Molecular and functional landscape of malignant serous effusions for precision oncology

Rebekka Wegmann, Lorenz Bankel, Yasmin Festl, Kate Lau, Sohyon Lee, Fabian Arnold, Valentina Cappelletti, Aaron Fehr, Paola Picotti, Konstantin J. Dedes, Daniel Franzen, Daniela Lenggenhager, Peter K. Bode, Martin Zoche, Holger Moch, Christian Britschgi and Berend Snijder ()
Additional contact information
Rebekka Wegmann: ETH Zurich
Lorenz Bankel: ETH Zurich
Yasmin Festl: ETH Zurich
Kate Lau: ETH Zurich
Sohyon Lee: ETH Zurich
Fabian Arnold: University Hospital Zurich
Valentina Cappelletti: ETH Zurich
Aaron Fehr: ETH Zurich
Paola Picotti: ETH Zurich
Konstantin J. Dedes: University Hospital Zurich
Daniel Franzen: University Hospital Zurich
Daniela Lenggenhager: University Hospital Zurich
Peter K. Bode: University Hospital Zurich
Martin Zoche: University Hospital Zurich
Holger Moch: Comprehensive Cancer Center Zurich (CCCZ)
Christian Britschgi: University Hospital Zurich
Berend Snijder: ETH Zurich

Nature Communications, 2024, vol. 15, issue 1, 1-21

Abstract: Abstract Personalized treatment for patients with advanced solid tumors critically depends on the deep characterization of tumor cells from patient biopsies. Here, we comprehensively characterize a pan-cancer cohort of 150 malignant serous effusion (MSE) samples at the cellular, molecular, and functional level. We find that MSE-derived cancer cells retain the genomic and transcriptomic profiles of their corresponding primary tumors, validating their use as a patient-relevant model system for solid tumor biology. Integrative analyses reveal that baseline gene expression patterns relate to global ex vivo drug sensitivity, while high-throughput drug-induced transcriptional changes in MSE samples are indicative of drug mode of action and acquired treatment resistance. A case study exemplifies the added value of multi-modal MSE profiling for patients who lack genetically stratified treatment options. In summary, our study provides a functional multi-omics view on a pan-cancer solid tumor cohort and underlines the feasibility and utility of MSE-based precision oncology.

Date: 2024
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-52694-8

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DOI: 10.1038/s41467-024-52694-8

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