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Kartal E, Schmidt TSB, Molina-Montes E, Rodríguez-Perales S, Wirbel J, Maistrenko OM, Akanni WA, Alashkar Alhamwe B, Alves RJ, Carrato A, Erasmus HP, Estudillo L, Finkelmeier F, Fullam A, Glazek AM, Gómez-Rubio P, Hercog R, Jung F, Kandels S, Kersting S, Langheinrich M, Márquez M, Molero X, Orakov A, Van Rossum T, Torres-Ruiz R, Telzerow A, Zych K, Benes V, Zeller G, Trebicka J, Real FX, Malats N, Bork P. A faecal microbiota signature with high specificity for pancreatic cancer. Gut 2022; 71:1359-1372. [PMID: 35260444 PMCID: PMC9185815 DOI: 10.1136/gutjnl-2021-324755] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 12/05/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Recent evidence suggests a role for the microbiome in pancreatic ductal adenocarcinoma (PDAC) aetiology and progression. OBJECTIVE To explore the faecal and salivary microbiota as potential diagnostic biomarkers. METHODS We applied shotgun metagenomic and 16S rRNA amplicon sequencing to samples from a Spanish case-control study (n=136), including 57 cases, 50 controls, and 29 patients with chronic pancreatitis in the discovery phase, and from a German case-control study (n=76), in the validation phase. RESULTS Faecal metagenomic classifiers performed much better than saliva-based classifiers and identified patients with PDAC with an accuracy of up to 0.84 area under the receiver operating characteristic curve (AUROC) based on a set of 27 microbial species, with consistent accuracy across early and late disease stages. Performance further improved to up to 0.94 AUROC when we combined our microbiome-based predictions with serum levels of carbohydrate antigen (CA) 19-9, the only current non-invasive, Food and Drug Administration approved, low specificity PDAC diagnostic biomarker. Furthermore, a microbiota-based classification model confined to PDAC-enriched species was highly disease-specific when validated against 25 publicly available metagenomic study populations for various health conditions (n=5792). Both microbiome-based models had a high prediction accuracy on a German validation population (n=76). Several faecal PDAC marker species were detectable in pancreatic tumour and non-tumour tissue using 16S rRNA sequencing and fluorescence in situ hybridisation. CONCLUSION Taken together, our results indicate that non-invasive, robust and specific faecal microbiota-based screening for the early detection of PDAC is feasible.
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Affiliation(s)
- Ece Kartal
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Collaboration for joint PhD degree, European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
| | - Thomas S B Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Esther Molina-Montes
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Sandra Rodríguez-Perales
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
- Molecular Cytogenetics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Jakob Wirbel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Collaboration for joint PhD degree, European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
| | - Oleksandr M Maistrenko
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Wasiu A Akanni
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Bilal Alashkar Alhamwe
- Member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung School (UGMLC), Philipps University Marburg Faculty of Medicine, Marburg, Germany
| | - Renato J Alves
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alfredo Carrato
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
- Medical Oncology Department of Oncology, Hospital Ramón y Cajal, Madrid, Spain
- University of Alcala de Henares, Alcala de Henares, Spain
| | - Hans-Peter Erasmus
- Translational Hepatology Department of Internal Medicine I, Goethe-Universitat Frankfurt am Main, Frankfurt am Main, Germany
| | - Lidia Estudillo
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Fabian Finkelmeier
- Translational Hepatology Department of Internal Medicine I, Goethe-Universitat Frankfurt am Main, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt am Main, Hessen, Germany
| | - Anthony Fullam
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anna M Glazek
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Paulina Gómez-Rubio
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Rajna Hercog
- Genomic Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ferris Jung
- Genomic Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Stefanie Kandels
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Stephan Kersting
- Department of Surgery, Erlangen University Hospital, Erlangen, Germany
- Department of Surgery, University of Greifswald, Greifswald, Germany
| | | | - Mirari Márquez
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Xavier Molero
- Hospital Universitari Vall d'Hebron, Institut de Recerca (VHIR), Barcelona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Askarbek Orakov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Thea Van Rossum
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Raul Torres-Ruiz
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
- Molecular Cytogenetics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Anja Telzerow
- Genomic Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Konrad Zych
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Vladimir Benes
- Genomic Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jonel Trebicka
- Translational Hepatology Department of Internal Medicine I, Goethe-Universitat Frankfurt am Main, Frankfurt am Main, Germany
- EF Clif, European Foundation for the Study of Chronic Liver Failure, Barcelona, Spain
| | - Francisco X Real
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nuria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
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