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Decoding and Re-Encoding Receptor Tyrosine Kinase/Fate Decision Signaling

English title Decoding and Re-Encoding Receptor Tyrosine Kinase/Fate Decision Signaling
Applicant Pertz Olivier
Number 185376
Funding scheme Project funding (Div. I-III)
Research institution Institut für Zellbiologie Departement Biologie Universität Bern
Institution of higher education University of Berne - BE
Main discipline Cellular Biology, Cytology
Start/End 01.06.2019 - 31.05.2023
Approved amount 759'360.00
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All Disciplines (2)

Discipline
Cellular Biology, Cytology
Biophysics

Keywords (6)

Proteomics; Live cell imaging; Mathematical Modelling; Optogenetics; Receptor Tyrosine Kinase signaling; MAPK signaling

Lay Summary (French)

Lead
Decodage de la structure des reseaux de signalisation de decision cellulaireLes cellules interpretent constamment les signaux extracellulaires par des processus de signalisation dynamique pour controller les processus de decision cellulaire (proliferation, mort cellulaire, migration, differentiation). Ceci implique des circuits de signalisation comportant des boucles de feedbacks qui convertissent des signaux chimiques ou mecaniques en ces etats de signalisation dynamique. Ces etats de signalisation sont on une seconde phase decodes en programmes transcriptionels qui induisent les decisions cellulaire. Dans ce projet, nous explorant comment ces etats de signalisation sont encodes puis decodes pour reguler les decisions cellulaire.
Lay summary

Contenu et objectifs du travail de recherche.

 

Dans ce projet nous utiliseront des circuits cellulaires qui consistent d’un recepteur synthetique optogenetique pour activer la signalisation cellulaire, et d’un biosenseur pour mesurer des etats de signalisation cellulaire. Ces nouvelles technologies, couplees a des methodes de microscopie et d’analyse d’image modernes, permettent de mesurer le flux de signalisation cellulaire dans des centaines de cellules vivantes avec un tres haut debit. Des methodes de transcriptomique et de proteomique modernes donneront une nouvelle vision de ces reseaux de signalisation. Comme preuve de concept, nous exploreront comment reprogrammer des decisions cellulaire de maniere robuste par simple application de lumiere bleue (pour activer les recepteurs optogenetiques).

 

Contexte scientifique et social du projet de recherche

 

Notre approche multidisciplinaire a le potentiel de donner des nouvelles idées pour contrôler des processus patho-physiologique comme le cancer, ou pour reprogrammer des cellules souches en type cellulaire desires.

 

Direct link to Lay Summary Last update: 29.03.2019

Responsible applicant and co-applicants

Employees

Project partner

Associated projects

Number Title Start Funding scheme
162195 Understanding single cell-level MAPK activation dynamics for manipulation of neuronal stem cell self-renewal and differentiation fates 01.03.2016 Bilateral programmes
183550 Real time Exploration of GTPase-Cytoskeletal feedback underlying Contractile Actomyosin Systems 01.09.2019 Sinergia
149923 Optogenetic control of receptor tyrosine kinase signaling to manipulate cell fate 01.02.2014 Project funding (Div. I-III)
149923 Optogenetic control of receptor tyrosine kinase signaling to manipulate cell fate 01.02.2014 Project funding (Div. I-III)
173462 Dissecting a Rho GTPase spatio-temporal signaling network regulating growth cone motility, neurite and axonal outgrowth 01.11.2017 Bilateral programmes
176008 Hunting for natural products targeting aberrant proliferative signaling in melanoma 01.01.2018 Project funding (Div. I-III)

Abstract

Complex signaling networks translate external stimuli into specific fates, with signaling dynamics rather than steady states controlling these fate decisions. These signaling states can be highly heterogeneous even within individual cells of an isogenic population. Measuring single-cell signaling dynamics is therefore key to understand fate decision signaling. Receptor tyrosine kinases (RTKs) are key regulators of fates such as proliferation, differentiation, cell motility and death. Recent work has shown that RTKs wire the downstream MAP kinase (MAPK) network with different feedback circuitries to encode specific ERK dynamics, that lead to distinct fates. A 2nd network layer then decodes these ERK dynamics to induce transcriptional programs that actuate these fates. Further, in cellular communities such as epithelial cells, sophisticated, collective spatial ERK dynamics co-ordinate fate decisions at the population level, enabling processes such as epithelial homeostasis. This proposal aims at characterizing to a new detail level: 1. How RTKs encode ERK dynamics; 2. How ERK dynamics are decoded into transcriptional programs actuating fates; 3. How spatio-temporal ERK dynamics emerge within epithelial cell communities to co-ordinate population-level fate decisions.In aims 1 and 2, we will use genetic circuits, that consist of optogenetic actuators coupled to fluorescent biosensors, to dynamically perturb (eg by applying light pulses) the signaling flux with high temporal resolution. This will allow us to dissect underlying signaling network circuitries, and to induce synthetic ERK dynamics of defined duration that (unlike using sustained GF stimulation) are population homogeneous and thus induce robust fate decisions. These circuits will to allow interrogate ERK dynamics at unprecedented scale through automated live cell microscopy. We will use a programmable optogenetic illuminator to induce synthetic ERK dynamics in large cell numbers for biochemical experiments. Using (phospho)-proteomics and transcriptomics techniques, we will comprehensively interrogate the signaling networks in an unbiased fashion. Large scale perturbation experiments will then be used to test hypothesizes derived from the omics datasets to identify new features of the ERK dynamics encoding/decoding network layers, allowing to refine current mathematical models. We will then genetically perturb the ERK dynamics encoding network layer to produce synthetic signaling states of desired duration, allowing to test how the decoding layer reacts. This will unveil the whole information flow from receptor to fate decision. As proof of concept, we will re-encode synthetic ERK dynamics to induce robust, desired fates across the cell population.In Aim 3, we will identify the mechanisms that generate random, stochastic ERK bursts, as well as spatially regulated ERK activity waves around extruding cells in epithelial cell communities. We will explore the significance of this ERK activity wave at minute timescales (eg closing the gap left by the extruding cell), and at multiple hours timescales (eg to explore if these ERK dynamics regulate proliferation to control epithelial homeostasis). Because this spatial signaling paradigm is not accessible using global perturbations, we will use a panel of optogenetic actuators to systematically perturb the monolayer at the single cell level. This will allow to locally control the mechanical landscape and cell extrusion events, allowing us to test how collective signaling dynamics control proliferation to ensure epithelial homeostasis. Understanding the signaling networks that control ERK dynamics and fate decisions will provide novel avenues to understand pathologies such as cancer, or to reprogram stem cell fates at will.
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