Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data
Abstract Background The association between microbes and cancer has been reported repeatedly; however, it is not clear if molecular tumour properties are connected to specific microbial colonisation patterns. This is due mainly to the current technical and analytical strategy limitations to characte...
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| Format: | Article |
| Language: | English |
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BMC
2023-05-01
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| Series: | Genome Medicine |
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| Online Access: | https://doi.org/10.1186/s13073-023-01180-9 |
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| author | Gaia Sambruni Angeli D. Macandog Jakob Wirbel Danilo Cagnina Carlotta Catozzi Tiziano Dallavilla Francesca Borgo Nicola Fazio Uberto Fumagalli-Romario Wanda L. Petz Teresa Manzo Simona P. Ravenda Georg Zeller Luigi Nezi Martin H. Schaefer |
| author_facet | Gaia Sambruni Angeli D. Macandog Jakob Wirbel Danilo Cagnina Carlotta Catozzi Tiziano Dallavilla Francesca Borgo Nicola Fazio Uberto Fumagalli-Romario Wanda L. Petz Teresa Manzo Simona P. Ravenda Georg Zeller Luigi Nezi Martin H. Schaefer |
| author_sort | Gaia Sambruni |
| collection | DOAJ |
| description | Abstract Background The association between microbes and cancer has been reported repeatedly; however, it is not clear if molecular tumour properties are connected to specific microbial colonisation patterns. This is due mainly to the current technical and analytical strategy limitations to characterise tumour-associated bacteria. Methods Here, we propose an approach to detect bacterial signals in human RNA sequencing data and associate them with the clinical and molecular properties of the tumours. The method was tested on public datasets from The Cancer Genome Atlas, and its accuracy was assessed on a new cohort of colorectal cancer patients. Results Our analysis shows that intratumoural microbiome composition is correlated with survival, anatomic location, microsatellite instability, consensus molecular subtype and immune cell infiltration in colon tumours. In particular, we find Faecalibacterium prausnitzii, Coprococcus comes, Bacteroides spp., Fusobacterium spp. and Clostridium spp. to be strongly associated with tumour properties. Conclusions We implemented an approach to concurrently analyse clinical and molecular properties of the tumour as well as the composition of the associated microbiome. Our results may improve patient stratification and pave the path for mechanistic studies on microbiota-tumour crosstalk. |
| first_indexed | 2024-04-09T14:00:49Z |
| format | Article |
| id | doaj.art-213f6dde22fd4445b062116b7522266d |
| institution | Directory Open Access Journal |
| issn | 1756-994X |
| language | English |
| last_indexed | 2024-04-09T14:00:49Z |
| publishDate | 2023-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Medicine |
| spelling | doaj.art-213f6dde22fd4445b062116b7522266d2023-05-07T11:19:32ZengBMCGenome Medicine1756-994X2023-05-0115111910.1186/s13073-023-01180-9Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing dataGaia Sambruni0Angeli D. Macandog1Jakob Wirbel2Danilo Cagnina3Carlotta Catozzi4Tiziano Dallavilla5Francesca Borgo6Nicola Fazio7Uberto Fumagalli-Romario8Wanda L. Petz9Teresa Manzo10Simona P. Ravenda11Georg Zeller12Luigi Nezi13Martin H. Schaefer14Department of Experimental Oncology, European Institute of Oncology-IRCCSDepartment of Experimental Oncology, European Institute of Oncology-IRCCSStructural and Computational Biology Unit, European Molecular Biology LaboratoryDepartment of Experimental Oncology, European Institute of Oncology-IRCCSDepartment of Experimental Oncology, European Institute of Oncology-IRCCSDepartment of Experimental Oncology, European Institute of Oncology-IRCCSDepartment of Experimental Oncology, European Institute of Oncology-IRCCSDivision of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology-IRCCSDigestive Surgery, European Institute of Oncology-IRCCSDigestive Surgery, European Institute of Oncology-IRCCSDepartment of Experimental Oncology, European Institute of Oncology-IRCCSDivision of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology-IRCCSStructural and Computational Biology Unit, European Molecular Biology LaboratoryDepartment of Experimental Oncology, European Institute of Oncology-IRCCSDepartment of Experimental Oncology, European Institute of Oncology-IRCCSAbstract Background The association between microbes and cancer has been reported repeatedly; however, it is not clear if molecular tumour properties are connected to specific microbial colonisation patterns. This is due mainly to the current technical and analytical strategy limitations to characterise tumour-associated bacteria. Methods Here, we propose an approach to detect bacterial signals in human RNA sequencing data and associate them with the clinical and molecular properties of the tumours. The method was tested on public datasets from The Cancer Genome Atlas, and its accuracy was assessed on a new cohort of colorectal cancer patients. Results Our analysis shows that intratumoural microbiome composition is correlated with survival, anatomic location, microsatellite instability, consensus molecular subtype and immune cell infiltration in colon tumours. In particular, we find Faecalibacterium prausnitzii, Coprococcus comes, Bacteroides spp., Fusobacterium spp. and Clostridium spp. to be strongly associated with tumour properties. Conclusions We implemented an approach to concurrently analyse clinical and molecular properties of the tumour as well as the composition of the associated microbiome. Our results may improve patient stratification and pave the path for mechanistic studies on microbiota-tumour crosstalk.https://doi.org/10.1186/s13073-023-01180-9Tumour microbiomeRNA-Seq data deconvolutionMicrobe-tumour interactionMicrobiome biomarker |
| spellingShingle | Gaia Sambruni Angeli D. Macandog Jakob Wirbel Danilo Cagnina Carlotta Catozzi Tiziano Dallavilla Francesca Borgo Nicola Fazio Uberto Fumagalli-Romario Wanda L. Petz Teresa Manzo Simona P. Ravenda Georg Zeller Luigi Nezi Martin H. Schaefer Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data Genome Medicine Tumour microbiome RNA-Seq data deconvolution Microbe-tumour interaction Microbiome biomarker |
| title | Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data |
| title_full | Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data |
| title_fullStr | Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data |
| title_full_unstemmed | Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data |
| title_short | Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data |
| title_sort | location and condition based reconstruction of colon cancer microbiome from human rna sequencing data |
| topic | Tumour microbiome RNA-Seq data deconvolution Microbe-tumour interaction Microbiome biomarker |
| url | https://doi.org/10.1186/s13073-023-01180-9 |
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