Performance of 16S Metagenomic Profiling in Formalin-Fixed Paraffin-Embedded versus Fresh-Frozen Colorectal Cancer Tissues

Formalin-fixed, paraffin-embedded (FFPE) tissues represent the most widely available clinical material to study colorectal cancer (CRC). However, the accuracy and clinical validity of FFPE microbiome profiling in CRC is uncertain. Here, we compared the microbial composition of 10 paired fresh-frozen...

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Autores principales:	Alessandra Borgognone, Garazi Serna, Marc Noguera-Julian, Lidia Alonso, Mariona Parera, Francesc Català-Moll, Lidia Sanchez, Roberta Fasani, Roger Paredes, Paolo Nuciforo
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	microbiome colorectal cancer 16S gene sequencing RNA in situ hybridization FFPE Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282
Acceso en línea:	https://doaj.org/article/1692101a09204778bd19fa92b728a0a8
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spelling	oai:doaj.org-article:1692101a09204778bd19fa92b728a0a82021-11-11T15:31:00ZPerformance of 16S Metagenomic Profiling in Formalin-Fixed Paraffin-Embedded versus Fresh-Frozen Colorectal Cancer Tissues10.3390/cancers132154212072-6694https://doaj.org/article/1692101a09204778bd19fa92b728a0a82021-10-01T00:00:00Zhttps://www.mdpi.com/2072-6694/13/21/5421https://doaj.org/toc/2072-6694Formalin-fixed, paraffin-embedded (FFPE) tissues represent the most widely available clinical material to study colorectal cancer (CRC). However, the accuracy and clinical validity of FFPE microbiome profiling in CRC is uncertain. Here, we compared the microbial composition of 10 paired fresh-frozen (FF) and FFPE CRC tissues using 16S rRNA sequencing and RNA-ISH. Both sample types showed different microbial diversity and composition. FF samples were enriched in archaea and representative CRC-associated bacteria, such as <i>Firmicutes</i>, <i>Bacteroidetes</i> and <i>Fusobacteria</i>. Conversely, FFPE samples were mainly enriched in typical contaminants, such as <i>Sphingomonadales</i> and <i>Rhodobacterales</i>. RNA-ISH in FFPE tissues confirmed the presence of CRC-associated bacteria, such as <i>Fusobacterium</i> and <i>Bacteroides</i>, as well as <i>Propionibacterium</i> allowing discrimination between tumor-associated and contaminant taxa. An internal quality index showed that the degree of similarity within sample pairs inversely correlated with the dominance of contaminant taxa. Given the importance of FFPE specimens for larger studies in human cancer genomics, our findings may provide useful indications on potential confounding factors to consider for accurate and reproducible metagenomics analyses.Alessandra BorgognoneGarazi SernaMarc Noguera-JulianLidia AlonsoMariona PareraFrancesc Català-MollLidia SanchezRoberta FasaniRoger ParedesPaolo NuciforoMDPI AGarticlemicrobiomecolorectal cancer16S gene sequencingRNA in situ hybridizationFFPENeoplasms. Tumors. Oncology. Including cancer and carcinogensRC254-282ENCancers, Vol 13, Iss 5421, p 5421 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	microbiome colorectal cancer 16S gene sequencing RNA in situ hybridization FFPE Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282
spellingShingle	microbiome colorectal cancer 16S gene sequencing RNA in situ hybridization FFPE Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282 Alessandra Borgognone Garazi Serna Marc Noguera-Julian Lidia Alonso Mariona Parera Francesc Català-Moll Lidia Sanchez Roberta Fasani Roger Paredes Paolo Nuciforo Performance of 16S Metagenomic Profiling in Formalin-Fixed Paraffin-Embedded versus Fresh-Frozen Colorectal Cancer Tissues
description	Formalin-fixed, paraffin-embedded (FFPE) tissues represent the most widely available clinical material to study colorectal cancer (CRC). However, the accuracy and clinical validity of FFPE microbiome profiling in CRC is uncertain. Here, we compared the microbial composition of 10 paired fresh-frozen (FF) and FFPE CRC tissues using 16S rRNA sequencing and RNA-ISH. Both sample types showed different microbial diversity and composition. FF samples were enriched in archaea and representative CRC-associated bacteria, such as <i>Firmicutes</i>, <i>Bacteroidetes</i> and <i>Fusobacteria</i>. Conversely, FFPE samples were mainly enriched in typical contaminants, such as <i>Sphingomonadales</i> and <i>Rhodobacterales</i>. RNA-ISH in FFPE tissues confirmed the presence of CRC-associated bacteria, such as <i>Fusobacterium</i> and <i>Bacteroides</i>, as well as <i>Propionibacterium</i> allowing discrimination between tumor-associated and contaminant taxa. An internal quality index showed that the degree of similarity within sample pairs inversely correlated with the dominance of contaminant taxa. Given the importance of FFPE specimens for larger studies in human cancer genomics, our findings may provide useful indications on potential confounding factors to consider for accurate and reproducible metagenomics analyses.
format	article
author	Alessandra Borgognone Garazi Serna Marc Noguera-Julian Lidia Alonso Mariona Parera Francesc Català-Moll Lidia Sanchez Roberta Fasani Roger Paredes Paolo Nuciforo
author_facet	Alessandra Borgognone Garazi Serna Marc Noguera-Julian Lidia Alonso Mariona Parera Francesc Català-Moll Lidia Sanchez Roberta Fasani Roger Paredes Paolo Nuciforo
author_sort	Alessandra Borgognone
title	Performance of 16S Metagenomic Profiling in Formalin-Fixed Paraffin-Embedded versus Fresh-Frozen Colorectal Cancer Tissues
title_short	Performance of 16S Metagenomic Profiling in Formalin-Fixed Paraffin-Embedded versus Fresh-Frozen Colorectal Cancer Tissues
title_full	Performance of 16S Metagenomic Profiling in Formalin-Fixed Paraffin-Embedded versus Fresh-Frozen Colorectal Cancer Tissues
title_fullStr	Performance of 16S Metagenomic Profiling in Formalin-Fixed Paraffin-Embedded versus Fresh-Frozen Colorectal Cancer Tissues
title_full_unstemmed	Performance of 16S Metagenomic Profiling in Formalin-Fixed Paraffin-Embedded versus Fresh-Frozen Colorectal Cancer Tissues
title_sort	performance of 16s metagenomic profiling in formalin-fixed paraffin-embedded versus fresh-frozen colorectal cancer tissues
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/1692101a09204778bd19fa92b728a0a8
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Performance of 16S Metagenomic Profiling in Formalin-Fixed Paraffin-Embedded versus Fresh-Frozen Colorectal Cancer Tissues

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