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

Project Information

Precision Motifs

Grant agreement ID: 866074

DOI 10.3030/866074

EC signature date 29 May 2020

Start date 1 September 2020

End date 31 August 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 2 000 000,00

EU contribution € 2 000 000,00

Coordinated by

UNIVERSITAT ZURICH
Switzerland

Publications

Peer reviewed articles (20)

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

Author(s): Luigi Tortola, Andrea Jacobs, Lea Pohlmeier, Franz-Josef Obermair, Franziska Ampenberger, Bernd Bodenmiller, Manfred Kopf.
Published in: Immunity, 2020, ISSN 2666-3791
Publisher: Elsevier
DOI: 10.1016/j.immuni.2020.07.001

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

Author(s): 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,
Published in: Nature, 2021, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-021-03648-3

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

Author(s): 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
Published in: Molecular Systems Biology, Issue 2021 Oct;17(10), 2021, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202110402

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

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

Establishing standardized immune phenotyping of metastatic melanoma by digital pathology.

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

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

Author(s): 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,
Published in: Nature Communications, Issue Mar 31;12(1), 2021, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-22303-z

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

Author(s): 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.
Published in: Allergy, Issue Apr 21, 2021, ISSN 0105-4538
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/all.14866

LifeTime improving European healthcare through cell-based interceptive medicine

Author(s): 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
Published in: Nature, 2020, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-020-2715-9

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

Author(s): Nils Eling, Nicolas Damond, Tobias Hoch, Bernd Bodenmiller
Published in: Bioinformatics, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa1061

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

Author(s): 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
Published in: Diabetes, Issue 2021 Aug;70(8), 2021, ISSN 0012-1797
Publisher: American Diabetes Association
DOI: 10.2337/db21-0070

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

Author(s): 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
Published in: Science, 2021, ISSN 0036-8075
Publisher: 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

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

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

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

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

Author(s): 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.
Published in: Nature Cancer, Issue 2021 Aug;2(8), 2021, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s43018-021-00216-6

SCIM: universal single-cell matching with unpaired feature sets

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

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

Author(s): 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.
Published in: Allergy, Issue 2021 Jun 22, 2021, ISSN 0105-4538
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/all.14983

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

Author(s): 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.
Published in: Nature Genetics, Issue 2022 Apr 18, 2022, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-022-01041-y

Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition.

Author(s): James D. Wade, Xiao-Kang Lun, Nevena Zivanovic, Eberhard O. Voit1, Bernd Bodenmiller1
Published in: Frontiers in Physiology, 2020, ISSN 1664-042x
Publisher: Frontiers Research Foundation
DOI: 10.3389/fphys.2020.579117

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

Author(s): 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.
Published in: Cell Reports Medicine, 2020, ISSN 2666-3791
Publisher: 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.

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