Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity

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 Loga, Caroline Hoffmann, George Coukos, Solange Peters, Vassili Soumelis, Eric Yves Durand, Laurence Leval (), Raphael Gottardo (), Krisztian Homicsko () and Elo Madissoon ()
Additional contact information
Yixing Dong: Lausanne University Hospital; University of Lausanne
Chiara Saglietti: Lausanne University Hospital and University of Lausanne
Quentin Bayard: Owkin
Almudena Espin Perez: Owkin
Sabrina Carpentier: Owkin
Daria Buszta: Lausanne University Hospital; Swiss Cancer Center Leman
Stephanie Tissot: Lausanne University Hospital; Swiss Cancer Center Leman
Rémy Dubois: Owkin
Atanas Kamburov: Owkin
Senbai Kang: Lausanne University Hospital; University of Lausanne
Carla Haignere: Owkin
Rita Sarkis: Lausanne University Hospital and University of Lausanne
Sylvie Andre: Lausanne University Hospital; Swiss Cancer Center Leman
Marina Alexandre Gaveta: Lausanne University Hospital; Swiss Cancer Center Leman
Silvia Lopez Lastra: Owkin
Nathalie Piazzon: Lausanne University Hospital and University of Lausanne
Rita Santos: Owkin
Katharina Loga: Owkin
Caroline Hoffmann: Owkin
George Coukos: Lausanne University Hospital; Swiss Cancer Center Leman
Solange Peters: Lausanne University Hospital; Swiss Cancer Center Leman
Vassili Soumelis: Owkin
Eric Yves Durand: Owkin
Laurence Leval: Lausanne University Hospital and University of Lausanne
Raphael Gottardo: Lausanne University Hospital; University of Lausanne
Krisztian Homicsko: Lausanne University Hospital; Swiss Cancer Center Leman
Elo Madissoon: Owkin

Nature Communications, 2025, vol. 16, issue 1, 1-18

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-59005-9

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