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Ulcerative colitis: functional analysis of the in-depth proteome

BACKGROUND: Ulcerative colitis (UC) is one major form of inflammatory bowel disease. The cause and the pathophysiology of the disease are not fully understood and we therefor aim in this study to identify important pathophysiological features in UC from proteomics data. METHODS: Colon mucosa biopsie...

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Autores principales: Schniers, Armin, Goll, Rasmus, Pasing, Yvonne, Sørbye, Sveinung Wergeland, Florholmen, Jon, Hansen, Terkel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350310/
https://www.ncbi.nlm.nih.gov/pubmed/30718987
http://dx.doi.org/10.1186/s12014-019-9224-6
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author Schniers, Armin
Goll, Rasmus
Pasing, Yvonne
Sørbye, Sveinung Wergeland
Florholmen, Jon
Hansen, Terkel
author_facet Schniers, Armin
Goll, Rasmus
Pasing, Yvonne
Sørbye, Sveinung Wergeland
Florholmen, Jon
Hansen, Terkel
author_sort Schniers, Armin
collection PubMed
description BACKGROUND: Ulcerative colitis (UC) is one major form of inflammatory bowel disease. The cause and the pathophysiology of the disease are not fully understood and we therefor aim in this study to identify important pathophysiological features in UC from proteomics data. METHODS: Colon mucosa biopsies from inflamed tissue of untreated UC patients at diagnosis and from healthy controls were obtained during colonoscopy. Quantitative protein data was acquired by bottom-up proteomics and furthermore processed with MaxQuant. The quantitative proteome data was analyzed with Perseus and enrichment data was analyzed by ClueGO for Cytoscape. RESULTS: The generated proteome dataset is to-date the deepest from colon mucosa biopsies with 8562 identified proteins whereof 6818 were quantified in > 70% of the samples. We report abundance differences between UC and healthy controls and the respective p values for all quantified proteins in the supporting information. From this data set enrichment analysis revealed decreased protein abundances in UC for metallothioneins, PPAR-inducible proteins, fibrillar collagens and proteins involved in bile acid transport as well as metabolic functions of nutrients, energy, steroids, xenobiotics and carbonate. On the other hand increased abundances were enriched in immune response and protein processing in the endoplasmic reticulum, e.g. unfolded protein response and signal peptidase complex proteins. CONCLUSIONS: This explorative study describes the most affected functions in UC tissue. Our results complemented previous findings substantially. Decreased abundances of signal peptidase complex proteins in UC are a new discovery. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12014-019-9224-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-63503102019-02-04 Ulcerative colitis: functional analysis of the in-depth proteome Schniers, Armin Goll, Rasmus Pasing, Yvonne Sørbye, Sveinung Wergeland Florholmen, Jon Hansen, Terkel Clin Proteomics Research BACKGROUND: Ulcerative colitis (UC) is one major form of inflammatory bowel disease. The cause and the pathophysiology of the disease are not fully understood and we therefor aim in this study to identify important pathophysiological features in UC from proteomics data. METHODS: Colon mucosa biopsies from inflamed tissue of untreated UC patients at diagnosis and from healthy controls were obtained during colonoscopy. Quantitative protein data was acquired by bottom-up proteomics and furthermore processed with MaxQuant. The quantitative proteome data was analyzed with Perseus and enrichment data was analyzed by ClueGO for Cytoscape. RESULTS: The generated proteome dataset is to-date the deepest from colon mucosa biopsies with 8562 identified proteins whereof 6818 were quantified in > 70% of the samples. We report abundance differences between UC and healthy controls and the respective p values for all quantified proteins in the supporting information. From this data set enrichment analysis revealed decreased protein abundances in UC for metallothioneins, PPAR-inducible proteins, fibrillar collagens and proteins involved in bile acid transport as well as metabolic functions of nutrients, energy, steroids, xenobiotics and carbonate. On the other hand increased abundances were enriched in immune response and protein processing in the endoplasmic reticulum, e.g. unfolded protein response and signal peptidase complex proteins. CONCLUSIONS: This explorative study describes the most affected functions in UC tissue. Our results complemented previous findings substantially. Decreased abundances of signal peptidase complex proteins in UC are a new discovery. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12014-019-9224-6) contains supplementary material, which is available to authorized users. BioMed Central 2019-01-29 /pmc/articles/PMC6350310/ /pubmed/30718987 http://dx.doi.org/10.1186/s12014-019-9224-6 Text en © The Author(s) 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Schniers, Armin
Goll, Rasmus
Pasing, Yvonne
Sørbye, Sveinung Wergeland
Florholmen, Jon
Hansen, Terkel
Ulcerative colitis: functional analysis of the in-depth proteome
title Ulcerative colitis: functional analysis of the in-depth proteome
title_full Ulcerative colitis: functional analysis of the in-depth proteome
title_fullStr Ulcerative colitis: functional analysis of the in-depth proteome
title_full_unstemmed Ulcerative colitis: functional analysis of the in-depth proteome
title_short Ulcerative colitis: functional analysis of the in-depth proteome
title_sort ulcerative colitis: functional analysis of the in-depth proteome
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350310/
https://www.ncbi.nlm.nih.gov/pubmed/30718987
http://dx.doi.org/10.1186/s12014-019-9224-6
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