Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity
Abstract Recent advancements in probe-based, full-transcriptome technologies for FFPE tissues, such as Visium CytAssist, Chromium Flex, and GeoMx DSP, enable analysis of archival samples, facilitating the generation of data from extensive cohorts. However, these methods can be labor-intensive and co...
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| Format: | Article |
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Nature Portfolio
2025-05-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-59005-9 |
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| author | Yixing Dong Chiara Saglietti Quentin Bayard Almudena Espin Perez Sabrina Carpentier Daria Buszta Stephanie Tissot Rémy Dubois Atanas Kamburov Senbai Kang Carla Haignere Rita Sarkis Sylvie Andre Marina Alexandre Gaveta Silvia Lopez Lastra Nathalie Piazzon Rita Santos Katharina von Loga Caroline Hoffmann George Coukos Solange Peters Vassili Soumelis Eric Yves Durand Laurence de Leval Raphael Gottardo Krisztian Homicsko Elo Madissoon |
| author_facet | Yixing Dong Chiara Saglietti Quentin Bayard Almudena Espin Perez Sabrina Carpentier Daria Buszta Stephanie Tissot Rémy Dubois Atanas Kamburov Senbai Kang Carla Haignere Rita Sarkis Sylvie Andre Marina Alexandre Gaveta Silvia Lopez Lastra Nathalie Piazzon Rita Santos Katharina von Loga Caroline Hoffmann George Coukos Solange Peters Vassili Soumelis Eric Yves Durand Laurence de Leval Raphael Gottardo Krisztian Homicsko Elo Madissoon |
| author_sort | Yixing Dong |
| collection | DOAJ |
| description | Abstract Recent advancements in probe-based, full-transcriptome technologies for FFPE tissues, such as Visium CytAssist, Chromium Flex, and GeoMx DSP, enable analysis of archival samples, facilitating the generation of data from extensive cohorts. However, these methods can be labor-intensive and costly, requiring informed selection based on research objectives. We compare these methods on FFPE tumor samples in Breast, NSCLC and DLBCL showing 1) good-quality, highly reproducible data from all methods; 2) GeoMx data containing cell mixtures despite marker-based preselection; 3) Visium and Chromium outperform GeoMx in discovering tumor heterogeneity and potential drug targets. We recommend the use of Visium and Chromium for high-throughput and discovery projects, while the manually more challenging GeoMx platform with targeted regions remains valuable for specialized questions. |
| format | Article |
| id | doaj-art-e63c8c51df484be4b26b236ff5fc5c30 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-e63c8c51df484be4b26b236ff5fc5c302025-08-20T03:53:58ZengNature PortfolioNature Communications2041-17232025-05-0116111810.1038/s41467-025-59005-9Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneityYixing Dong0Chiara Saglietti1Quentin Bayard2Almudena Espin Perez3Sabrina Carpentier4Daria Buszta5Stephanie Tissot6Rémy Dubois7Atanas Kamburov8Senbai Kang9Carla Haignere10Rita Sarkis11Sylvie Andre12Marina Alexandre Gaveta13Silvia Lopez Lastra14Nathalie Piazzon15Rita Santos16Katharina von Loga17Caroline Hoffmann18George Coukos19Solange Peters20Vassili Soumelis21Eric Yves Durand22Laurence de Leval23Raphael Gottardo24Krisztian Homicsko25Elo Madissoon26Biomedical Data Science Center, Lausanne University Hospital; University of LausanneInstitute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of LausanneOwkinOwkinOwkinDepartment of Oncology, Lausanne University Hospital; Swiss Cancer Center LemanDepartment of Oncology, Lausanne University Hospital; Swiss Cancer Center LemanOwkinOwkinBiomedical Data Science Center, Lausanne University Hospital; University of LausanneOwkinInstitute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of LausanneDepartment of Oncology, Lausanne University Hospital; Swiss Cancer Center LemanDepartment of Oncology, Lausanne University Hospital; Swiss Cancer Center LemanOwkinInstitute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of LausanneOwkinOwkinOwkinDepartment of Oncology, Lausanne University Hospital; Swiss Cancer Center LemanDepartment of Oncology, Lausanne University Hospital; Swiss Cancer Center LemanOwkinOwkinInstitute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of LausanneBiomedical Data Science Center, Lausanne University Hospital; University of LausanneDepartment of Oncology, Lausanne University Hospital; Swiss Cancer Center LemanOwkinAbstract Recent advancements in probe-based, full-transcriptome technologies for FFPE tissues, such as Visium CytAssist, Chromium Flex, and GeoMx DSP, enable analysis of archival samples, facilitating the generation of data from extensive cohorts. However, these methods can be labor-intensive and costly, requiring informed selection based on research objectives. We compare these methods on FFPE tumor samples in Breast, NSCLC and DLBCL showing 1) good-quality, highly reproducible data from all methods; 2) GeoMx data containing cell mixtures despite marker-based preselection; 3) Visium and Chromium outperform GeoMx in discovering tumor heterogeneity and potential drug targets. We recommend the use of Visium and Chromium for high-throughput and discovery projects, while the manually more challenging GeoMx platform with targeted regions remains valuable for specialized questions.https://doi.org/10.1038/s41467-025-59005-9 |
| spellingShingle | Yixing Dong Chiara Saglietti Quentin Bayard Almudena Espin Perez Sabrina Carpentier Daria Buszta Stephanie Tissot Rémy Dubois Atanas Kamburov Senbai Kang Carla Haignere Rita Sarkis Sylvie Andre Marina Alexandre Gaveta Silvia Lopez Lastra Nathalie Piazzon Rita Santos Katharina von Loga Caroline Hoffmann George Coukos Solange Peters Vassili Soumelis Eric Yves Durand Laurence de Leval Raphael Gottardo Krisztian Homicsko Elo Madissoon Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity Nature Communications |
| title | Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity |
| title_full | Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity |
| title_fullStr | Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity |
| title_full_unstemmed | Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity |
| title_short | Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity |
| title_sort | transcriptome analysis of archived tumors by visium geomx dsp and chromium reveals patient heterogeneity |
| url | https://doi.org/10.1038/s41467-025-59005-9 |
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