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Installing a Hyperion CyTOF mass cytometry platform for high-dimensional single cell analysis at the University of Bern

English title Installing a Hyperion CyTOF mass cytometry platform for high-dimensional single cell analysis at the University of Bern
Applicant Keogh-Stroka Deborah
Number 183501
Funding scheme R'EQUIP
Research institution Department for BioMedical Research Universität Bern
Institution of higher education University of Berne - BE
Main discipline Immunology, Immunopathology
Start/End 01.10.2019 - 30.11.2021
Approved amount 759'800.00
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All Disciplines (2)

Immunology, Immunopathology
Experimental Cancer Research

Keywords (3)

multidimensional single cell analysis; mass cytometry; Hyperion

Lay Summary (German)

Komplexe Krankheiten, wie z.B. Krebserkrankungen, weisen in der Regel eine große Anzahl genetischer und/oder epigenetischer Veränderungen in verschiedenen Zelltypen auf. Diese Veränderungen können von unterschiedlicher pathologischer und therapeutischer Bedeutung sein. Die neue Plattform leistet einen Beitrag zum Entdecken von diesen Veränderungen.
Lay summary

Inhalt und Ziele des Forschungsprojekts

Für die Umsetzung der Präzisionsmedizin ist das Erkennen und Verstehen, ob und wie solche Veränderungen die zelluläre Dysfunktion beeinflussen, zwingend. Technologien, welche es erlauben, derartige Veränderungen auf Einzelzellbasis zu untersuchen, erbringen einen hohen Nutzen in der Aufklärung solcher komplexen biologischen Phänomene. Darüber hinaus werden derartige Einzelzellmessungen für das Studium der Krankheitsbiologie routinemäßig unverzichtbar und sind zielführend für zukünftige klinische Anwendungen wie z.B. die Identifizierung von neuen Biomarkern.

Die geplante Anschaffung dient zur Etablierung einer Plattform zur hochdimensionalen Analyse von Einzelzellen mittels bildgebender Massenzytometrie, namentlich der HyperionTMImaging Plattform. Diese Plattform ermöglicht eine multiparametrische zelluläre Analyse und das Studium von komplexen zellulären Strukturen in Zellpopulationen und deren Interaktion mit Gewebezellen.

Wissenschaftlicher und gesellschaftlicher Kontext des Forschungsprojekts

Wir sind überzeugt, dass diese neue Plattform den Forschenden der Universität Bern und des Inselspitals den Zugang zu einem Instrument der nächsten Generation ermöglicht, welcher das Erforschen komplexer Pathologien und das Studium der interzellulären Kommunikation in kombinierter Form von chemischen und räumlichen Informationen erlaubt.


Direct link to Lay Summary Last update: 21.09.2019

Responsible applicant and co-applicants

Project partner


The LIM Protein Ajuba Augments Tumor Metastasis in Colon Cancer
Dommann Noëlle, Sánchez-Taltavull Daniel, Eggs Linda, Birrer Fabienne, Brodie Tess, Salm Lilian, Baier Felix Alexander, Medová Michaela, Humbert Magali, Tschan Mario P., Beldi Guido, Candinas Daniel, Stroka Deborah (2020), The LIM Protein Ajuba Augments Tumor Metastasis in Colon Cancer, in Cancers, 12(7), 1913-1913.


Group / person Country
Types of collaboration
Fabian Blank/Pneumology Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure
Thomas Marti in Thoracic surgery at Inselspital Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure
Hans-Uwe Simon/Institute of Pharmacology Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
University of Bern Flow Cytometry Course Individual talk Introduction to Helios, Hyperion and the IMC Platform in Bern 14.03.2022 Bern, Switzerland Keogh-Stroka Deborah;
BIC 20th International Summer School Talk given at a conference Welcome to the IMC Platform 05.07.2021 Emmetten, Switzerland Keogh-Stroka Deborah; Fux Michaela;
BIC 20th International Summer School, University of Bern Poster Studying the Liver with Imaging Mass Cytometry 05.07.2021 Emmetten, Switzerland Keogh-Stroka Deborah;


Title Date Place
Introductory course for Helios 11.01.2022 Zoom, remote, Switzerland
IMC Platform kickoff 01.09.2021 Bern, Switzerland
Introductory course for Helios 15.07.2021 Remote via Zoom, Switzerland
Introductory course for Helios 27.01.2021 Remote via Zoom, Switzerland
Introducing Mass Cytometry Bern Edition 20.08.2020 Bern, Switzerland

