Analysis of functional tissue motifs for precision medicine in metastatic breast cancer

Informazioni relative al progetto

Precision Motifs

ID dell’accordo di sovvenzione: 866074

DOI

10.3030/866074

Progetto chiuso

Data della firma CE 29 Maggio 2020

Data di avvio 1 Settembre 2020

Data di completamento 31 Agosto 2025

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale

€ 2 000 000,00

Contributo UE

€ 2 000 000,00

Coordinato da

UNIVERSITAT ZURICH
Switzerland

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Pubblicazioni

Peer reviewed articles (39)

High-Dimensional T Helper Cell Profiling Reveals a Broad Diversity of Stably Committed Effector States Uncovers Interlineage Relationships

Autori: Luigi Tortola, Andrea Jacobs, Lea Pohlmeier, Franz-Josef Obermair, Franziska Ampenberger, Bernd Bodenmiller, Manfred Kopf.
Pubblicato in: Immunity, 2020, ISSN 2666-3791
Editore: Elsevier
DOI: 10.1016/j.immuni.2020.07.001

Clonal fitness inferred from time-series modelling of single-cell cancer genomes

Autori: Sohrab Salehi, Farhia Kabeer, Nicholas Ceglia, Mirela Andronescu, Marc J. Williams, Kieran R. Campbell, Themina Masud, Beixi Wang, Justina Biele, Jazmine Brimhall, David Gee, Hakwoo Lee, Jerome Ting, Allen W. Zhang, Hoa Tran, Ciara O'Flanagan, Fatemeh Dorri, Nicole Rusk, Teresa de Algara, So Ra Lee, Brian Y.C. Cheng, Peter Eirew, Takako Kono, Jenifer Pham, Diljot Grewal, Daniel Lai, Richard Moore,
Pubblicato in: Nature, 2021, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s41586-021-03648-3

Standardization of Suspension and Imaging Mass Cytometry Single‐Cell Readouts for Clinical Decision Making

Autori: Ruben Casanova, Shuhan Xu, Pierre Bost, Sujana Sivapatham, Andrea Jacobs, Stefanie Engler, null null, Mitchell P. Levesque, Reinhard Dummer, Bernd Bodenmiller, Stéphane Chevrier
Pubblicato in: Cytometry Part A, Numero 107, 2025, Pagina/e 390-403, ISSN 1552-4922
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/cyto.a.24940

Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd

Autori: Attila Gabor, Marco Tognetti, Alice Driessen, Jovan Tanevski, Baosen Guo, Wencai Cao, He Shen, Thomas Yu Verena Chung, Single Cell Signaling in Breast Cancer DREAM Consortium members, Bernd Bodenmiller1, Julio Saez-Rodriguez1
Pubblicato in: Molecular Systems Biology, Numero 2021 Oct;17(10), 2021, ISSN 1744-4292
Editore: Nature Publishing Group
DOI: 10.15252/msb.202110402

Multiplex protein imaging in tumour biology

Autori: Natalie de Souza, Shan Zhao, Bernd Bodenmiller
Pubblicato in: Nature Reviews Cancer, Numero 24, 2024, Pagina/e 171-191, ISSN 1474-175X
Editore: Nature Publishing Group
DOI: 10.1038/s41568-023-00657-4

Mass cytometric and transcriptomic profiling of epithelial-mesenchymal transitions in human mammary cell lines.

Autori: Johanna Wagner, Markus, Masek, Andrea Jacobs, Charlotte Soneson, Sujana Sivapatham, Nicolas Damond, Natalie de Souza, Mark D. Robinson, Bernd Bodenmiller.
Pubblicato in: Scientific Data, Numero 2022 Apr;7(70), 2022, ISSN 2052-4463
Editore: Nature Publishing Group
DOI: 10.1038/s41597-022-01137-4

Establishing standardized immune phenotyping of metastatic melanoma by digital pathology.

