PXD062507

PXD062507 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-02 02:31:37	ID requested
⏵ 1	2025-04-11 09:26:03	announced

10.1111/ALL.15779;

submitter keyword: basic mechanisms

eosinophilic esophagitis

epithelium

proteomic

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

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PRIDE project URI

• PRIDE
  1. PXD062507
     1. Label: PRIDE project
     2. Name: Proteomic analysis of the esophageal epithelium reveals key features of eosinophilic esophagitis pathophysiology