Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Adherens junction protein expression is associated with poor response to neoadjuvant FLOT chemotherapy and pro-inflammatory tumor microenvironment in esophageal adenocarcinoma

ABSTRACT: Esophageal adenocarcinomas represent aggressive gastrointestinal malignancies, characterized by poor survival and variable responses to perioperative therapies. Our study identified a significant association between adherens junction (AJ) protein expression and treatment response to FLOT chemotherapy. We demonstrate that AJ dysregulation occurs across histological subtypes and correlates with pro-inflammatory tumor microenvironment and extracellular matrix remodeling. These findings provide a foundation which could guide treatment selection, potentially avoiding ineffective therapies while identifying patients for alternative approaches. The adenocarcinoma samples analyzed in this study were part of a larger cohort for mass spectrometry proteomic analysis that also included esophageal squamous cell carcinomas (PEC) and normal esophageal tissue. All samples from this comprehensive cohort were preprocessed together up to and including the analysis of protein expression quantification, and the complete dataset is deposited in this upload.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Esophagus

SUBMITTER: Proteomics Facility

LAB HEAD: Alexander Quaas

PROVIDER: PXD071328 | Pride | 2026-01-06

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	3099_001.raw	Raw
	3099_002.raw	Raw
	3099_003.raw	Raw
	3099_004.raw	Raw
	3099_005.raw	Raw

Items per page:

1 - 5 of 350

Similar Datasets

Proteomic analysis of the esophageal epithelium reveals key features of eosinophilic esophagitis pathophysiology

Project description:Background: Eosinophilic esophagitis (EoE) is a chronic non-IgE-mediated allergic disease of the esophagus. An unbiased proteomics approach was performed to investigate pathophysiological changes in esophageal epithelium. Additionally, an RNAseq-based transcriptomic analysis in paired samples was also carried out. Methods: Total proteins were purified from esophageal endoscopic biopsies in a cohort of adult EoE patients (n = 25) and healthy esophagus controls (n = 10). Differentially accumulated (DA) proteins in EoE patients compared to control tissues were characterized to identify altered biological processes and signaling pathways. Results were also compared with a quantitative proteome dataset of the human esophageal mucosa. Next, results were contrasted with those obtained after RNAseq analysis in paired samples. Finally, we matched up protein expression with two EoE-specific mRNA panels (EDP and Eso-EoE panel). Results: A total of 1667 proteins were identified, of which 363 were DA in EoE. RNA sequencing in paired samples identified 1993 differentially expressed (DE) genes. Total RNA and protein levels positively correlated, especially in DE mRNA-proteins pairs. Pathway analysis of these proteins in EoE showed alterations in immune and inflammatory responses for the upregulated proteins, and in epithelial differentiation, cornification and keratinization in those downregulated. Interestingly, a set of DA proteins, including eosinophil-related and secreted proteins, were not detected at the mRNA level. Protein expression positively correlated with EDP and Eso-EoE, and corresponded with the most abundant proteins of the human esophageal proteome. Conclusions: We unraveled for the first time key proteomic features involved in EoE pathogenesis. An integrative analysis of transcriptomic and proteomic datasets provides a deeper insight than transcriptomic alone into understanding complex disease mechanisms.

2025-04-11 | PXD062507 | Pride

Characterisation of corneal defects in ATG7-deficient mice

Project description:Proteomic analysis of mouse cornea lysates. ATG7 is an autophagy component necessary for thedegradation and recycling of cellular components. We aim to characterise the difference in corneal phenotype between an ATG7 knockdown mouse model and a control mouse model.

2025-11-10 | PXD068453 | Pride

CLIPPER 2.0: Peptide level annotation and data analysis for positional proteomics

Project description:Positional proteomics methodologies have transformed protease research and have brought mass spectrometry (MS)-based degradomics studies to the forefront of protease characterization and system-wide interrogation of protease signaling. Considerable advancements in sensitivity and throughput of liquid chromatography (LC)-MS/MS instrumentation enable generation of enormous positional proteomics datasets of protein termini and neo-termini of cleaved protease substrates. However, such progress has not been observed to the same extent in data analysis and post-processing steps, which arguably constitute the largest bottleneck in positional proteomics workflows. Here, we present a computational tool, CLIPPER 2.0, that builds on prior algorithms developed for MS-based protein termini analysis, facilitating peptide level annotation and data analysis. CLIPPER 2.0 can be used with several sample preparation workflows and proteomics search algorithms, and enables fast and automated database information retrieval, statistical and network analysis, as well as visualization of terminomic datasets. We demonstrate our tool by analyzing GluC and MMP9 cleavages in HeLa lysates. CLIPPER 2.0 is available at https://github.com/UadKLab/CLIPPER-2.0.

2024-05-02 | PXD047261 | Pride

Integrative Analysis of Saliva-Derived Exosomal Proteome and Lipidome for the Diagnosis of Esophageal Squamous Cell Carcinoma

Project description:Early diagnosis of esophageal squamous cell carcinoma (ESCC) is crucial for improving patient prognosis. Currently, the diagnosis of ESCC primarily relies on endoscopic biopsy. Salivary exosomes have shown great potential in non-invasive screening, but their proteomic and lipidomic characteristics remain to be reported. Exosomes were isolated from salivary samples of 54 patients with ESCC and 62 healthy controls using ultracentrifugation, and subsequently subjected to non-targeted proteomic and lipidomic analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Differentially expressed proteins and lipids in salivary exosomes were identified through differential analysis, and a comprehensive analysis of multi-omics data was performed using correlation analysis.

