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- Vessby, Johan, 1972-, et al.
(author)
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A two-step proteomic approach identifies candidate biomarker in ulcerative colitis with concomitant primary sclerosing cholangitis.
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Other publication (other academic/artistic)abstract
- Introduction: Ulcerative colitis (UC) with concomitant primary sclerosing cholangitis (PSC-UC or PSC-IBD) is today considered a unique IBD entity, including a more malignant disease course compared with classical UC. Biomarkers for identifying UC patients at risk of developing PSC is lacking, which may delay the onset of endoscopy surveillance. Mass spectrometric development has enabled the use of formalin-fixed paraffin embedded tissue (FFPE) for high resolution proteome analysis. In this study, we search for PSC-IBD proteomic fingerprints in FFPE by utilizing mass spectrometry.Methods: Protein was extracted out of FFPE colon archival samples from PSC-IBD (n=9), UC (n=7), and healthy controls (n=7). IBD-patients were all in clinical remission, without biologics or steroids, and all UC patients had a history of pancolitis. Samples were processed by the Multienzyme Digestion FASP and were analysed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Proteins were quantified using the Total Protein Approach. Data was analysed using linear regression and in a multiple manner using random forest algorithms. Candidate findings were validated in a second cohort (n: PSC-IBD=16 UC=21) using the same proteomic technique. To make an over-all proteome comparison, we performed principal component analysis, as well as a meta-analysis for the most prominent findings.Results: In the exploratory proteomic step, 7279 unique proteins were detected. After statistical analysis including multiple testing, the top-5 proteins (CD47, LSM7, NDUFAF4, AGPAT1 and THEM192) were selected as candidate proteins. When validating these findings in a confirmatory cohort, AGPAT1 was verified (p=0.009). According to meta-analysis, AGPAT1 was also found to be the most distinctive protein between PSC-IBD and UC. The overall proteomic profiles in step 1 and step 2 (7706 proteins) confirmed small biologic variations between the IBD-groups.Conclusions: In this two-step proteomic study on remissive IBD, we were able to verify AGPAT1 as a colonic PSC-IBD biomarker. We found high overall proteome resemblance, in contrast to the phenotypical differences existing between PSC-IBD and UC. Our findings have possible implication in future PSC-IBD diagnostics, and adds further knowledge to the evasive PSC-IBD phenotype.
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| 2. |
- Vessby, Johan, 1972-, et al.
(author)
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AGPAT1 as a Novel Colonic Biomarker for Discriminating Between Ulcerative Colitis With and Without Primary Sclerosing Cholangitis
- 2022
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In: Clinical and Translational Gastroenterology. - : Ovid Technologies (Wolters Kluwer Health). - 2155-384X. ; 13:5
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Journal article (peer-reviewed)abstract
- INTRODUCTION: Ulcerative colitis (UC) associated with primary sclerosing cholangitis (PSC-UC) is considered a unique inflammatory bowel disease (IBD) entity. PSC diagnosis in an IBD individual entails a significantly higher risk of gastrointestinal cancer; however, biomarkers for identifying patients with UC at risk for PSC are lacking. We, therefore, performed a thorough PSC-UC biomarker study, starting from archived colonic tissue.METHODS: Proteins were extracted out of formalin-fixed paraffin-embedded proximal colon samples from PSC-UC (n = 9), UC (n = 7), and healthy controls (n = 7). Patients with IBD were in clinical and histological remission, and all patients with UC had a history of pancolitis. Samples were processed by the multienzyme digestion FASP and subsequently analyzed by liquid chromatography-tandem mass spectrometry. Candidate proteins were replicated in an independent cohort (n: PSC-UC = 16 and UC = 21) and further validated by immunohistochemistry.RESULTS: In the discovery step, 7,279 unique proteins were detected. The top 5 most differentiating proteins (PSC-UC vs UC) based on linear regression analysis were selected for replication. Of these, 1-acetylglycerol-3-phosphate O-acyltransferase 1 (AGPAT1) was verified as higher in PSC-UC than UC (P = 0.009) in the replication cohort. A difference on the group level was also confirmed by immunohistochemistry, showing more intense AGPAT1 staining in patients with PSC-UC compared with UC.DISCUSSION: We present AGPAT1 as a potential colonic biomarker for differentiating PSC-UC from UC. Our findings have possible implication for future PSC-IBD diagnostics and surveillance.
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| 4. |
- Wegler, Christine, et al.
(author)
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Global variability analysis of mRNA and protein concentrations across and within human tissues
- 2020
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In: NAR Genomics and Bioinformatics. - : Oxford University Press (OUP). - 2631-9268. ; 2:1
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Journal article (peer-reviewed)abstract
- Genes and proteins show variable expression patterns throughout the human body. However, it is not clear whether relative differences in mRNA concentrations are retained on the protein level. Furthermore, inter-individual protein concentration variability within single tissue types has not been comprehensively explored. Here, we used the Gini index for in-depth concentration variability analysis of publicly available transcriptomics and proteomics data, and of an in-house proteomics dataset of human liver and jejunum from 38 donors. We found that the transfer of concentration variability from mRNA to protein is limited, that established ‘reference genes’ for data normalization vary markedly at the protein level, that protein concentrations cover a wide variability spectrum within single tissue types, and that concentration variability analysis can be a convenient starting point for identifying disease-associated proteins and novel biomarkers. Our results emphasize the importance of considering individual concentration levels, as opposed to population averages, for personalized systems biology analysis.
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