Project

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Single cell analysis using mass cytometry

English title Single cell analysis using mass cytometry
Applicant Bodenmiller Bernd
Number 139220
Funding scheme R'EQUIP
Research institution Institut für Molekulare Biologie Universität Zürich
Institution of higher education University of Zurich - ZH
Main discipline Biochemistry
Start/End 01.02.2012 - 31.05.2013
Approved amount 289'750.00
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All Disciplines (6)

Discipline
Biochemistry
Experimental Cancer Research
Molecular Biology
Chemical Engineering
Immunology, Immunopathology
Genetics

Keywords (6)

Single cell analysis; Mass cytometry; Systems Biology; Signaling Networks; Model organisms; Immunology

Lay Summary (English)

Lead
Lay summary

Cells constantly sense environmental cues, integrate this information with their internal state and ultimately adapt their phenotype. Understanding these events and to accurately measure the resulting phenotypes on the single cell level is one of the central challenges of current biology. Cellular states and phenotypes, even in populations of genetically identical cells, must be considered to be highly heterogeneous, due to multiple cell subsets with a unique cellular memory, cell cycle stage, age or environment. These differences explode in multicellular organisms, as cells ranging from early stem-cell like cells to fully specialized cells constituting healthy or cancer tissue are present. Furthermore, depending on the cellular location and context, cells of a tissue will display unique behavior and the history of an organism is e.g. well reflected in the cells of the immune system. Although highly relevant for biological and biomedical research, the cellular phenotypes and the underlying structure of genetic programs or signaling networks and their changes during growth, development or disease and the spatial interplay of cell (clusters) within a tissue or tumor are largely unknown. However, this is not surprising as current immunohistochemistry/immune fluorescence microscopy and flow cytometry methods typically used to analyze single cells can only measure few molecules simultaneously, impeding to capture cellular state, phenotype and context. In this project, we exploit a novel method called mass cytometry which overcomes these limitations. Mass cytometry couples flow cytometry to a novel single cell mass spectrometer, called CyTOF, and allows accurately quantifying up to 100 (signaling) molecules and phenotypes on the single-cell level in a multiplexed manner. Mass cytometry not only expands analyses already performed with flow cytometry, but opens exciting new avenues for research: The quantitative and correlative nature of up to 100 molecules quantified on each cell (phenotype, signaling stats, etc.) allows for the mathematical reconstruction of single cell networks, cellular continua or the spatial interplay of cells while capturing the underlying signaling networks. The projects of this application will use mass cytometry to first, analyze signaling network structure driving cellular plasticity in human tumors, second, generate a 3D model of growth and shape control in the developing Drosophila wing, third, to built an accurate mechanistic model of hedgehog signaling and fourth, to thoroughly characterize peripheral CD4+ T cell differentiation.

Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Collaboration

Group / person Country
Types of collaboration
Prof. Detlef Guenther / ETH Zuerich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Nature Webcast 27.03.2013 Online
FP7 Marie Curie Training Network HEM_ID – Hematopoietic Cell Identity 12.03.2013 Vienna, Austria
USGEB Annual Meeting Life Sciences Switzerland (LS2) 31.01.2013 Zurich, Switzerland
Annual Symposium of the Danish Proteomics Society (DAPSOC) 20.11.2012 Odense, Denmark
CRG Core Facilities Technology Symposium 18.11.2012 Barcelone, Spain
Pharmaceutical Flow Cytometry & Imaging 10.10.2012 Alderley Park, UK
Guy’s Hospital Seminar Series 09.10.2012 London, UK
12th Euroconference of the European Society of Clinical Cell Analysis (ESCCA) 12.09.2012 Budapest, Hungary
XXVII Congress of the International Society for Advancement of Cytometry (CYTO) 23.06.2012 Leipzig, Germany
Inauguration of Mass Cytometer suite & Immunomonitoring Core Labs, Commissariat à l’Energie Atomique (CEA) 05.06.2012 Paris, France
XXVth International Symposium on Technological Innovations in Laboratory Hematology (ISLH) 21.05.2012 Nice, France
32nd Blankenese Conference 19.05.2012 Hamburg, Germany
Fourth Annual ENBDC workshop 13.04.2012 Weggis, Switzerland
Spring Meeting of the Swiss Chemical Society (SCS) 16.02.2012 Geneva, Switzerland
Society for Laboratory Automation and Screening (SLAS) 04.02.2012 San Diego, USA


Knowledge transfer events

Active participation

Title Type of contribution Date Place Persons involved
Maxquant summer school 27.06.2013 Munich, Germany
UCD Conway Core Technology Summer School 21.06.2013 Dublin, Ireland


Communication with the public

Communication Title Media Place Year
Media relations: print media, online media Exploiting Flow Cytometry’s Full Capabilities Genetic Engineering & Biotechnology News International 01.12.2012
Media relations: print media, online media Fatale Metamorphose Uni Magazin German-speaking Switzerland 04.12.2012

Awards

Title Year
SNF Assistant Professorship 2013
Genome Technology Tomorrows PI 2012

Associated projects

Number Title Start Funding scheme
135699 Genetic Dissection of Growth and Size Control in the Model Organism Drosophila 01.04.2011 Project funding
143877 Epithelial-Mesenchymal Transition Single-Cell Signaling States and Phenotypes through Time and Space 01.11.2012 Project funding
124922 Effects of Interleukin-21 on T cell responses and diseases 01.07.2009 Project funding
135688 Microbial networks and their functional capabilities in the environment 01.04.2011 Project funding

