Getting a grip on signalling dynamics in single-cells

Cells live in a continuously changing (dynamic) and noisy environment. It is fascinating how cells respond to relevant changes in their environment while staying ignorant of the noise.

Protein-kinases play a central role in transmitting the relevant ‘input-signals’ throughout the cell, sequentially catalysing or inhibiting chemical reactions, thereby forming a connected network of intracellular signalling.

Identifying the components of this signalling roadmap in a variety of cell-types has helped us to intervene in many different diseases.

However, we do not truly understand how these networks function in dynamic environments, as we lack a ‘timetable’ summarising ‘when’, and ‘how fast’ the signals are transferred throughout the roadmap: there is a gap in knowledge on kinetic properties of the signalling networks.

In this project, I propose to develop a technology platform to determine the kinetic properties of an intracellular-signalling network in response to dynamic input-signals.

In particular, I will focus on the activation of the B-cell receptor signalling pathway, crucial for B-cell survival and playing a significant role in our immune system. Objective 1. To control input signals, I will implement a fluidics-based cell culture system.

Then, I will develop microfluidics-based ‘multi-omics single-cell sequencing technology’ that measures (phospho-)protein and RNA-levels. Objective 2. Exploring the kinetic properties of signal propagation over time requires state-of-the-art computational tools.

I will develop a computational workflow including data-processing and normalisation, determining cell state, (pseudo)time inference and determining signalling levels to calculate kinetic properties of the signalling network. Objective 3.

As a proof-of-concept, I will build a ‘timetable’ with kinetic properties for the B-cell receptor signalling network in response to a variety of input signals.

This information allows me to explore the effect of dynamic activation and inhibitory drugs on how the signalling network processes input signals and affects B-cell state or function.