Autori: Bettina Sobottka, Marta Nowak, Anja L. Frei, Martina Haberecker, Samuel Merki, Tumor Profiler consortium, Mitchell P. Levesque, Reinhard Dummer, Holger Moch, Viktor H. Koelzer.
Pubblicato in: Laboratory Investigation, Numero 2021 Dec;101(12, 2021, ISSN 0023-6837
Editore: Nature Publishing Group
DOI: 10.1038/s41374-021-00653-y

A stratification system for breast cancer based on basoluminal tumor cells and spatial tumor architecture

Autori: Lasse Meyer, Hartland W. Jackson, Nils Eling, Shan Zhao, Genki Usui, Haithem Dakhli, Peter Schraml, Susanne Dettwiler, Constanze Elfgen, Zsuzsanna Varga, Holger Moch, Natalie de Souza, Bernd Bodenmiller
Pubblicato in: Cancer Cell, Numero 43, 2025, Pagina/e 1637-1655.e9, ISSN 1535-6108
Editore: Cell Press
DOI: 10.1016/j.ccell.2025.06.019

A comprehensive single-cell map of T cell exhaustion-associated immune environments in human breast cancer

Autori: Sandra Tietscher, Johanna Wagner, Tobias Anzeneder, Claus Langwieder, Martin Rees, Bettina Sobottka, Natalie de Souza, Bernd Bodenmiller
Pubblicato in: Nature Communications, Numero 14, 2023, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-022-35238-w

Cancer Research in the Age of Spatial Omics: Lessons from IMAXT

Autori: Dario Bressan, null null, Nicholas Walton, Gregory J. Hannon, null null, Mohammad Al Sa’d, Bruno Albuquerque, Hamid Raza Ali, Martina Alini, Samuel Aparicio, Heather Ashmore, Thomas Ashmore, Vinci Au, Shankar Balasubramanian, Caroline Baril, Giorgia Battistoni, Sean Beatty, Robby Becker, Bernd Bodenmiller, Alina Bollhagen, Carla Boquetale, Edward S. Boyden, Dario Bressan, Alejandra Bruna, Marcel
Pubblicato in: Cancer Discovery, Numero 15, 2025, Pagina/e 16-21, ISSN 2159-8274
Editore: American Association for Cancer Research Inc.
DOI: 10.1158/2159-8290.cd-24-1686

Landscapes of cellular phenotypic diversity in breast cancer xenografts and their impact on drug response

Autori: Dimitra Georgopoulou, Maurizio Callari, Oscar M. Rueda, Abigail Shea,. Alistair Martin, Agnese Giovannetti, Fatime Qosaj, Ali Dariush, Suet-Feung Chin, Larissa S. Carnevalli, Elena Provenzano, Wendy Greenwood, Giulia Lerda, Elham Esmaeilishirazifard, Martin O'Reilly, Violeta Serra, Dario Bressan, IMAXT Consortium, Gordon B. Mills, H. Raza Ali, Sabina S Cosulich, Gregory J. Hannon, Alejandra Bruna,
Pubblicato in: Nature Communications, Numero Mar 31;12(1), 2021, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-22303-z

Profound dysregulation of T cell homeostasisand function in patients with severe COVID-19.

Autori: Sarah Adamo, Stéphane Chevrier, Carlo Cervia, Yves Zurbuchen, Miro E. Raeber, Lilinae Yang, Sujana Sivapatham, Andrea Jacobs, Esther Baechli, Alain Rudiger, Melina Stüssi-Helbling, Lars C. Huber, Dominik J. Schaer, Bernd Bodenmiller1, Onur Boyman1, Jakob Nilsson1.
Pubblicato in: Allergy, Numero Apr 21, 2021, ISSN 0105-4538
Editore: Blackwell Publishing Inc.
DOI: 10.1111/all.14866

LifeTime improving European healthcare through cell-based interceptive medicine

Autori: Nikolaus Rajewsky, Geneviève Almouzni, Stanislaw A. Gorski, Stein Aerts, Ido Amit, Michela G. Bertero, Christoph Bock, Annelien L. Bredenoord, Giacomo Cavall, Susanne Chiocca, Hans Clevers, Bart De Strooper, Angelika Eggert, Jan Ellenberg, Xosé M. Fernández, Marek Figlerowicz, Susan M. Gasser, Norbert Hubner, Jorgen Kjems, Jürgen A. Knoblich, Grietje Krabbe, Peter Lichter, Sten Linnarsson, Jea
Pubblicato in: Nature, 2020, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s41586-020-2715-9

Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data

Autori: Nils Eling, Nicolas Damond, Tobias Hoch, Bernd Bodenmiller
Pubblicato in: Bioinformatics, 2020, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btaa1061

Monogenic Diabetes and Integrated Stress Response Genes Display Altered Gene Expression in Type 1 Diabetes.

Autori: Helmut Hiller, Dawn E. Beachy, Jospeh J. Lebowitz, Stefanie Engler, Justin R. Mason, Douglas R. Miller, Irina Kusmarteva, Laura M. Jacobsen, Amanda L. Posgai, Habibeh Khoshbouei, Richard A. Oram, Desmond A. Schatz, Andrew T. Hattersley, Bernd Bodenmiller, Mark A. Atkinson, Harry S. Nick, Clive H. Wasserfall
Pubblicato in: Diabetes, Numero 2021 Aug;70(8), 2021, ISSN 0012-1797
Editore: American Diabetes Association
DOI: 10.2337/db21-0070

Statistical modeling and analysis of cell counts from multiplexed imaging data

Autori: Pierre Bost, Ruben Casanova, Uria Mor, Martina Haberecker, Chantal Pauli, Susanne Dettwiler, Bernd Bodenmiller
Pubblicato in: Cell Systems, Numero 16, 2025, Pagina/e 101296, ISSN 2405-4712
Editore: Elsevier BV
DOI: 10.1016/j.cels.2025.101296

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

Autori: Shahar Alon, Daniel R. Goodwin, Anubhav Sinha, Asmamaw T. Wassie, Fei Chen, Evan R. Daugharthy, Yosuke Bando, Atsushi Kajita, Andrew Xue, Karl Marrett, Robert Prior, Yi Cui, Andrew C. Payne, Chun-Chen Yao, Ho-Jun Suk, Ru Wang, Chih-Chieh Jay Yu, Paul Tillberg, Paul Reginato, Nikita Pak, Songlei Liu, Sukanya Punthambaker, Eswar P.R. Iyer, Richie E. Kohman, Jeremy A. Miller, Ed S. Lein, Ana Lako, Ni
Pubblicato in: Science, 2021, ISSN 0036-8075
Editore: American Association for the Advancement of Science
DOI: 10.1126/science.aax2656

A quantitative analysis of the interplay of environment, neighborhood, cell state in 3D spheroids

Autori: Vito R.T. Zanotelli, Matthias Leutenegger, Xiao-Kang Lun, Fanny Georgi, Natalie de Souza, Bernd Bodenmiller
Pubblicato in: Molecular Systems Biology, 2020, ISSN 1744-4292
Editore: Nature Publishing Group
DOI: 10.15252/msb.20209798

Precision Oncology Program (POP), an observational study using real-world data and imaging mass cytometry to explore decision support for the Molecular Tumor Board: study protocol

Autori: Laura Amanda Boos, Christian Doerig, Gabriele Gut, Nicola Miglino, Luis Fábregas Ibáñez, Shemra Rizzo, Charlotta Schärfe Fruechtenicht, Nandini Chitale, Charles Lu, Martin Zoche, Bernd Bodenmiller, Stephane Chevrier, Alexandra Sophia Eklund, Marta Nowak, Sepehr Rahmani Khajouei, Carmen Galani Berardo, Lukasz Kaczmarek, Karin Bosshard, William Archey, Matthias Bodmer, Dominik Glinz, Eva Camaril
Pubblicato in: BMJ Open, Numero 15, 2025, Pagina/e e096591, ISSN 2044-6055
Editore: BMJ Publishing Group
DOI: 10.1136/bmjopen-2024-096591

Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment

Autori: Laura Kuett, Raul Catena, Alaz Özcan, Alex Plüss A, Cancer Grand Challenges IMAXT Consortium, Peter Schraml, Holger Moch, Natalie de Souza, Bernd Bodenmiller.
Pubblicato in: Nature Cancer, Numero 2022 Jan;3(1):, 2022, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s43018-021-00301-w

cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data

Autori: Lasse Meyer, Nils Eling, Bernd Bodenmiller
Pubblicato in: BMC Bioinformatics, Numero 25, 2024, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859-023-05546-z

Sensitive detection of minimal residual disease and immunotherapy targets by multi-modal bone marrow analysis in high-risk neuroblastoma – a multi-center study

Autori: Nina U. Gelineau, Eva Bozsaky, Lieke M. J. van Zogchel, Fikret Rifatbegovic, Daria Lazic, Andrea Ziegler, Ahmad Javadi, Lily Zappeij-Kannegieter, Ulrike Pötschger, Marta Fiocco, Peter F. Ambros, Inge M. Ambros, Bernd Bodenmiller, Ellen C. van der Schoot, Ruth Ladenstein, Marie Bernkopf, Godelieve A. M. Tytgat, Sabine Taschner-Mandl
Pubblicato in: Journal of Experimental & Clinical Cancer Research, Numero 44, 2025, ISSN 1756-9966
Editore: Springer Science and Business Media LLC
DOI: 10.1186/s13046-025-03481-w