Communication with the public

Communication Title Media Place Year
Media relations: print media, online media IMC_UniBe Twitter Rhaeto-Romanic Switzerland International German-speaking Switzerland Western Switzerland Italian-speaking Switzerland 2021
Media relations: print media, online media Imaging Mass Cytometry and Mass Cytometry Platform Website Italian-speaking Switzerland German-speaking Switzerland Western Switzerland International Rhaeto-Romanic Switzerland 2020

Associated projects

Number Title Start Funding scheme
175609 Towards understanding the importance of non-canonical phosphatidylinositol kinases in the maintenance of prostate metabolism. 01.12.2017 Project funding (Div. I-III)
170084 Intestinal tissue resident memory T cells in inflammation and homeostasis 01.11.2016 Project funding (Div. I-III)
170170 Targeting TNF receptor TNIK signaling to eliminate cancer stem cells 01.01.2017 Project funding (Div. I-III)
177523 Swiss Inflammatory Bowel Disease Cohort Study (SIBDCS) 01.04.2018 Cohort Studies Large
179394 Deciphering the Interplay of Regulatory T Cells and the Gut Microbiota in the Regulation of Myeloid Leukemia Stem Cells 01.05.2018 Project funding (Div. I-III)
173157 Fuelling hepatic resistance against irradiation-induced damage and disease 01.03.2018 Project funding (Div. I-III)
166578 Analyzing and modulating the epigenetic landscape of CDX2 as well as studying its function in colorectal cancer pathology 01.06.2016 Project funding (Div. I-III)
166594 Purinergic control of innate lymphoid cells in liver injury and repair 01.04.2016 Project funding (Div. I-III)
198543 Functional chemoinformatic modelling of the host cell metabolome to fight apicomplexan parasites 01.03.2021 Sinergia
207635 Towards understanding non-canonical phosphatidylinositol kinases as vulnerabilities in prostate cancer metabolism 01.04.2022 Project funding (Div. I-III)
170131 Anatomical routes and molecular mechanisms of T cell migration across the brain barriers 01.10.2016 Project funding (Div. I-III)
173219 Identification and analysis of PU.1 cell death pathways to improve leukemia therapy 01.05.2017 Project funding (Div. I-III)
157486 Role of Ribonuclease inhibitor (RNH1) in Hematopoiesis and Inflammation 01.04.2015 SNSF Professorships
168012 Role of maternal microbiota and aryl hydrocarbon receptor signalling in establishing neonatal skin homeostasis 01.01.2017 Ambizione
156869 Mechanisms of PARP inhibitor resistance of BRCA2-deficient mouse mammary tumors 01.08.2015 Project funding (Div. I-III)
177164 Intermicrobial and host-microbial interactions that determine the trajectory of mammalian microbial colonization in early life 01.05.2018 Sinergia
160269 Acquired and hereditary thrombotic microangiopathies exemplar diseases to understand ADAMTS13 function and pathophysiology 01.01.2016 Project funding (Div. I-III)
169352 Phenotypic and genomic characterization of stem-like cancer cells surviving castration in human prostate cancer 01.12.2016 Project funding (Div. I-III)
163205 PhenoTox: Pharmacometabolomics of early-onset fluoropyrimdine-related toxicity in cancer patients: hunting the missing heritability 01.09.2016 Project funding (Div. I-III)
173127 Gas6 and protein S pathways in hemostasis, thrombosis and inflammation 01.09.2017 Project funding (special)
163086 mRNA splicing and epithelial integrity 01.04.2016 Project funding (special)
179265 The role of the tumor microenvironment on prostate cancer stem cell phenotype and metastasis 01.08.2018 Project funding (Div. I-III)


Complex diseases commonly involve large numbers of genetic or epigenetic changes across several cell types, each of variable pathologic and therapeutic relevance. Identifying and understanding how such alterations collectively drive cellular dysfunction is a mandatory requirement in the implementation of precision medicine and requires complex technological efforts along with state-of-the-art computational tools. In that respect, single-cell technologies are entering the mainstream, providing an important utility to elucidate a diverse range of complex biological phenomena. Moreover, single-cell measurements are routinely becoming indispensable for the study of disease biology since heterogeneous cell populations undergo dynamic changes, differentiating toward many distinct identities a fact that has a key role in adjusting the appropriate therapies. This project will install a Hyperion CyTOF Imaging System that will enable comprehensive analysis of cellular phenotypes and their interrelationships through Imaging Mass Cytometry. This platform will be used to measure multiple protein markers in the spatial context of the tissue microenvironment and in single cell suspensions, gain full microenvironment and tissue architecture data, run panels of over 40 detection parameters, and avoid non-specific signals obtained from fluorescence reporter overlap.This new platform instrument will provide the researchers at the University of Bern with a next generation state-of-the-art tool to study complex disease biology and to delve into intercellular communication with a higher degree of combined chemical and spatial information.