Cracking it - successful mRNA extraction for digital gene expression analysis from decalcified, formalin-fixed and paraffinembedded bone tissue

Alireza Saraji; Anne Offermann; Janine Stegmann-Frehse; Katharina Hempel; Duan Kang; Rosemarie Krupar; Christian Watermann; Danny Jonigk; Mark Philipp Kuhnel; Jutta Kirfel; Sven Perner; Verena Sailer

doi:10.1371/journal.pone.0257416

Cracking it - successful mRNA extraction for digital gene expression analysis from decalcified, formalin-fixed and paraffinembedded bone tissue

Alireza Saraji, Anne Offermann, Janine Stegmann-Frehse, Katharina Hempel, Duan Kang, Rosemarie Krupar, Christian Watermann, Danny Jonigk, Mark Philipp Kuhnel, Jutta Kirfel, Sven Perner, Verena Sailer^*

^*Corresponding author for this work

Institute of Pathology

6 Citations (Scopus)

Abstract

With the advance of precision medicine, the availability of tumor tissue for molecular analysis has become a limiting factor. This is particularly the case for bone metastases which are frequently occurring in cancer types such as prostate cancer. Due to the necessary decalcification process it was long thought that transcriptome analysis will not be feasible from decalcified formalin-fixed, paraffin-embedded (DFFPE) in a large manner. Here we demonstrate that mRNA extraction from DFFPE is feasible, quick, robust and reproducible and that decalcification does not hamper subsequent gene expression analysis. This might assist in implementing transcriptome analysis from DFFPE into every day practice.

Original language	English
Article number	e0257416
Journal	PLoS ONE
Volume	16
Issue number	9 September
DOIs	https://doi.org/10.1371/journal.pone.0257416
Publication status	Published - 09.2021

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This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Research Areas and Centers

Centers: University Cancer Center Schleswig-Holstein (UCCSH)

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Saraji, A., Offermann, A., Stegmann-Frehse, J., Hempel, K., Kang, D., Krupar, R., Watermann, C., Jonigk, D., Kuhnel, M. P., Kirfel, J., Perner, S., & Sailer, V. (2021). Cracking it - successful mRNA extraction for digital gene expression analysis from decalcified, formalin-fixed and paraffinembedded bone tissue. PLoS ONE, 16(9 September), Article e0257416. https://doi.org/10.1371/journal.pone.0257416

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title = "Cracking it - successful mRNA extraction for digital gene expression analysis from decalcified, formalin-fixed and paraffinembedded bone tissue",

abstract = "With the advance of precision medicine, the availability of tumor tissue for molecular analysis has become a limiting factor. This is particularly the case for bone metastases which are frequently occurring in cancer types such as prostate cancer. Due to the necessary decalcification process it was long thought that transcriptome analysis will not be feasible from decalcified formalin-fixed, paraffin-embedded (DFFPE) in a large manner. Here we demonstrate that mRNA extraction from DFFPE is feasible, quick, robust and reproducible and that decalcification does not hamper subsequent gene expression analysis. This might assist in implementing transcriptome analysis from DFFPE into every day practice. ",

author = "Alireza Saraji and Anne Offermann and Janine Stegmann-Frehse and Katharina Hempel and Duan Kang and Rosemarie Krupar and Christian Watermann and Danny Jonigk and Kuhnel, \{Mark Philipp\} and Jutta Kirfel and Sven Perner and Verena Sailer",

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Saraji, A, Offermann, A, Stegmann-Frehse, J, Hempel, K, Kang, D, Krupar, R, Watermann, C, Jonigk, D, Kuhnel, MP, Kirfel, J, Perner, S & Sailer, V 2021, 'Cracking it - successful mRNA extraction for digital gene expression analysis from decalcified, formalin-fixed and paraffinembedded bone tissue', PLoS ONE, vol. 16, no. 9 September, e0257416. https://doi.org/10.1371/journal.pone.0257416

TY - JOUR

T1 - Cracking it - successful mRNA extraction for digital gene expression analysis from decalcified, formalin-fixed and paraffinembedded bone tissue

AU - Saraji, Alireza

AU - Offermann, Anne

AU - Stegmann-Frehse, Janine

AU - Hempel, Katharina

AU - Kang, Duan

AU - Krupar, Rosemarie

AU - Watermann, Christian

AU - Jonigk, Danny

AU - Kuhnel, Mark Philipp

AU - Kirfel, Jutta

AU - Perner, Sven

AU - Sailer, Verena

N1 - Publisher Copyright: © 2021 Saraji et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

PY - 2021/9

Y1 - 2021/9

N2 - With the advance of precision medicine, the availability of tumor tissue for molecular analysis has become a limiting factor. This is particularly the case for bone metastases which are frequently occurring in cancer types such as prostate cancer. Due to the necessary decalcification process it was long thought that transcriptome analysis will not be feasible from decalcified formalin-fixed, paraffin-embedded (DFFPE) in a large manner. Here we demonstrate that mRNA extraction from DFFPE is feasible, quick, robust and reproducible and that decalcification does not hamper subsequent gene expression analysis. This might assist in implementing transcriptome analysis from DFFPE into every day practice.

AB - With the advance of precision medicine, the availability of tumor tissue for molecular analysis has become a limiting factor. This is particularly the case for bone metastases which are frequently occurring in cancer types such as prostate cancer. Due to the necessary decalcification process it was long thought that transcriptome analysis will not be feasible from decalcified formalin-fixed, paraffin-embedded (DFFPE) in a large manner. Here we demonstrate that mRNA extraction from DFFPE is feasible, quick, robust and reproducible and that decalcification does not hamper subsequent gene expression analysis. This might assist in implementing transcriptome analysis from DFFPE into every day practice.

UR - https://www.scopus.com/pages/publications/85115050138

U2 - 10.1371/journal.pone.0257416

DO - 10.1371/journal.pone.0257416

M3 - Journal articles

C2 - 34529723

AN - SCOPUS:85115050138

VL - 16

JO - PLoS ONE

JF - PLoS ONE

IS - 9 September

M1 - e0257416

ER -

Cracking it - successful mRNA extraction for digital gene expression analysis from decalcified, formalin-fixed and paraffinembedded bone tissue

Abstract

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