Metagenomic analysis of formalin-fixed paraffin-embedded tumor and normal mucosa reveals differences in the microbiome of colorectal cancer patients
Autor: | Vicente Pérez-Brocal, Gabriela Debesa-Tur, Susana Ruiz-Ruiz, Amparo Latorre, Adela Castillejo, Andrés Moya, José Luis Soto |
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Přispěvatelé: | Fundación Científica Asociación Española Contra el Cáncer, Generalitat Valenciana, European Commission, Universidad de Alicante. Departamento de Biotecnología, Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Biotecnología, Genética Humana y de Mamíferos (GHM) |
Rok vydání: | 2021 |
Předmět: |
Male
0301 basic medicine Tissue Fixation Colorectal cancer Cohort Studies 0302 clinical medicine Sequencing Intestinal Mucosa Cancer Aged 80 and over Paraffin Embedding Multidisciplinary biology Middle Aged Lynch syndrome 030220 oncology & carcinogenesis Medicine Female DNA mismatch repair Bacteroides fragilis Colorectal Neoplasms Microbial genetics Adult Science Microbial communities Biología Celular Microbiology Article 03 medical and health sciences Formalin-fixed paraffin embedded Germline mutation Formaldehyde medicine Humans Microbiome Clinical microbiology Aged biology.organism_classification medicine.disease Genética Gastrointestinal Microbiome genomic DNA 030104 developmental biology Metagenomics Case-Control Studies Cancer research Metagenome |
Zdroj: | Scientific Reports, Vol 11, Iss 1, Pp 1-15 (2021) Scientific Reports RUA. Repositorio Institucional de la Universidad de Alicante Universidad de Alicante (UA) Digital.CSIC. Repositorio Institucional del CSIC instname Digital.CSIC: Repositorio Institucional del CSIC Consejo Superior de Investigaciones Científicas (CSIC) |
Popis: | An increased risk of developing colorectal cancer (CRC) and other types of tumor is associated to Lynch syndrome (LS), an inherited condition caused by germline mutations in mismatch repair genes. We selected a cohort of LS patients that had developed CRC and had undergone surgical resection. Formalin-fixed paraffin embedded (FFPE) tissue blocks from matched colorectal and normal mucosa were used for genomic DNA extraction with a commercial kit and sequenced by high-throughput sequencing. A metagenomic approach enabled the taxonomic and functional identification of the microbial community and associated genes detected in the specimens. Slightly lower taxonomic diversity was observed in the tumor compared to the non-tumor tissue. Furthermore, the most remarkable differences between tumors and healthy tissue was the significant increase in the genus Fusobacterium in the former, in particular the species F. nucleatum, as well as Camplylobacter or Bacteroides fragilis, in accordance with previous studies of CRC. However, unlike prior studies, the present work is not based on directed detection by qPCR but instead uses a metagenomic approach to retrieve the whole bacterial community, and addresses the additional difficulty of using long-term stored FFPE samples. We want to particularly acknowledge the patients and the Biobank IBSP-CV (PT17/0015/0017) integrated in the Spanish National Biobanks Network and in the Valencian Biobanking Network, especially A. Ahicart, D. Molina and J. Martínez, for their collaboration. This research was funded by grants to AM from the Fundación Científica de la Asociación Española contra el Cancer (project AECC 2017-1485), including a post-doctoral contract to VPB first and to SRR later. GD is recipient of a PhD fellowship from the Junta Asociada Provincial de Valencia AECC. Action co-financed by the European Union through the Operational Program of European Regional Development Fund (ERDF) of Valencia Region (Spain) 2014-2020. |
Databáze: | OpenAIRE |
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