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FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers

The majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically important to understand gene regulation in human disease. T...

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Autores principales: Zhao, Linxuan, Xing, Pengwei, Polavarapu, Vamsi Krishna, Zhao, Miao, Valero-Martínez, Blanca, Dang, Yonglong, Maturi, Nagaprathyusha, Mathot, Lucy, Neves, Inês, Yildirim, Irem, Swartling, Fredrik Johansson, Sjöblom, Tobias, Uhrbom, Lene, Chen, Xingqi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8643707/
https://www.ncbi.nlm.nih.gov/pubmed/34534335
http://dx.doi.org/10.1093/nar/gkab813
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author Zhao, Linxuan
Xing, Pengwei
Polavarapu, Vamsi Krishna
Zhao, Miao
Valero-Martínez, Blanca
Dang, Yonglong
Maturi, Nagaprathyusha
Mathot, Lucy
Neves, Inês
Yildirim, Irem
Swartling, Fredrik Johansson
Sjöblom, Tobias
Uhrbom, Lene
Chen, Xingqi
author_facet Zhao, Linxuan
Xing, Pengwei
Polavarapu, Vamsi Krishna
Zhao, Miao
Valero-Martínez, Blanca
Dang, Yonglong
Maturi, Nagaprathyusha
Mathot, Lucy
Neves, Inês
Yildirim, Irem
Swartling, Fredrik Johansson
Sjöblom, Tobias
Uhrbom, Lene
Chen, Xingqi
author_sort Zhao, Linxuan
collection PubMed
description The majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically important to understand gene regulation in human disease. The required input for current genome-wide histone modification profiling studies from FFPE samples is either 10–20 tissue sections or whole tissue blocks, which prevents better resolved analyses. But it is desirable to consume a minimal amount of FFPE tissue sections in the analysis as clinical tissues of interest are limited. Here, we present FFPE tissue with antibody-guided chromatin tagmentation with sequencing (FACT-seq), the first highly sensitive method to efficiently profile histone modifications in FFPE tissues by combining a novel fusion protein of hyperactive Tn5 transposase and protein A (T7−pA−Tn5) transposition and T7 in vitro transcription. FACT-seq generates high-quality chromatin profiles from different histone modifications with low number of FFPE nuclei. We proved a very small piece of FFPE tissue section containing ∼4000 nuclei is sufficient to decode H3K27ac modifications with FACT-seq. H3K27ac FACT-seq revealed disease-specific super enhancers in the archived FFPE human colorectal and human glioblastoma cancer tissue. In summary, FACT-seq allows decoding the histone modifications in archival FFPE tissues with high sensitivity and help researchers to better understand epigenetic regulation in cancer and human disease.
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spelling pubmed-86437072021-12-06 FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers Zhao, Linxuan Xing, Pengwei Polavarapu, Vamsi Krishna Zhao, Miao Valero-Martínez, Blanca Dang, Yonglong Maturi, Nagaprathyusha Mathot, Lucy Neves, Inês Yildirim, Irem Swartling, Fredrik Johansson Sjöblom, Tobias Uhrbom, Lene Chen, Xingqi Nucleic Acids Res Methods Online The majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically important to understand gene regulation in human disease. The required input for current genome-wide histone modification profiling studies from FFPE samples is either 10–20 tissue sections or whole tissue blocks, which prevents better resolved analyses. But it is desirable to consume a minimal amount of FFPE tissue sections in the analysis as clinical tissues of interest are limited. Here, we present FFPE tissue with antibody-guided chromatin tagmentation with sequencing (FACT-seq), the first highly sensitive method to efficiently profile histone modifications in FFPE tissues by combining a novel fusion protein of hyperactive Tn5 transposase and protein A (T7−pA−Tn5) transposition and T7 in vitro transcription. FACT-seq generates high-quality chromatin profiles from different histone modifications with low number of FFPE nuclei. We proved a very small piece of FFPE tissue section containing ∼4000 nuclei is sufficient to decode H3K27ac modifications with FACT-seq. H3K27ac FACT-seq revealed disease-specific super enhancers in the archived FFPE human colorectal and human glioblastoma cancer tissue. In summary, FACT-seq allows decoding the histone modifications in archival FFPE tissues with high sensitivity and help researchers to better understand epigenetic regulation in cancer and human disease. Oxford University Press 2021-09-17 /pmc/articles/PMC8643707/ /pubmed/34534335 http://dx.doi.org/10.1093/nar/gkab813 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Methods Online
Zhao, Linxuan
Xing, Pengwei
Polavarapu, Vamsi Krishna
Zhao, Miao
Valero-Martínez, Blanca
Dang, Yonglong
Maturi, Nagaprathyusha
Mathot, Lucy
Neves, Inês
Yildirim, Irem
Swartling, Fredrik Johansson
Sjöblom, Tobias
Uhrbom, Lene
Chen, Xingqi
FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers
title FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers
title_full FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers
title_fullStr FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers
title_full_unstemmed FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers
title_short FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers
title_sort fact-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8643707/
https://www.ncbi.nlm.nih.gov/pubmed/34534335
http://dx.doi.org/10.1093/nar/gkab813
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