Summary
The Molecular Nose
Mammalian
cells use more genes to regulate biological processes than to carry them out.
These include all fundamental processes such as cell growth, differentiation,
survival, metabolism and the ability to sense and produce the correct
complement of biomolecules to communicate with the environment. Complexity is
further enhanced by the organization of biological processes as networks. Understanding
the behaviour and responses of such complex networks will be crucial to solve
eminent questions in biology.
To
address this need we will build a
multiplexed sensor platform that can assess and quantify dynamic changes in the
functional state of biochemical networks in mammalian cells, and use these data
to reconstruct cell network interactions and their dynamic behaviour on a
systems wide level. The concept underpinning this platform is fundamentally
different from existing methods used in the biological sciences to assess cell
function, and similar to the “Electronic Nose”, where an array of sensors is
first trained with individual stimuli to establish a library of response
patterns which subsequently are used to deconvolute complex inputs.
The
“Molecular Nose” will monitor the
outputs of several hundred network components simultaneously in cell
populations or single cells using artificial transcriptional reporters, and
design a software framework and algorithms for their functional analysis. The
Molecular Nose will be built in three versions. One will be constructed using
molecular biology tools, and will permit to use a large array (up to 1000) of
sensors. However, it requires the cell being lysed for the measurement as the
detector is outside of the cell. This version will be particularly useful for
training the system and establishing a large library of response patterns. The
second version will be built by integrating both individual sensors and their
corresponding detectors onto bar-coded nanoparticles which will be introduced
into cells and read using surface enhanced
resonance Raman scattering spectroscopy. This setup
will use a smaller number of sensors (up to 30), but can be used to monitor
responses in living cells in real time. In parallel we will develop methods for
the controlled introduction of these particle libraries into cells. The third
version is the stable integration of a plasmid based sensor library into the
embryonic mouse stem cells with the aim to generate a transgenic sensor mouse. The
stem cells also can be used for organotypic cultures and in vitro
differentiation systems.
The
Molecular Nose will enable the systematic testing and rational interpretation
of the behaviour of cellular networks. The technique is generic with a wide range
of applications in both single cells and cell populations, including eminent
biological problems such as the analysis of drug effects and prediction of side
effects; stem cell
differentiation with a view to eventually control differentiation; cell fate
specification in order to support tissue engineering; genetic and biochemical
networks for the production of desired proteins and metabolites by
synthetically engineered pathways; and the
investigation of adaptive network responses and evolution. Currently, we are
lacking efficient experimental tools to analyse these complex interactions.
OBjectives
The overall objectives of this proposal are:
·
to construct and establish a
Sensor-Detector platform in single cells, cell population, tissues and
eventually mice
·
to design an Analyser and
associated algorithms that will decode the cellular responses measured by the
Sensor-Detector
·
to prove application of this
technology for the measurements of drug responses and signalling network
adaptation
Beneficiaries