Dataset Information

An efficient urine peptidomics workflow identifies chemically defined dietary gluten peptides from patients with celiac disease

ABSTRACT: This study sought to identify proteins derived from dietary wheat, rye, and barley in human urine samples. The urinary peptidomes of celiac disease patients and healthy controls were compared.

INSTRUMENT(S): Orbitrap Fusion Lumos, LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human) Hordeum Vulgare (barley) Secale Cereale Triticum Aestivum (wheat)

TISSUE(S): Urine

DISEASE(S): Celiac Disease

SUBMITTER: Brad Palanski

LAB HEAD: Joshua Elias

PROVIDER: PXD031048 | Pride | 2022-01-18

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	CeD1_ClinicalStudy_Rep1.RAW	Raw
	CeD1_ClinicalStudy_Rep1.csv	Csv
	CeD1_ClinicalStudy_Rep2.RAW	Raw
	CeD1_ClinicalStudy_Rep2.csv	Csv
	CeD2_ClinicalStudy_Rep1.RAW	Raw

Items per page:

1 - 5 of 181

Similar Datasets

Project description:Background & Aims: Traditional celiac disease diagnostics based on histomorphometric evaluations are liable to misinterpretations due to the common technical flaws e.g. wrong orientation of the biopsy and subjective errors are relatively common e.g. interobserver errors. We envisioned that there is a need for molecular histomorphometric tool that obviates these error sources yielding an objective ratio instead. Gene expression determine the state of a tissue, so the changes in expression may be associated with the severity of lesions during CD and can be used to classify it. Methods: 15 CD patients, who have been at least one year on gluten-free diet, were enrolled. All participants were biopsied before and after the gluten challenge (10 weeks, 4 grams of gluten daily). 6 healthy non-CD individuals were included as controls. Biopsies were taken on PAXgene biological fixative and embedded in paraffin and Vh/Cd ratio was assessed. RNA was extracted from the same sections and subjected to genome-wide 3’RNA-sequencing. Sequencing data was used to determine differentially expressed genes and regression model, that successfully describes the mucosal damage, was created and tested in independent material. Results: 167 differentially expressed genes were identified in healthy vs. treated CD comparisons with 117 genes downregulated and 50 genes upregulated. 415 differentially expressed genes were identified in Post gluten challenge to Treated CD comparisons with 195 genes downregulated and 220 genes upregulated. 119 genes whose expression highly correlates to Vh/Cd ratio (Spearman’s rank correlation coefficient, |rho|>0.7) were identified. Gene ontology analyses show that genes involved in cellular response to cytokines, including interferons, were over-represented. Stepwise regression allowed us computationally cut down the number of genes, that describe Vh/Cd ratio changes, to 7 and IELs number to 5. Created models describe 98.9% of observed Vh/Cd and 97.5% of IELs number variabilities; there is a strong correlation between the model’s predicted and observed ratios. Conclusions: Adoption of molecular histomorphometry, with our selected set of target genes, is quantitative and reliable way of estimating gluten-induced mucosal injury and inflammation. By including this technology one can overcome the typical shortcomings common in celiac disease diagnostics based on traditional histomorphometry analyses alone. Likewise, molecular histomorphometry is a promising instrument when incorporated in clinical trials where assessing drug efficacy on mucosal health is paramount. In addition, despite deemed healthy, based on traditional histomorphometric analyses, celiac patients on gluten free diet have significantly distinctive molecular histomorphometric pattern when compared to healthy controls.

Dataset Information

An efficient urine peptidomics workflow identifies chemically defined dietary gluten peptides from patients with celiac disease

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets