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

Informacje na temat projektu

Precision Motifs

Identyfikator umowy o grant: 866074

DOI

10.3030/866074

Projekt został zamknięty

Data podpisania przez KE 29 Maja 2020

Data rozpoczęcia 1 Września 2020

Data zakończenia 31 Sierpnia 2025

Finansowanie w ramach

• EXCELLENT SCIENCE - European Research Council (ERC)

Koszt całkowity

€ 2 000 000,00

Wkład UE

€ 2 000 000,00

Koordynowany przez

UNIVERSITAT ZURICH
Switzerland

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Publikacje

Peer reviewed articles (39)

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

Autorzy: Luigi Tortola, Andrea Jacobs, Lea Pohlmeier, Franz-Josef Obermair, Franziska Ampenberger, Bernd Bodenmiller, Manfred Kopf.
Opublikowane w: Immunity, 2020, ISSN 2666-3791
Wydawca: Elsevier
DOI: 10.1016/j.immuni.2020.07.001

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

Autorzy: 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,
Opublikowane w: Nature, 2021, ISSN 0028-0836
Wydawca: Nature Publishing Group
DOI: 10.1038/s41586-021-03648-3

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

Autorzy: Ruben Casanova, Shuhan Xu, Pierre Bost, Sujana Sivapatham, Andrea Jacobs, Stefanie Engler, null null, Mitchell P. Levesque, Reinhard Dummer, Bernd Bodenmiller, Stéphane Chevrier
Opublikowane w: Cytometry Part A, Numer 107, 2025, Strona(/y) 390-403, ISSN 1552-4922
Wydawca: 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

Autorzy: 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
Opublikowane w: Molecular Systems Biology, Numer 2021 Oct;17(10), 2021, ISSN 1744-4292
Wydawca: Nature Publishing Group
DOI: 10.15252/msb.202110402

Multiplex protein imaging in tumour biology

Autorzy: Natalie de Souza, Shan Zhao, Bernd Bodenmiller
Opublikowane w: Nature Reviews Cancer, Numer 24, 2024, Strona(/y) 171-191, ISSN 1474-175X
Wydawca: Nature Publishing Group
DOI: 10.1038/s41568-023-00657-4

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

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

Establishing standardized immune phenotyping of metastatic melanoma by digital pathology.

Autorzy: Bettina Sobottka, Marta Nowak, Anja L. Frei, Martina Haberecker, Samuel Merki, Tumor Profiler consortium, Mitchell P. Levesque, Reinhard Dummer, Holger Moch, Viktor H. Koelzer.
Opublikowane w: Laboratory Investigation, Numer 2021 Dec;101(12, 2021, ISSN 0023-6837
Wydawca: 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

Autorzy: 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
Opublikowane w: Cancer Cell, Numer 43, 2025, Strona(/y) 1637-1655.e9, ISSN 1535-6108
Wydawca: 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

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

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

Autorzy: 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
Opublikowane w: Cancer Discovery, Numer 15, 2025, Strona(/y) 16-21, ISSN 2159-8274
Wydawca: 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

Autorzy: 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,
Opublikowane w: Nature Communications, Numer Mar 31;12(1), 2021, ISSN 0028-0836
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-021-22303-z

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

Autorzy: 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.
Opublikowane w: Allergy, Numer Apr 21, 2021, ISSN 0105-4538
Wydawca: Blackwell Publishing Inc.
DOI: 10.1111/all.14866

LifeTime improving European healthcare through cell-based interceptive medicine

Autorzy: 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
Opublikowane w: Nature, 2020, ISSN 0028-0836
Wydawca: Nature Publishing Group
DOI: 10.1038/s41586-020-2715-9

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

Autorzy: Nils Eling, Nicolas Damond, Tobias Hoch, Bernd Bodenmiller
Opublikowane w: Bioinformatics, 2020, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btaa1061

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

Autorzy: 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
Opublikowane w: Diabetes, Numer 2021 Aug;70(8), 2021, ISSN 0012-1797
Wydawca: American Diabetes Association
DOI: 10.2337/db21-0070

Statistical modeling and analysis of cell counts from multiplexed imaging data

Autorzy: Pierre Bost, Ruben Casanova, Uria Mor, Martina Haberecker, Chantal Pauli, Susanne Dettwiler, Bernd Bodenmiller
Opublikowane w: Cell Systems, Numer 16, 2025, Strona(/y) 101296, ISSN 2405-4712
Wydawca: Elsevier BV
DOI: 10.1016/j.cels.2025.101296

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

Autorzy: 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
Opublikowane w: Science, 2021, ISSN 0036-8075
Wydawca: 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

Autorzy: Vito R.T. Zanotelli, Matthias Leutenegger, Xiao-Kang Lun, Fanny Georgi, Natalie de Souza, Bernd Bodenmiller
Opublikowane w: Molecular Systems Biology, 2020, ISSN 1744-4292
Wydawca: 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

Autorzy: 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
Opublikowane w: BMJ Open, Numer 15, 2025, Strona(/y) e096591, ISSN 2044-6055
Wydawca: 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

