Towards Reliable Methodology: Microbiome Analysis of Fresh Frozen vs. Formalin-Fixed Paraffin-Embedded Bladder Tissue Samples: A Feasibility Study
Studies have shown that the human microbiome influences the response to systemic immunotherapy. However, only scarce data exist on the impact of the urinary microbiome on the response rates of bladder cancer (BC) to local <i>Bacillus Calmette-Guérin</i> instillation therapy. We launched...
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MDPI AG
2024-12-01
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| Online Access: | https://www.mdpi.com/2076-2607/12/12/2594 |
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| author | Dominik Enderlin Uwe Bieri Jana Gadient Yasser Morsy Michael Scharl Jan Hendrik Rüschoff Lukas John Hefermehl Anna Nikitin Janine Langenauer Daniel Stephan Engeler Beat Förster Fabian Obrecht Jonathan Surber Thomas Paul Scherer Daniel Eberli Cédric Poyet |
| author_facet | Dominik Enderlin Uwe Bieri Jana Gadient Yasser Morsy Michael Scharl Jan Hendrik Rüschoff Lukas John Hefermehl Anna Nikitin Janine Langenauer Daniel Stephan Engeler Beat Förster Fabian Obrecht Jonathan Surber Thomas Paul Scherer Daniel Eberli Cédric Poyet |
| author_sort | Dominik Enderlin |
| collection | DOAJ |
| description | Studies have shown that the human microbiome influences the response to systemic immunotherapy. However, only scarce data exist on the impact of the urinary microbiome on the response rates of bladder cancer (BC) to local <i>Bacillus Calmette-Guérin</i> instillation therapy. We launched the prospective SILENT-EMPIRE study in 2022 to address this question. We report the results of the pilot study of SILENT-EMPIRE, which aimed to compare the microbiome between fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) samples in the cancerous tissue and adjacent healthy tissue of BC patients. Our results show that alpha diversity is increased in FF samples compared to FFPE (coverage index <i>p</i> = 0.041, core abundance index <i>p</i> = 0.008). No significant differences concerning alpha diversity could be detected between cancerous and non-cancerous tissue in the same BC patients. This study demonstrates that microbiome analysis from both FF and FFPE samples is feasible. Implementing this finding could aid in the translation of research findings into clinical practice. |
| format | Article |
| id | doaj-art-3a04dedf64d443ea8642349c3e62bcf9 |
| institution | DOAJ |
| issn | 2076-2607 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj-art-3a04dedf64d443ea8642349c3e62bcf92025-08-20T02:56:50ZengMDPI AGMicroorganisms2076-26072024-12-011212259410.3390/microorganisms12122594Towards Reliable Methodology: Microbiome Analysis of Fresh Frozen vs. Formalin-Fixed Paraffin-Embedded Bladder Tissue Samples: A Feasibility StudyDominik Enderlin0Uwe Bieri1Jana Gadient2Yasser Morsy3Michael Scharl4Jan Hendrik Rüschoff5Lukas John Hefermehl6Anna Nikitin7Janine Langenauer8Daniel Stephan Engeler9Beat Förster10Fabian Obrecht11Jonathan Surber12Thomas Paul Scherer13Daniel Eberli14Cédric Poyet15Department of Urology, University Hospital of Zurich, University of Zurich, 8091 Zurich, SwitzerlandDepartment of Urology, University Hospital of Zurich, University of Zurich, 8091 Zurich, SwitzerlandDepartment of Urology, University Hospital of Zurich, University of Zurich, 8091 Zurich, SwitzerlandDepartment of Gastroenterology and Hepatology, University Hospital of Zurich, University of Zurich, 8091 Zurich, SwitzerlandDepartment of Gastroenterology and Hepatology, University Hospital of Zurich, University of Zurich, 8091 Zurich, SwitzerlandDepartment of Pathology, and Molecular Pathology, University Hospital of Zurich, University of Zurich, 8091 Zurich, SwitzerlandDivision of Urology, Department of Surgery, Kantonsspital Baden, 5404 