Distant Metastases of Breast Cancer Resemble Primary Tumors in Cancer Cell Composition but Differ in Immune Cell Phenotypes

Autori: Laura Kuett, Alina Bollhagen, Sandra Tietscher, Bettina Sobottka, Nils Eling, Zsuzsanna Varga, Holger Moch, Natalie de Souza, Bernd Bodenmiller
Pubblicato in: Cancer Research, Numero 85, 2025, Pagina/e 15-31, ISSN 0008-5472
Editore: American Association for Cancer Research
DOI: 10.1158/0008-5472.can-24-1211

Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia.

Autori: Junyan Lu, Ester Cannizzaro, Fabienne Meier-Abt, Sebastian Scheinost, Peter-Martin Bruch, Holly A. Giles, Almut Lütge, Jennifer Hüllein, Lena Wagner, Brian Giacopelli, Ferran Nadeu, Julio Delgado, Elias Campo, Maurizio Mangolini, Ingo Ringshausen, Martin Böttcher, Dimitros Mougiakakos, Andrea Jacobs, Bernd Bodenmiller, Sascha Dietrich, Christopher C. Oakes, Thorsten Zenz, Wolfgang Huber.
Pubblicato in: Nature Cancer, Numero 2021 Aug;2(8), 2021, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s43018-021-00216-6

SCIM: universal single-cell matching with unpaired feature sets

Autori: Stefan G. Stark, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Tumor Profiler Consortium, Gunnar Rätsch, Kjong-Van Lehmann
Pubblicato in: Bioinformatics, 2020, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btaa843

Cutaneous and systemic hyperinflammation drives maculopapular drug exanthema in severely ill COVID-19 patients.

Autori: Ysutaka Mitamura, Daniel Schulz, Saskia Oro, Nick Li, Isabel Kolm, Claudia Lang, Reihane Ziadlou, Ge Tan, Bernd Bodenmiller, Peter Steiger, Angelo Marzano, Nicolas de Prost, Olivier Caudin, Mitchell Levesque, Corinne Stoffel, Peter Schmid-Grendelmeier, Emanual Maverakis, Cezim A. Akdis, Marie-Charlotte Brüggen.
Pubblicato in: Allergy, Numero 2021 Jun 22, 2021, ISSN 0105-4538
Editore: Blackwell Publishing Inc.
DOI: 10.1111/all.14983

Feasibility of multiomics tumor profiling for guiding treatment of melanoma

Autori: Nicola Miglino, Nora C. Toussaint, Alexander Ring, Ximena Bonilla, Marina Tusup, Benedict Gosztonyi, Tarun Mehra, Gabriele Gut, Francis Jacob, Stephane Chevrier, Kjong-Van Lehmann, Ruben Casanova, Andrea Jacobs, Sujana Sivapatham, Laura Boos, Parisa Rahimzadeh, Manuel Schuerch, Bettina Sobottka, Natalia Chicherova, Shuqing Yu, Rebekka Wegmann, Julien Mena, Emanuela S. Milani, Sandra Goetze, Cinzia
Pubblicato in: Nature Medicine, Numero 31, 2025, Pagina/e 2430-2441, ISSN 1078-8956
Editore: Nature Publishing Group
DOI: 10.1038/s41591-025-03715-6

An end-to-end workflow for multiplexed image processing and analysis

Autori: Jonas Windhager, Vito Riccardo Tomaso Zanotelli, Daniel Schulz, Lasse Meyer, Michelle Daniel, Bernd Bodenmiller, Nils Eling
Pubblicato in: Nature Protocols, Numero 18, 2023, Pagina/e 3565-3613, ISSN 1754-2189
Editore: Nature Publishing Group
DOI: 10.1038/s41596-023-00881-0

Breast tumor microenvironment structures are associated with genomic features and clinical outcome.

