Performance of 16S Metagenomic Profiling in Formalin-Fixed Paraffin-Embedded versus Fresh-Frozen Colorectal Cancer Tissues
Borgognone, Alessandra (Institut Germans Trias i Pujol. Institut de Recerca de la Sida IrsiCaixa)
Serna, Garazi (Vall d'Hebron Institut d'Oncologia)
Noguera-Julian, Marc (Institut Germans Trias i Pujol. Institut de Recerca de la Sida IrsiCaixa)
Alonso, Lidia (Vall d'Hebron Institut d'Oncologia)
Parera, Mariona (Institut Germans Trias i Pujol. Institut de Recerca de la Sida IrsiCaixa)
Català-Moll, Francesc (Institut Germans Trias i Pujol. Institut de Recerca de la Sida IrsiCaixa)
Sanchez, Lidia (Vall d'Hebron Institut d'Oncologia)
Fasani, Roberta (Vall d'Hebron Institut d'Oncologia)
Paredes, Roger (Institut Germans Trias i Pujol. Institut de Recerca de la Sida IrsiCaixa)
Nuciforo, Paolo (Vall d'Hebron Institut d'Oncologia)
Universitat Autònoma de Barcelona. Departament de Medicina

Date:	2021
Abstract:	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 Firmicutes, Bacteroidetes and Fusobacteria. Conversely, FFPE samples were mainly enriched in typical contaminants, such as Sphingomonadales and Rhodobacterales. RNA-ISH in FFPE tissues confirmed the presence of CRC-associated bacteria, such as Fusobacterium and Bacteroides, as well as Propionibacterium 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.
Grants:	"la Caixa" Foundation LCF/PR/CE07/5061000 Instituto de Salud Carlos III PI20/00889
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Microbiome ; Colorectal cancer ; 16S gene sequencing ; RNA in situ hybridization ; FFPE
Published in:	Cancers, Vol. 13, Num. 21 (october 2021) , ISSN 2072-6694

DOI: 10.3390/cancers13215421
PMID: 34771584

18 p, 3.0 MB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Health sciences and biosciences > Institut d'Investigació en Ciencies de la Salut Germans Trias i Pujol (IGTP)
Articles > Research articles
Articles > Published articles