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Proteomic comparison between different tissue preservation methods for identification of promising biomarkers of urothelial bladder cancer

Samples in biobanks are generally preserved by formalin-fixation and paraffin-embedding (FFPE) and/or optimal cutting temperature compound (OCT)-embedding and subsequently frozen. Mass spectrometry (MS)-based analysis of these samples is now available via developed protocols, however, the difference...

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Autores principales: Valdés, Alberto, Bitzios, Athanasios, Kassa, Eszter, Shevchenko, Ganna, Falk, Alexander, Malmström, Per-Uno, Dragomir, Anca, Segersten, Ulrika, Lind, Sara Bergström
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8027873/
https://www.ncbi.nlm.nih.gov/pubmed/33828141
http://dx.doi.org/10.1038/s41598-021-87003-6
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author Valdés, Alberto
Bitzios, Athanasios
Kassa, Eszter
Shevchenko, Ganna
Falk, Alexander
Malmström, Per-Uno
Dragomir, Anca
Segersten, Ulrika
Lind, Sara Bergström
author_facet Valdés, Alberto
Bitzios, Athanasios
Kassa, Eszter
Shevchenko, Ganna
Falk, Alexander
Malmström, Per-Uno
Dragomir, Anca
Segersten, Ulrika
Lind, Sara Bergström
author_sort Valdés, Alberto
collection PubMed
description Samples in biobanks are generally preserved by formalin-fixation and paraffin-embedding (FFPE) and/or optimal cutting temperature compound (OCT)-embedding and subsequently frozen. Mass spectrometry (MS)-based analysis of these samples is now available via developed protocols, however, the differences in results with respect to preservation methods needs further investigation. Here we use bladder urothelial carcinoma tissue of two different tumor stages (Ta/T1—non-muscle invasive bladder cancer (NMIBC), and T2/T3—muscle invasive bladder cancer (MIBC)) which, upon sampling, were divided and preserved by FFPE and OCT. Samples were parallel processed from the two methods and proteins were analyzed with label-free quantitative MS. Over 700 and 1200 proteins were quantified in FFPE and OCT samples, respectively. Multivariate analysis indicates that the preservation method is the main source of variation, but also tumors of different stages could be differentiated. Proteins involved in mitochondrial function were overrepresented in OCT data but missing in the FFPE data, indicating that these proteins are not well preserved by FFPE. Concordant results for proteins such as HMGCS2 (uniquely quantified in Ta/T1 tumors), and LGALS1, ANXA5 and plastin (upregulated in T2/T3 tumors) were observed in both FFPE and OCT data, which supports the use of MS technology for biobank samples and encourages the further evaluation of these proteins as biomarkers.
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spelling pubmed-80278732021-04-09 Proteomic comparison between different tissue preservation methods for identification of promising biomarkers of urothelial bladder cancer Valdés, Alberto Bitzios, Athanasios Kassa, Eszter Shevchenko, Ganna Falk, Alexander Malmström, Per-Uno Dragomir, Anca Segersten, Ulrika Lind, Sara Bergström Sci Rep Article Samples in biobanks are generally preserved by formalin-fixation and paraffin-embedding (FFPE) and/or optimal cutting temperature compound (OCT)-embedding and subsequently frozen. Mass spectrometry (MS)-based analysis of these samples is now available via developed protocols, however, the differences in results with respect to preservation methods needs further investigation. Here we use bladder urothelial carcinoma tissue of two different tumor stages (Ta/T1—non-muscle invasive bladder cancer (NMIBC), and T2/T3—muscle invasive bladder cancer (MIBC)) which, upon sampling, were divided and preserved by FFPE and OCT. Samples were parallel processed from the two methods and proteins were analyzed with label-free quantitative MS. Over 700 and 1200 proteins were quantified in FFPE and OCT samples, respectively. Multivariate analysis indicates that the preservation method is the main source of variation, but also tumors of different stages could be differentiated. Proteins involved in mitochondrial function were overrepresented in OCT data but missing in the FFPE data, indicating that these proteins are not well preserved by FFPE. Concordant results for proteins such as HMGCS2 (uniquely quantified in Ta/T1 tumors), and LGALS1, ANXA5 and plastin (upregulated in T2/T3 tumors) were observed in both FFPE and OCT data, which supports the use of MS technology for biobank samples and encourages the further evaluation of these proteins as biomarkers. Nature Publishing Group UK 2021-04-07 /pmc/articles/PMC8027873/ /pubmed/33828141 http://dx.doi.org/10.1038/s41598-021-87003-6 Text en © The Author(s) 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Valdés, Alberto
Bitzios, Athanasios
Kassa, Eszter
Shevchenko, Ganna
Falk, Alexander
Malmström, Per-Uno
Dragomir, Anca
Segersten, Ulrika
Lind, Sara Bergström
Proteomic comparison between different tissue preservation methods for identification of promising biomarkers of urothelial bladder cancer
title Proteomic comparison between different tissue preservation methods for identification of promising biomarkers of urothelial bladder cancer
title_full Proteomic comparison between different tissue preservation methods for identification of promising biomarkers of urothelial bladder cancer
title_fullStr Proteomic comparison between different tissue preservation methods for identification of promising biomarkers of urothelial bladder cancer
title_full_unstemmed Proteomic comparison between different tissue preservation methods for identification of promising biomarkers of urothelial bladder cancer
title_short Proteomic comparison between different tissue preservation methods for identification of promising biomarkers of urothelial bladder cancer
title_sort proteomic comparison between different tissue preservation methods for identification of promising biomarkers of urothelial bladder cancer
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8027873/
https://www.ncbi.nlm.nih.gov/pubmed/33828141
http://dx.doi.org/10.1038/s41598-021-87003-6
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