2025-08-25 | PXD062319 | Pride

Cells from PCSK9D374Y minipigs HFHC and LF/MTPi LC-MS/MS

Project description:Positron emission tomography (PET) imaging with the radiolabeled glucose analogue fluorodeoxyglucose (18FDG) is widely used to monitor atherosclerosis in clinical trials, but there is uncertainty regarding the plaque cell types that accumulate FDG and how uptake is regulated. The longstanding view that 18FDG is mainly taken up by macrophages is at odds with human and experimental data, and the impact of disease activity on 18FDG uptake has not been examined directly. To analyze the ability of 18FDG-PET to monitor disease activity, we developed a large-animal model of plaque regression in minipigs with hepatic overexpression of a gain-of-function mutant of proprotein convertase subtilisin kexin type 9 (PCSK9). Atherosclerosis was induced through 12 months of high-fat feeding, and disease activity was then lowered for 3 months by reducing plasma cholesterol with a low-fat diet alone or in combination with microsomal transfer protein inhibition. Plaque regression was evident from reduced lipid content, reduced necrotic core size, and partial resolution of plaque inflammation. These changes were accompanied by lowering of the 18FDG-PET signal to that in non-atherosclerotic control pigs. Single-cell gene expression profiling revealed that the reduction of disease activity in regressing plaques occurred with substantial downregulation versus progressing plaques of genes encoding glycolytic enzymes in SMCs, modulated SMCs, macrophages, and lymphocytes. The ability of 18FDG-PET imaging to monitor atherosclerosis thus reflects the tight link between disease activity and glycolytic activity in all major cell types of minipig atherosclerotic plaque.

2025-07-07 | PXD060147 | Pride

Integrative MHC-I peptidome quantitation with isobaric tagging mass spectrometry

Project description:Despite the appreciation of CD8+ T cell anti-tumor immune responses towards improvement patient outcomes, the MHC-I peptides that facilitate the response are poorly described. Alternatively, whether cancer therapies alter the MHC-I peptide repertoire has not been fully assessed due to the lack of quantitative strategies. In this regard, anthracyclines and ionizing radiation both increase the infiltration of CD8+ T cells into tumors but whether they do so by altering the MHC-I peptidome repertoire is not known. To investigate this, we developed a platform for screening therapy-induced MHC-I peptides by quantitative, multiplexed measurement of MHC-I peptides with tandem mass tags (TMT). We show that both ionizing radiation and the anthracycline doxorubicin induce MHC-I peptides that are largely derived from mitotic progression and cell cycle proteins. Our approach enables further strategies to understand how small molecules and other therapies alter MHC-I peptide presentation that may be harnessed for CD8+ T cell-based immunotherapies.

2019-03-05 | PXD011464 | Pride

Unveiling Multi-Omics and Immune Landscapes in COVID-19 Patients' Ovaries Microenvironment for Oocyte Competency Biomarkers Identification

Project description:Background: The outbreak of coronavirus disease 2019 (COVID-19) poses a considerable health threat to humanity, with potential implications for the ovarian microenvironment remaining uncertain. Methods: Transcriptomic and proteomic analyses of ovarian granulosa cells, along with metabolomic and lipidomic profiling of follicular fluid, were conducted on 17 non-COVID-19 cases and 9 COVID-19 cases. This study received approval from the ethics committee (KYLL-2022-581). Generalized estimating equations model was performed to identify oocyte competency biomarkers. Additionally, cell proliferation, apoptosis, and altered pathways were examined following lentivirus transfection. Methods: Transcriptomic and proteomic analyses of ovarian granulosa cells, along with metabolomic and lipidomic profiling of follicular fluid, were conducted on 17 non-COVID-19 cases and 9 COVID-19 cases. This study received approval from the ethics committee (KYLL-2022-581). Generalized estimating equations model was performed to identify oocyte competency biomarkers. Additionally, cell proliferation, apoptosis, and altered pathways were examined following lentivirus transfection. Conclusions: By integrating untargeted metabolomic and lipidomic features, we identified biomarkers indicative of oocyte competency influenced by COVID-19.

2025-05-07 | PXD058234 | Pride

Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics - Library Build, concentration response, structure activity relationships and in-cell treatment

Project description:In this manuscript we describe our work on the development of a label-free chemoproteomics screening platform for cysteine reactive covalent fragments on a 96 well plate format. Within this workflow, we profile cysteine reactive fragments by competition with the hyper-reactive iodoacetamide desthiobiotin (IA-DTB) in cell lysates and live cells. We employ label free quantification and data independent acquisition (DIA) on an Evosep One – Bruker timsTOF Pro. The platform was used to screen a library of 80 Cys-reactive covalent fragments in HEK293T and Jurkat cell lysate, identifying functionally relevant hit fragments for numerous cysteine sites and demonstrating the utility of the approach in expanding the ligandable proteome. We have also validated a number of selective interactions through dose response and further expanded our proteomics platform to perform hit expansion studies and in-cell validation.

2024-11-18 | PXD054145 | Pride

Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics - 80 compound screen (HEK293T and Jurkat)

2024-11-18 | PXD054127 | Pride

Proteomic analysis of the role of chaperone-mediated autophagy (CMA) in muscle stem cells (MuSCs) regenerative functions

Project description:Proteomic analysis of the role of chaperone-mediated autophagy (CMA) in muscle stem cells (MuSCs) regenerative functions. Here, cultured WT (Lamp2a WT) and CMA-deficient (Lamp2a Pax7CreER) MuSCs. 6 replicates per group, and 300.000 cells per sample.

2025-10-17 | PXD069565 | 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