Feasibility of multiomics tumor profiling for guiding treatment of melanoma

There is limited evidence supporting the feasibility of using omics and functional technologies to inform treatment decisions. Here we present results from a cohort of 116 melanoma patients in the prospective, multicentric observational Tumor Profiler (TuPro) precision oncology project. Nine independent technologies, mostly at single-cell level, were used to analyze 126 patient samples, generating up to 500 Gb of data per sample (40,000 potential markers) within 4 weeks. Among established and experimental markers, the molecular tumor board selected 54 to inform its treatment recommendations. In 75% of cases, TuPro-based data were judged to be useful in informing recommendations. Patients received either standard of care (SOC) treatments or highly individualized, polybiomarker-driven treatments (beyond SOC). The objective response rate in difficult-to-treat palliative, beyond SOC patients (n = 37) was 38%, with a disease control rate of 54%. Progression-free survival of patients with TuPro-informed therapy decisions was 6.04 months, (95% confidence interval, 3.75-12.06) and 5.35 months (95% confidence interval, 2.89-12.06) in ≥third therapy lines. The proof-of-concept TuPro project demonstrated the feasibility and relevance of omics-based tumor profiling to support data-guided clinical decision-making. ClinicalTrials.gov identifier: NCT06463509 .

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Publication Details

Journal
Nature Medicine
Published
2025-05-27
DOI
https://doi.org/10.1038/s41591-025-03715-6
Citations
9
Primary Topic
CAR-T cell therapy research
Type
article
Field-Weighted Citation Impact
9.41

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article

Feasibility of multiomics tumor profiling for guiding treatment of melanoma

Rebekka Wegmann, René Holtackers, Viktor Hendrik Koelzer, Faisal Alquaddoomi et al.
9 citations
Nature Medicine
CAR-T cell therapy research
9.41
article

Feasibility of multiomics tumor profiling for guiding treatment of melanoma

Rebekka Wegmann, René Holtackers, Viktor Hendrik Koelzer, Faisal Alquaddoomi, Laurie Prélot, Marina Bacac, Jonas Albinus, Audrey van Drogen, María Lourdes Rosano-González, André Fedier, Marina Tusup, Marcus Vetter, Sujana Sivapatham, Franziska Singer, Stefanie Engler, Ricardo Coelho, Markus Gabriel Manz, Patrick G. A. Pedrioli, Bernd Bodenmiller, Lars Bosshard, Andreas N. WICKI, Linda Grob, Natalia Chicherova, Daniel Baumhoer, Michael Weller, Tobias Schär, Beatrice Beck‐Schimmer, Gabriela Senti, Stefan Nicolet, Petra Catalina Schwalie, Christian P. Kunze, Kjong-Van Lehmann, Martin Mehnert, Fabian Wendt, Cinzia Esposito, Lara Bernasconi, Flavio C. Lombardo, Katja Eschbach, Lucas Pelkmans, Martin Erkens, Alexander Ring, Severin Schwan, Gregor Zuend, Laura Boos, Alice K. Jacobs, Mitchell Paul Levesque, Bettina Sobottka, Vipin T. Sreedharan, Shuqing Yu, Abdullah Kahraman, Detlef Günther, Melike Ak, Nicola Miglino, Gunnar Rätsch, Niko Beerenwinkel, Michael Prummer, Sandra Goetze, Stefan G. Stark, Jack Kuipers, Tatjana Vlajnic, Esther Danenberg, Ruben Casanova, Francis Jacob, Per-Olof Attinger, Johanna Ziegler, Pedro Ferreira, Tamara Huesser, Berend Snijder, Anja Frei, Julian M. Metzler, Bruno S. Frey, Gabriele Gut, Ximena Bonilla, Wenguang Shao, Salvatore Piscuoglio, Ilaria Alborelli, Simone E. Muenst, Mattheus H. E. Wildschut, Mónica Núñez López, Ruedi Aebersold, Norbert Wey, Christian Beisel, Tinu M. Thomas, Viola A Heinzelmann-Schwarz, Ramona Schlenker, Charlotte K.Y. Ng, Anne Bertolini, Christian Rommel, Martin Zoche, Maya D’Costa, Alva Rani James, Ulrike Lischetti, Anja Irmisch, Alexander Immer, Werner Kuebler, Stéphane Chevrier, André Kahles, Bernd Wollscheid, Mustafa A. Tuncel, Philip M. Jermann, Sandra Weber, Emanuela S. Milani, Natascha Santacroce, Benedict Gosztonyi, Tarun Mehra, Julien Mena, Markus Tolnay, Holger Moch, Natalie R. Davidson, Pirmin Haeuptle, Nora C. Toussaint, Vinko Toševski, Jacobo Sarabia del Castillo, William P. Weber, Sebastian Lugert, Tanmay Tanna, Daniel J. Stekhoven, Natalie Rimmer, Monica-Andreea Baciu-Drăgan, Reinhard Dummer, Alexandre Theocharides, Philipp Markolin, Christian Kurzeder, Joanna Ficek-Pascual, Marta Nowak, Riccardo Murri, Gerd Maass, Marc Zimmermann, Tim M. Jaeger, Mathilde Ritter, Silvana I. Albert, Parisa Rahimzadeh, Manuel Schuerch
article en
9 citations

Abstract

There is limited evidence supporting the feasibility of using omics and functional technologies to inform treatment decisions. Here we present results from a cohort of 116 melanoma patients in the prospective, multicentric observational Tumor Profiler (TuPro) precision oncology project. Nine independent technologies, mostly at single-cell level, were used to analyze 126 patient samples, generating up to 500 Gb of data per sample (40,000 potential markers) within 4 weeks. Among established and experimental markers, the molecular tumor board selected 54 to inform its treatment recommendations. In 75% of cases, TuPro-based data were judged to be useful in informing recommendations. Patients received either standard of care (SOC) treatments or highly individualized, polybiomarker-driven treatments (beyond SOC). The objective response rate in difficult-to-treat palliative, beyond SOC patients (n = 37) was 38%, with a disease control rate of 54%. Progression-free survival of patients with TuPro-informed therapy decisions was 6.04 months, (95% confidence interval, 3.75-12.06) and 5.35 months (95% confidence interval, 2.89-12.06) in ≥third therapy lines. The proof-of-concept TuPro project demonstrated the feasibility and relevance of omics-based tumor profiling to support data-guided clinical decision-making. ClinicalTrials.gov identifier: NCT06463509 .

Nature MedicineVol. 31(7)
Roche (Switzerland) (CH), University of Bern (CH), SIB Swiss Institute of Bioinformatics (CH), University of Basel (CH), University of Zurich (CH), University Hospital of Basel (CH), FHNW University of Applied Sciences and Arts Northwestern Switzerland (CH), ETH Zurich (CH), Institute for Biomedical Engineering (CH), Roche Pharma AG (Germany) (DE), University Hospital of Zurich (CH), Life Science Zurich (CH), Swiss Data Science Center (CH), CS Diagnostics (DE), RWTH Aachen University (DE)
F. Hoffmann-La Roche, Eidgenössische Technische Hochschule Zürich, Universität Zürich, Universitätsspital Zürich
Peace, Justice and strong institutions
Openalex Percentile: Top 2%
CAR-T cell therapy research
9.41
DOIOpen Access PDFOpenAlex
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