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

Abstract 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 d...

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Autores principales:	Alberto Valdés, Athanasios Bitzios, Eszter Kassa, Ganna Shevchenko, Alexander Falk, Per-Uno Malmström, Anca Dragomir, Ulrika Segersten, Sara Bergström Lind
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ee191a1deab3421e87b93c60e49c7a1b
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spelling	oai:doaj.org-article:ee191a1deab3421e87b93c60e49c7a1b2021-12-02T14:37:39ZProteomic comparison between different tissue preservation methods for identification of promising biomarkers of urothelial bladder cancer10.1038/s41598-021-87003-62045-2322https://doaj.org/article/ee191a1deab3421e87b93c60e49c7a1b2021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-87003-6https://doaj.org/toc/2045-2322Abstract 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.Alberto ValdésAthanasios BitziosEszter KassaGanna ShevchenkoAlexander FalkPer-Uno MalmströmAnca DragomirUlrika SegerstenSara Bergström LindNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Alberto Valdés Athanasios Bitzios Eszter Kassa Ganna Shevchenko Alexander Falk Per-Uno Malmström Anca Dragomir Ulrika Segersten Sara Bergström Lind Proteomic comparison between different tissue preservation methods for identification of promising biomarkers of urothelial bladder cancer
description	Abstract 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.
format	article
author	Alberto Valdés Athanasios Bitzios Eszter Kassa Ganna Shevchenko Alexander Falk Per-Uno Malmström Anca Dragomir Ulrika Segersten Sara Bergström Lind
author_facet	Alberto Valdés Athanasios Bitzios Eszter Kassa Ganna Shevchenko Alexander Falk Per-Uno Malmström Anca Dragomir Ulrika Segersten Sara Bergström Lind
author_sort	Alberto Valdés
title	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_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_sort	proteomic comparison between different tissue preservation methods for identification of promising biomarkers of urothelial bladder cancer
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/ee191a1deab3421e87b93c60e49c7a1b
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Proteomic comparison between different tissue preservation methods for identification of promising biomarkers of urothelial bladder cancer

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