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Multidimensional immune profiling of single cells using mass cytometry

English title Multidimensional immune profiling of single cells using mass cytometry
Applicant Zippelius Alfred
Number 189780
Funding scheme R'EQUIP
Research institution Abteilung für Onkologie Medizinische Universitätsklinik B Universitätsspital Basel
Institution of higher education University of Basel - BS
Main discipline Immunology, Immunopathology
Start/End 01.01.2020 - 31.12.2020
Approved amount 358'318.00
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All Disciplines (3)

Discipline
Immunology, Immunopathology
Clinical Cancer Research
Clinical Immunology and Immunopathology

Keywords (4)

single cell analysis; multidimensional analysis ; mass cytometry; immune phenotyping

Lay Summary (German)

Lead
Das CyTOF System ist ein Massenzytometer, das hochdimensionale Analysen von einzelnen Zellen ermöglicht. Die Bereitstellung dieser Plattform an der Universität Basel erlaubt interessierten Forschungsgruppen an zahlreichen Insitutionen und Einrichtungen den Zugang für wissenschaftliche Untersuchungen.
Lay summary

Die rasche und umfassende Analyse von einzelnen Zellen ist in der Wissenschaft wie beispielsweise in der immunologischen Forschung entscheidend, um deren Identität und Funktion mehrdimensional zu erfassen. Das CyTOF System ist ein Massenzytometer, welches Einzelzell-Suspensionen, markiert mit stabilen Schwermetall-Isotopen, analysiert. Die atomisierten Ionen werden nach Masse separiert und nur nicht-biologische Ionen der Sonden werden gezählt. Mit über 130 Detektionskanälen ermöglicht dieses System über 50 Isotopen-Sonden mit hoher Aquisitionsrate zu detektieren, dies ohne Kompensation. Die Probenvorbereitung und Proteindetektion sind, mit wenigen Unterschieden, vergleichbar mit fluoreszenzbasierter Durchflusszytometrie.  Damit werden vielfältige Anwendungen möglich, wie die Analyse des zellulären Verhaltens, einschließlich Zellsignalisierung, -proliferation, -tod oder -kommunikation und der Analyse der zellulären Differenzierung bzw. Funktion. Der Antrag erlaubt uns, ein CyTOF System an der Universität Basel, insbesondere im Bereich der immunologischen Forschung, einem eindeutigen Schwerpunkt der Universität, einzurichten. Obgleich die Universität Basel über eine hohe Dichte an herausragenden Wissenschaftlern und Aerzten in diesem Bereich verfügt, gibt es derzeit kein CyTOF System im akademischen Umfeld. Somit handelt es sich dabei um ein multi-institutionelles und multidisziplinäres Projekt, das von folgenden Antragstellern getragen wird:

  • Reaktion und Resistenz gegen Krebsimmuntherapie (A. Zippelius, DBM)
  • Vielfalt der Entwicklung und Funktion von Thymusepithelzellen (G.Holländer, DBM)
  • Mechanismen zur Aufrechterhaltung der peripheren naiven T-Zell-Homöostase (J.Pieters, Biozentrum)
  • Beziehung zwischen follikulären Lymphomzellen und der Mikroumgebung zur personalisierten Immuntherapie (S. Dirnhofer, Institut für Pathologie)
  • Längsschnittuntersuchung der phänotypischen und funktionellen Differenzierung antiviraler B-Zellen (D. Pinschewer, DBM)
  • Beitrag des Zellstoffwechsels zur klinisch relevanten Dysregulation des Immunsystems (C.Hess, DBM)