Baden, SwitzerlandDivision of Urology, Department of Surgery, Kantonsspital Baden, 5404 Baden, SwitzerlandDepartment of Urology, Cantonal Hospital of St. Gallen, School of Medicine, University of St. Gallen, 9007 St. Gallen, SwitzerlandDepartment of Urology, Cantonal Hospital of St. Gallen, School of Medicine, University of St. Gallen, 9007 St. Gallen, SwitzerlandDepartment of Urology, Kantonsspital Winterthur, 8401 Winterthur, SwitzerlandDepartment of Urology, Kantonsspital Winterthur, 8401 Winterthur, SwitzerlandDepartment of Urology, University Hospital of Zurich, University of Zurich, 8091 Zurich, SwitzerlandDepartment of Urology, University Hospital of Zurich, University of Zurich, 8091 Zurich, SwitzerlandDepartment of Urology, University Hospital of Zurich, University of Zurich, 8091 Zurich, SwitzerlandDepartment of Urology, University Hospital of Zurich, University of Zurich, 8091 Zurich, SwitzerlandStudies have shown that the human microbiome influences the response to systemic immunotherapy. However, only scarce data exist on the impact of the urinary microbiome on the response rates of bladder cancer (BC) to local <i>Bacillus Calmette-Guérin</i> instillation therapy. We launched the prospective SILENT-EMPIRE study in 2022 to address this question. We report the results of the pilot study of SILENT-EMPIRE, which aimed to compare the microbiome between fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) samples in the cancerous tissue and adjacent healthy tissue of BC patients. Our results show that alpha diversity is increased in FF samples compared to FFPE (coverage index <i>p</i> = 0.041, core abundance index <i>p</i> = 0.008). No significant differences concerning alpha diversity could be detected between cancerous and non-cancerous tissue in the same BC patients. This study demonstrates that microbiome analysis from both FF and FFPE samples is feasible. Implementing this finding could aid in the translation of research findings into clinical practice.https://www.mdpi.com/2076-2607/12/12/2594fresh frozenformalin-fixed paraffin-embeddedmicrobiomebladder canceralpha diversity |
| spellingShingle | Dominik Enderlin Uwe Bieri Jana Gadient Yasser Morsy Michael Scharl Jan Hendrik Rüschoff Lukas John Hefermehl Anna Nikitin Janine Langenauer Daniel Stephan Engeler Beat Förster Fabian Obrecht Jonathan Surber Thomas Paul Scherer Daniel Eberli Cédric Poyet Towards Reliable Methodology: Microbiome Analysis of Fresh Frozen vs. Formalin-Fixed Paraffin-Embedded Bladder Tissue Samples: A Feasibility Study Microorganisms fresh frozen formalin-fixed paraffin-embedded microbiome bladder cancer alpha diversity |
| title | Towards Reliable Methodology: Microbiome Analysis of Fresh Frozen vs. Formalin-Fixed Paraffin-Embedded Bladder Tissue Samples: A Feasibility Study |
| title_full | Towards Reliable Methodology: Microbiome Analysis of Fresh Frozen vs. Formalin-Fixed Paraffin-Embedded Bladder Tissue Samples: A Feasibility Study |
| title_fullStr | Towards Reliable Methodology: Microbiome Analysis of Fresh Frozen vs. Formalin-Fixed Paraffin-Embedded Bladder Tissue Samples: A Feasibility Study |
| title_full_unstemmed | Towards Reliable Methodology: Microbiome Analysis of Fresh Frozen vs. Formalin-Fixed Paraffin-Embedded Bladder Tissue Samples: A Feasibility Study |
| title_short | Towards Reliable Methodology: Microbiome Analysis of Fresh Frozen vs. Formalin-Fixed Paraffin-Embedded Bladder Tissue Samples: A Feasibility Study |
| title_sort | towards reliable methodology microbiome analysis of fresh frozen vs formalin fixed paraffin embedded bladder tissue samples a feasibility study |
| topic | fresh frozen formalin-fixed paraffin-embedded microbiome bladder cancer alpha diversity |
| url | https://www.mdpi.com/2076-2607/12/12/2594 |
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