PXD030775-2

PXD030775 is an original dataset announced via ProteomeXchange.

Title	Exploring post-genomic biomarker signatures based on pathomechanisms of ulcerative colitis
Description	Objective: Ulcerative colitis (UC) is a chronic disease with rising incidence and unclear etiology. The application of mass spectrometry-based post-genomic analysis methods shall support the development of molecular biomarker signatures providing status information with regard to UC pathomechanisms. Design: Pathomechanisms characteristic for UC were assessed by proteome profiling of human tissue specimen, obtained from five distinct colon locations each of 12 patients. Systemic disease-associated alterations were investigated by mass spectrometry-based multi-omics analyses comprising proteins, metabolites and eicosanoids of plasma obtained from UC patients during disease and upon remission in comparison to healthy controls. Results: Proteome profiling results identified colitis-associated activation of neutrophils, macrophages, B- and T-cells, platelets, fibroblasts and endothelial cells and indicated hypoxic stress, as well as a general reduction of mitochondrial proteins accompanying the establishment of apparent healing-promoting activities as well as scar formation. While the immune cells mainly contributed pro-inflammatory proteins, the colitis-associated epithelial cells, fibroblasts, endothelial cells and platelets predominantly formed anti-inflammatory and healing-promoting proteins. Blood plasma proteomics indicated chronic inflammation and platelet activation, whereas plasma metabolomics identified disease-associated deregulation of bile acids, eicosanoids and gut microbiome-derived metabolites. Upon remission, several, but not all, molecular candidate biomarker levels recovered to normal levels. These findings may indicate that pathomechanisms related to gut functions, gut microbiome status, microvascular damage and metabolic dysregulation associated with hypoxia may do not resolve uniformly upon remission. Conclusions: The establishment of disease-associated biomarker profiles related to molecular UC pathomechanisms may support the establishment of bioassays with improved prognostic power aiding individualized therapy.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:44:49.815.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christopher Gerner
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2022-01-06 01:39:16	ID requested
1	2023-04-11 13:59:45	announced
⏵ 2	2023-11-14 08:45:09	announced	2023-11-14: Updated project metadata.

Janker L, Schuster D, Bortel P, Hagn G, Meier-Menches SM, Mohr T, Mader JC, Slany A, Bileck A, Brunmair J, Madl C, Unger L, Hennlich B, Weitmayr B, Del Favero G, Pils D, Pukrop T, Pfisterer N, Feichtenschlager T, Gerner C, Multiomics-empowered Deep Phenotyping of Ulcerative Colitis Identifies Biomarker Signatures Reporting Functional Remission States. J Crohns Colitis, 17(9):1514-1527(2023) [pubmed]

submitter keyword: Chronic inflammation, Plasma proteomics, Remission signature, Tissue proteomics,Ulcerative colitis

Univ.-Prof. Dr. Christopher Gerner
contact affiliation	Department of Analytical Chemistry, University of Vienna, Vienna, Austria Joint Metabolome Facility, University of Vienna & Medical University of Vienna, Vienna, Austria
contact email	christopher.gerner@univie.ac.at
lab head
Christopher Gerner
contact affiliation	University of Vienna
contact email	christopher.gerner@univie.ac.at
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD030775
     1. Label: PRIDE project
     2. Name: Exploring post-genomic biomarker signatures based on pathomechanisms of ulcerative colitis