Direct link to Lay Summary Last update: 27.05.2020

Responsible applicant and co-applicants

Project partner

Associated projects

Number Title Start Funding scheme
192730 Investigating the role for coronin 1 in T cell homeostasis and immune tolerance 01.04.2020 Project funding (Div. I-III)
185318 Alarmin' for T cell self-renewal 01.04.2019 Project funding (Div. I-III)
184672 Cellular and molecular analysis of thymus organogenesis and maintenance 01.07.2019 Project funding (Div. I-III)
171050 Transcriptional control and Epigenetic Mechanisms of Thymic Epithelial Cell Development and Function 01.03.2017 Bilateral programmes
173132 Immunity and tolerance in persistent viral infection 01.04.2017 Project funding (Div. I-III)
166663 Dissection of the coronin 1-mediated signal transduction pathway 01.10.2016 Project funding (Div. I-III)
172848 Role of glucose and serine metabolism in regulating the CD8+ T cell memory response 01.04.2017 Project funding (Div. I-III)
170929 Paracrine delivery of therapeutic biologicals: developing a new technology for personalized cancer immunotherapy 01.01.2017 Sinergia

Abstract

Technological advances have allowed multiplexing of single-cell measurements on an “-omics” scale for capturing multi-dimensional information that clarifies cellular identity and function. Mass cytometry is one such progress, which uniquely enables the quantification of over 40 parameters on single cells. This allows investigating complex coordinated cellular systems by assessing the diversity of cellular phenotypes and behaviours in a single sample. Fluorescence-based flow cytometry has balanced these goals to fill a critical need. However, fluorophore emission spectra overlap, making them difficult to distinguish from one another. Particularly, as more parameters are measured in a single experiment, ultimately contributing to unambiguous data. In contrast, elemental mass spectrometry analyses individual cells labelled with stable heavy metal isotopes over 130 detection channels. CyTOF has the exquisite ability to simultaneously resolve more than 50 elemental probes per cell at high acquisition rates without the need for compensation, thereby maximizing the per-cell information obtained from a single sample in a single experiment. This fundamental difference enables significantly more cellular features to be assayed simultaneously using a mass-based platform including:- Cellular behaviour, including cell signalling, mediators of proliferation, cell death, or intercellular communication (i.e., cytokines, growth factors, etc.) - Cellular progression, such as a differentiation trajectory from a primitive to a mature cell type- Cellular diversity and possible fates a cell can adoptOverall, CyTOF is capable to identify cellular populations of interest while simultaneously assessing cellular features from a single experiment.With this grant we propose the acquisition of the first Basel-based Mass CyTOF. In addition to the six multi-institutional and multi-disciplinary projects outlined by the main and co-applicants we have more than 15 research groups that have committed to use mass CyTOF within their research projects, some of whom are utilizing CyTOF already in collaboration. We strongly believe that for the reasons outlined below we will urgently benefit from a local mass cytometry facility.•Mass cytometry has become a significant advance for studies in basic research including immunology research, the latter being a distinct key focal area of the University of Basel.•In addition, mass cytometry is increasingly being utilised for translational clinical research. Basel has an exceptionally high density of outstanding physician scientists committed to using mass CyTOF for immune monitoring in their mandatory translational studies.•Given the lack of mass CyTOF in the Basel academic area, the only way to perform mass cytometry experiments are through collaborations. The demand in Basel for projects requiring mass cytometry however is simply too high for collaborations to be a solution•Several already funded projects (as outlined in the grant) urgently require mass cytometry assessments• We have recently acquired a novel multiplex (up to 50 markers) imaging platform called CODEX at the University of Basel. Data from CODEX when paired with mass CyTOF data will resolve phenotypic, functional as well as spatial information of distinct cell types during disease progression This will allow us to be at the forefront of deep multidimensional immune profiling. The six proposed projects here all aim to perform single cell immune phenotyping to characterize very rare cell populations for assessing •cancer immunotherapy response and resistance (A. Zippelius, DBM)•diversity of thymic epithelial cell development and function in health and disease (G. Holländer, DBM)•mechanisms involved in maintenance of peripheral naïve T cell homeostasis (J. Pieters, Biozentrum)•complex relationship between follicular lymphoma cells and the microenvironment for better personalized immunotherapies (S. Dirnhofer, Institute of Pathology)•longitudinal assess the phenotypic and functional differentiation of antiviral B cells (D. Pinschewer, DBM)•contribution of cellular metabolism to clinically relevant immune dysregulation (C. Hess, DBM)Therefore, these projects clearly highlight the urgent need for a mass CyTOF instrument to generate impactful and clinically relevant data within the scientific community of the Basel academic area.
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