PXD062507 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Proteomic analysis of the esophageal epithelium reveals key features of eosinophilic esophagitis pathophysiology |
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. |
HostingRepository | PRIDE |
AnnounceDate | 2025-04-11 |
AnnouncementXML | Submission_2025-04-11_09:26:03.127.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Pedro Majano |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | timsTOF Pro |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2025-04-02 02:31:37 | ID requested | |
⏵ 1 | 2025-04-11 09:26:03 | announced | |
Publication List
Keyword List
submitter keyword: basic mechanisms |
eosinophilic esophagitis |
epithelium |
proteomic |
Contact List
Pedro L.Majano |
contact affiliation | Instituto investigación sanitaria la Princesa |
contact email | pedro.majano@salud.madrid.org |
lab head | |
Pedro Majano |
contact affiliation | Instituto Investigacion Sanitaria Hospital Universitario de la Princesa |
contact email | pedro.majano@salud.madrid.org |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD062507
- Label: PRIDE project
- Name: Proteomic analysis of the esophageal epithelium reveals key features of eosinophilic esophagitis pathophysiology