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 von Loga; Caroline Hoffmann; George Coukos; Solange Peters; Vassili Soumelis; Eric Yves Durand; Laurence de Leval; Raphael Gottardo; Krisztian Homicsko; Elo Madissoon

doi:10.1038/s41467-025-59005-9

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

Nat Commun. 2025 May 12;16(1):4400. doi: 10.1038/s41467-025-59005-9.

Authors

Yixing Dong¹, Chiara Saglietti², Quentin Bayard³, Almudena Espin Perez³, Sabrina Carpentier³, Daria Buszta⁴, Stephanie Tissot^{4

5}, Rémy Dubois³, Atanas Kamburov³, Senbai Kang¹, Carla Haignere³, Rita Sarkis², Sylvie Andre^{4

5

6}, Marina Alexandre Gaveta^{4

5

6}, Silvia Lopez Lastra³, Nathalie Piazzon², Rita Santos³, Katharina von Loga³, Caroline Hoffmann³, George Coukos^{4

5

6}, Solange Peters⁴, Vassili Soumelis³, Eric Yves Durand³, Laurence de Leval^#⁷, Raphael Gottardo^#^{8

9

10

11}, Krisztian Homicsko^#^{12

13

14}, Elo Madissoon^#¹⁵

Affiliations

¹ Biomedical Data Science Center, Lausanne University Hospital; University of Lausanne, Lausanne, Switzerland.
² Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
³ Owkin, Paris, France.
⁴ Department of Oncology, Lausanne University Hospital; Swiss Cancer Center Leman, Lausanne, Switzerland.
⁵ Ludwig Insitute for Cancer Research, Lausanne, Switzerland.
⁶ Agora Translational Research Center, Lausanne, Switzerland.
⁷ Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland. Laurence.DeLeval@chuv.ch.
⁸ Biomedical Data Science Center, Lausanne University Hospital; University of Lausanne, Lausanne, Switzerland. Raphael.Gottardo@chuv.ch.
⁹ Agora Translational Research Center, Lausanne, Switzerland. Raphael.Gottardo@chuv.ch.
¹⁰ Swiss Institute of Bioinformatics, Lausanne, Switzerland. Raphael.Gottardo@chuv.ch.
¹¹ School of Life Sciences, Ecole Polytechnique Fédérale de, Lausanne, Switzerland. Raphael.Gottardo@chuv.ch.
¹² Department of Oncology, Lausanne University Hospital; Swiss Cancer Center Leman, Lausanne, Switzerland. Krisztian.Homicsko@chuv.ch.
¹³ Ludwig Insitute for Cancer Research, Lausanne, Switzerland. Krisztian.Homicsko@chuv.ch.
¹⁴ Agora Translational Research Center, Lausanne, Switzerland. Krisztian.Homicsko@chuv.ch.
¹⁵ Owkin, Paris, France. elo.madissoon@owkin.com.

^# Contributed equally.

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.

MeSH terms

Breast Neoplasms / genetics
Female
Gene Expression Profiling* / methods
Humans
Lung Neoplasms / genetics
Neoplasms* / genetics
Paraffin Embedding
Transcriptome*

Grants and funding

320030_215550/Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)