Autori: Esther Danenberg, Helen Bardwell, Vito R.T.Zanotelli, Elena Provenzano, Suet-Fueng Chin, Oscar M. Rueda Andrew Green, Emad Rakha, Samuel Aparicio, Ian O. Ellis, Bernd Bodenmiller1, Carlos Caldas1, H. Raza Ali1.
Pubblicato in: Nature Genetics, Numero 2022 Apr 18, 2022, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s41588-022-01041-y

Multielement Z-tag imaging by X-ray fluorescence microscopy for next-generation multiplex imaging

Autori: Merrick Strotton, Tsuyoshi Hosogane, Marco di Michiel, Holger Moch, Zsuzsanna Varga, Bernd Bodenmiller
Pubblicato in: Nature Methods, Numero 20, 2023, Pagina/e 1310-1322, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-023-01977-x

Classifying cancer-associated fibroblasts—The good, the bad, and the target

Autori: Lena Cords, Natalie de Souza, Bernd Bodenmiller
Pubblicato in: Cancer Cell, Numero 42, 2025, Pagina/e 1480-1485, ISSN 1535-6108
Editore: Cell Press
DOI: 10.1016/j.ccell.2024.08.011

Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition.

Autori: James D. Wade, Xiao-Kang Lun, Nevena Zivanovic, Eberhard O. Voit1, Bernd Bodenmiller1
Pubblicato in: Frontiers in Physiology, 2020, ISSN 1664-042x
Editore: Frontiers Research Foundation
DOI: 10.3389/fphys.2020.579117

A distinct innate immune signature marks progression from mild to severe COVID-19

Autori: Stéphane Chevrier, Yves Zurbuchen, Carlo Cervia, Sarah Adamo, Miro E. Raeber, Natalie de Souza, Sujana Sivapatham, Andrea Jacobs, Esther Bachli, Alain Rudiger, Melina Stüssi-Helbling, Lars C. Huber, Dominik J. Schaer, Jakob Nilsson1, Onur Boyman1, Bernd Bodenmiller1.
Pubblicato in: Cell Reports Medicine, 2020, ISSN 2666-3791
Editore: Cell Press (Elsevier)
DOI: 10.1016/j.xcrm.2020.100166

Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy.

Autori: Tobias Hoch, Daniel Schulz, Nils Eling, Julia Martínez Gómez, Mitchell P. Levesque, Bernd Bodenmiller
Pubblicato in: Science Immunology, Numero 2022 Apr;7(70, 2022, ISSN 2470-9468
Editore: American Association for the Advancement of Science
DOI: 10.1126/sciimmunol.abk1692

DNA-barcoded signal amplification for imaging mass cytometry enables sensitive and highly multiplexed tissue imaging

Autori: Tsuyoshi Hosogane, Ruben Casanova, Bernd Bodenmiller
Pubblicato in: Nature Methods, Numero 20, 2023, Pagina/e 1304-1309, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-023-01976-y

Compressed sensing expands the multiplexity of imaging mass cytometry

Autori: Tsuyoshi Hosogane, Leonor Schubert Santana, Nils Eling, Holger Moch, Bernd Bodenmiller
Pubblicato in: Nature Communications, Numero 16, 2025, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-025-66629-4

Cancer-associated fibroblast classification in single-cell and spatial proteomics data

Autori: Lena Cords, Sandra Tietscher, Tobias Anzeneder, Claus Langwieder, Martin Rees, Natalie de Souza, Bernd Bodenmiller
Pubblicato in: Nature Communications, Numero 14, 2023, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-023-39762-1

Integrating Formalin-Fixed, Paraffin-Embedded–Derived Whole-Genome Sequencing into Routine Molecular Pathology

Autori: Cassandra Litchfield, Ronny Nienhold, Andreas Wicki, Michael Schmid, Domingo Aguilera-Garcia, Viktor Hendrik Koelzer, Rudolf Aebersold, Melike Ak, Faisal S. Al-Quaddoomi, Silvana I. Albert, Jonas Albinus, Ilaria Alborelli, Sonali Andani, Per-Olof Attinger, Marina Bacac, Monica-Andreea Baciu-Drăgan, Daniel Baumhoer, Beatrice Beck-Schimmer, Niko Beerenwinkel, Christian Beisel, Lara Bernasconi, Anne
Pubblicato in: The Journal of Molecular Diagnostics, Numero 27, 2025, Pagina/e 722-735, ISSN 1525-1578
Editore: American Society for Investigative Pathology
DOI: 10.1016/j.jmoldx.2025.04.011

Optimizing multiplexed imaging experimental design through tissue spatial segregation estimation

Autori: Pierre Bost, Daniel Schulz, Stefanie Engler, Clive Wasserfall, Bernd Bodenmiller
Pubblicato in: Nature Methods, Numero 20, 2023, Pagina/e 418-423, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-022-01692-z