Autorzy: Laura Kuett, Raul Catena, Alaz Özcan, Alex Plüss A, Cancer Grand Challenges IMAXT Consortium, Peter Schraml, Holger Moch, Natalie de Souza, Bernd Bodenmiller.
Opublikowane w: Nature Cancer, Numer 2022 Jan;3(1):, 2022, ISSN 0028-0836
Wydawca: 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

Autorzy: Lasse Meyer, Nils Eling, Bernd Bodenmiller
Opublikowane w: BMC Bioinformatics, Numer 25, 2024, ISSN 1471-2105
Wydawca: 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

Autorzy: 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
Opublikowane w: Journal of Experimental & Clinical Cancer Research, Numer 44, 2025, ISSN 1756-9966
Wydawca: 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

Autorzy: Laura Kuett, Alina Bollhagen, Sandra Tietscher, Bettina Sobottka, Nils Eling, Zsuzsanna Varga, Holger Moch, Natalie de Souza, Bernd Bodenmiller
Opublikowane w: Cancer Research, Numer 85, 2025, Strona(/y) 15-31, ISSN 0008-5472
Wydawca: 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.

Autorzy: 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.
Opublikowane w: Nature Cancer, Numer 2021 Aug;2(8), 2021, ISSN 0028-0836
Wydawca: Nature Publishing Group
DOI: 10.1038/s43018-021-00216-6

SCIM: universal single-cell matching with unpaired feature sets

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

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

Autorzy: 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.
Opublikowane w: Allergy, Numer 2021 Jun 22, 2021, ISSN 0105-4538
Wydawca: Blackwell Publishing Inc.
DOI: 10.1111/all.14983

Feasibility of multiomics tumor profiling for guiding treatment of melanoma

Autorzy: 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
Opublikowane w: Nature Medicine, Numer 31, 2025, Strona(/y) 2430-2441, ISSN 1078-8956
Wydawca: Nature Publishing Group
DOI: 10.1038/s41591-025-03715-6

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

Autorzy: Jonas Windhager, Vito Riccardo Tomaso Zanotelli, Daniel Schulz, Lasse Meyer, Michelle Daniel, Bernd Bodenmiller, Nils Eling
Opublikowane w: Nature Protocols, Numer 18, 2023, Strona(/y) 3565-3613, ISSN 1754-2189
Wydawca: Nature Publishing Group
DOI: 10.1038/s41596-023-00881-0

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

Autorzy: 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.
Opublikowane w: Nature Genetics, Numer 2022 Apr 18, 2022, ISSN 0028-0836
Wydawca: Nature Publishing Group
DOI: 10.1038/s41588-022-01041-y

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

Autorzy: Merrick Strotton, Tsuyoshi Hosogane, Marco di Michiel, Holger Moch, Zsuzsanna Varga, Bernd Bodenmiller
Opublikowane w: Nature Methods, Numer 20, 2023, Strona(/y) 1310-1322, ISSN 1548-7091
Wydawca: Nature Publishing Group
DOI: 10.1038/s41592-023-01977-x

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

Autorzy: Lena Cords, Natalie de Souza, Bernd Bodenmiller
Opublikowane w: Cancer Cell, Numer 42, 2025, Strona(/y) 1480-1485, ISSN 1535-6108
Wydawca: Cell Press
DOI: 10.1016/j.ccell.2024.08.011

Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition.

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

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

Autorzy: 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.
Opublikowane w: Cell Reports Medicine, 2020, ISSN 2666-3791
Wydawca: 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.

Autorzy: Tobias Hoch, Daniel Schulz, Nils Eling, Julia Martínez Gómez, Mitchell P. Levesque, Bernd Bodenmiller
Opublikowane w: Science Immunology, Numer 2022 Apr;7(70, 2022, ISSN 2470-9468
Wydawca: 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

Autorzy: Tsuyoshi Hosogane, Ruben Casanova, Bernd Bodenmiller
Opublikowane w: Nature Methods, Numer 20, 2023, Strona(/y) 1304-1309, ISSN 1548-7091
Wydawca: Nature Publishing Group
DOI: 10.1038/s41592-023-01976-y

Compressed sensing expands the multiplexity of imaging mass cytometry

Autorzy: Tsuyoshi Hosogane, Leonor Schubert Santana, Nils Eling, Holger Moch, Bernd Bodenmiller
Opublikowane w: Nature Communications, Numer 16, 2025, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-025-66629-4

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

Autorzy: Lena Cords, Sandra Tietscher, Tobias Anzeneder, Claus Langwieder, Martin Rees, Natalie de Souza, Bernd Bodenmiller
Opublikowane w: Nature Communications, Numer 14, 2023, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-023-39762-1

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

Autorzy: 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
Opublikowane w: The Journal of Molecular Diagnostics, Numer 27, 2025, Strona(/y) 722-735, ISSN 1525-1578
Wydawca: American Society for Investigative Pathology
DOI: 10.1016/j.jmoldx.2025.04.011

Optimizing multiplexed imaging experimental design through tissue spatial segregation estimation

Autorzy: Pierre Bost, Daniel Schulz, Stefanie Engler, Clive Wasserfall, Bernd Bodenmiller
Opublikowane w: Nature Methods, Numer 20, 2023, Strona(/y) 418-423, ISSN 1548-7091
Wydawca: Nature Publishing Group
DOI: 10.1038/s41592-022-01692-z