Abstract

Cells constantly sense environmental cues, integrate this information with their internal state and ultimately adapt their phenotype. Understanding these events and to accurately measure the resulting phenotypes on the single cell level is one of the central challenges of current biology. Cellular states and phenotypes, even in populations of genetically identical cells, must be considered to be highly heterogeneous, due to multiple cell subsets with a unique cellular memory, cell cycle stage, age or environment. These differences explode in multicellular organisms, as cells ranging from early stem-cell like cells to fully specialized cells constituting healthy or cancer tissue are present. Furthermore, depending on the cellular location and context, cells of a tissue will display unique behavior and the history of an organism is e.g. well reflected in the cells of the immune system. Although highly relevant for biological and biomedical research, the cellular phenotypes and the underlying structure of genetic programs or signaling networks and their changes during growth, development or disease and the spatial interplay of cell (clusters) within a tissue or tumor are largely unknown. However, this is not surprising as current immunohistochemistry/immune fluorescence microscopy and flow cytometry methods typically used to analyze single cells can only measure few molecules simultaneously, impeding to capture cellular state, phenotype and context.Here we apply to support the equipment needed to exploit a revolutionary method called mass cytometry which overcomes these limitations. Mass cytometry couples flow cytometry to a novel single cell mass spectrometer, called CyTOF, and allows accurately quantifying up to 100 (signaling) molecules and phenotypes on the single-cell level in a multiplexed manner. Already over 300 single cell assays that cover the most important immunological, growth, cell cycle, apoptosis and stem cell signaling molecules and phosphorylation sites are available and the first application to study immune signaling was just published in Science. In the near future it can be also be expected that besides increasing the number of single cell assays also absolute epitope copy numbers and mRNA levels can be measured on the single cell level.Mass cytometry not only expands analyses already performed with flow cytometry, but opens exciting new avenues for research: The quantitative and correlative nature of up to 100 molecules quantified on each cell (phenotype, signaling state, mRNA level etc.) allows for the mathematical reconstruction of single cell networks, cellular developmental continua and the underlying signaling can be captured, and the spatial interplay of cells can be resolved by location markers or by coupling mass cytometry to laser ablation methods.The projects proposed in this application cover most of these aspects and range from the 3-dimensional analysis of model organism tissues, via immune biology to cell plasticity in cancer to generating accurate mathematical models of development. The leading group is deeply involved in the development of methods for mass cytometry since two years and all groups are leaders in their respective field. In short these includeDr. Bernd Bodenmiller (University of Zurich or ETH Zurich) will host the CyTOF instrument. During his postdoctoral training at Stanford University he developed novel methods for one of the first mass cytometry instruments available (see attached manuscript). With his new group starting this autumn in Zurich, he will bring all expertise to exploit mass cytometry and will use it to analyze signaling network structure driving cellular plasticity in human tumors. Prof. Ernst Hafen (ETH Zurich and University of Zurich) is a renowned leader in the field of growth control in the model organism Drosophila melanogaster. The project planned in his lab intends to apply 3D mass cytometry to study growth and shape control in the developing Drosophila wing. His lab will combine a state-of-the-art systems genetics QTL study with mass cytometry to study the individual contribution of quantitative loci to growth control network dynamics. His lab will contribute important reagents for mass cytometry in Drosophila melanogaster. Prof. Christian von Mering (University of Zurich) is a well-known computational biologist focusing on network analysis and the generation of computational models based on large scale “omics” data. In his planned project in collaboration with Prof. Koni Basler (University of Zurich) he planes to generate and exploit CyTOF data to accurately parameterize a mechanistic model of hedgehog signaling. Prof. Manfred Kopf (ETH Zurich) studies the roles of cytokines in infectious diseases and made substantial discoveries in defining the cytokines that determine the fate and function of CD4+ T cells. In his proposal, he plans using mass cytometry to thoroughly characterize peripheral CD4+ T cell differentiation as defined by a battery of cytokines, chemokines, co-stimulatory molecules and phosphorylation of signalling molecules.Research groups profiting from mass cytometry will not only be the four groups participating in this proposal. Synergies can be also be expected between groups of University of Zurich, ETH Zurich, Functional Genomic Center and the University Hospital. Furthermore, every research group working currently using fluorescence based flow cytometry or working in the fields of immunology, cellular plasticity/stem cell biology, cancer biology, basic biology or any research in which single cell analysis are of interest, can profit from mass cytometry. As such, the user base is very broad and while the four groups participating in this application will use a high percentage of the capacity of the mass cytometer, the already existing requests from other Swiss research groups to access the instrument will make sure that the instrument will be constantly operated at full capacity. In fact, as the user base is very broad, the result will be that once it will be known that a mass cytometer exists in Switzerland, the demand will greatly exceed the supply, making the acquisition in other places necessary (this happened e.g. to the lab of Prof. Nolan@Stanford). Finally, all developed methods and reagents developed within the here proposed projects will be made available to other research groups within Switzerland. Therefore, a this mass cytometry platform will significantly contribute to increase the competitiveness of Swiss research.
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