic transport and establishes the sTurbo TauRD system as a valuable tool for exploring the tau interactome.

2025-11-12 | PXD066874 | Pride

Construction, debugging and iterative redesign of synXVI, a 903-kb synthetic chromosome of Saccharomyces cerevisiae

Project description:Assembly and debugging of the 902,994-bp synthetic Saccharomyces cerevisiae chromosome synXVI of the Sc2.0 project is described. Application of the CRISPR D-BUGS protocol identified defective loci, which were modified to improve sporulation and recover wild-type like growth when grown on glycerol as a sole carbon source when grown at 37˚C. LoxPsym sites inserted downstream of dubious open reading frames impacted the 5’ UTR of genes required for optimal growth and were identified as a systematic cause of defective growth. Based on lessons learned from analysis of Sc2.0 defects and synXVI, an in-silico redesign of the synXVI chromosome was performed, which can be used as a blueprint for future synthetic yeast genome designs. The in-silico redesign of synXVI includes reduced PCR tag frequency, modified chunk and megachunk termini, and adjustments to allocation of loxPsym sites and TAA stop codons to dubious ORFs. This redesign provides a roadmap into applications of Sc2.0 strategies in non-yeast organisms.

2025-05-07 | PXD058199 | Pride

mini-Complexome Profiling, an FDR-controlled workflow for global targeted Detection of protein complexes (Heart Data)

2024-07-25 | PXD049426 | Pride

mini-Complexome Profiling, an FDR-controlled workflow for global targeted Detection of protein complexes (Hek293 data)

Project description:Co-fractionation mass spectrometry experiments (CF-MS) using native-like protein separations such as Blue Native electrophoresis (BNE) or size exclusion chromatography (SEC) enable a global characterization of protein networks, and a better understanding of cellular functions. They do, however, pose significant requirements on sample amounts, on wet lab and on instrument time, which frequently renders statistically useful replication or comparative experiments between multiple biological states non-feasible. Here we present a fast workflow called mini-Complexome Profiling (mCP) for global targeted detection of annotated protein-protein complexes. It comprises mild extraction of complexes, fractionation by BNE and analysis by data independent acquisition mass spectrometry (DIA-MS). Of note, BNE fractionation into 35 fractions is achieved using commercial mini-gels, with minimal requirements on sample amounts. Complexes are detected using a novel, bespoke R package with a controlled false discovery rate (FDR) approach. The tool is available to the community on a Github repository (https://github.com/hugoagno3/mCP ). We first benchmarked our workflow using Hek293 cell lysates as a well established cell line model. We then challenged mCP by investigating changes in the complexome of mouse cardiomyocytes isolated from different heart cavities of single mice. In these challenging and limited samples we detected 48 annotated protein complexes per compartment on average and were able to perform differential inter-cavity comparisons from single animals. These reduced sample and instrument time requirements suggest the suitability of our workflow for complexome screening in sparse samples, e.g. in human patient biopsies.

2024-07-25 | PXD049340 | Pride

Proteome Analysis of Phylogenetically Distant Yeast Species

Project description:A dataset of nine diverse yeast species cultivated in different media.

2025-07-04 | PXD064343 | Pride

Multi-Omic and Functional Analysis for Classification and Treatment of Sarcomas with FUS-TFCP2 or EWSR1-TFCP2 Fusions

Project description:Linking clinical multi-omics analyses with mechanistic studies may improve the understanding of rare cancers. We leveraged two precision oncology programs to investigate rhabdomyosarcoma with FUS/EWSR1-TFCP2 fusions, an orphan malignancy without effective therapies. All tumors exhibited outlier ALK expression, partly accompanied by intragenic deletions and aberrant splicing. This resulted in the expression of ALK variants, i.e. short transcripts (ST), which we named ALK-ST1 (consisting of exons 1-2:18–29), ALK-ST2 (1:18–29), ALK-ST3 (18–29), and ALK-ST4 (1–5:12–17). To systematically investigate the oncogenic capacity of these ALK variants, we stably expressed them in p53-deficient MCF10A human mammary epithelial cells and performed different transformation assays. These experiments demonstrated that ALK-ST1, ALK-ST2, and ALK-ST3 are oncogenic variants, while ALK-ST4 could not transform MCF10A cells. We confirmed protein expression of ALK-ST1, ALK-ST2, and ALK-ST3 by western blotting, which was not possible for ALK-ST4 due to lack of a specific antibody that binds to the N-terminus of ALK that is lost in ALK-ST4. We therefore performed mass spectrometry-based label-free quantitative proteomics on lysates from MCF10A cells stably expressing empty vector (EV), wildtype ALK (ALK-WT), or ALK-ST4 to confirm its expression.

2023-11-13 | PXD045522 | Pride

Assessing Customized Multivalent Chemokine-Binding Peptide Treatment in a Murine Model of Coxsackievirus B3 Infection

Project description:This study investigates the therapeutic potential of BK1.3, a synthetic Evasin-derived peptide, in a murine model of Coxsackievirus B3 (CVB3)-induced viral myocarditis. Myocarditis, an inflammatory disease of the heart muscle, is often triggered by viral infections and driven by excessive immune cell infiltration, mediated by chemokines. BK1.3 selectively targets and inhibits key CC chemokines involved in inflammation, potentially mitigating immune-mediated cardiac damage while preserving essential host defense mechanisms. Beyond its impact on cardiac inflammation, CVB3 infection induces systemic effects, including metabolic disturbances and liver dysfunction. The liver plays a critical role in regulating energy homeostasis and immune responses during infection, making it essential to understand how CVB3 alters hepatic metabolism and whether BK1.3 treatment influences these changes. To explore the metabolic adaptations of the liver during CVB3 infection and under BK1.3 treatment, we conducted a comprehensive proteomic analysis of liver tissue. Our goal was to assess infection-induced changes in protein expression related to metabolism, as well as to determine the extent to which BK1.3 modulates these processes. To interpret the functional implications of the observed proteomic changes, we applied HepatoKin1, a computational liver metabolism model, integrating protein abundance data to simulate metabolic pathway activity. This approach provided insights into how viral infection reprograms hepatic metabolism and how targeted chemokine inhibition may affect these adapatations. The dataset offers a valuable resource for understanding systemic metabolic responses in murine viral myocarditis and evaluating the potential benefits of chemokine-targeted therapy.

2025-05-07 | PXD060461 | Pride

Global proteome of mid- and late-development Petunia inflata flower petal protoplasts

Project description:Establishing the global proteomes of Petunia inflata flower protoplasts at S3 and S5 developmental stages to assess the presence of anthocyanin biosynthetic enzymes and determine the suitability of flowers in different developmental stages as material for transient expression of TurboID-tagged bait proteins for proximity labeling.

2024-09-11 | PXD055749 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data