■ Combinatorial drug screening with droplet microfluidics

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Description of the PhD project

Drug combination is a strongly rising therapeutic strategy as it does not require synthesis of novel molecules. Indeed, synergistic effects can increase treatment efficacy at constant toxicity levels, and is now being increasingly used for antibiotics and cancer chemotherapy. Furthermore, combinations can lower the emergence of treatment resistance causing relapse, which has proven extremely potent for HIV. However the pharmaceutical industry is currently lacking methods to screen for such combinations at a sufficient high throughput and low cost, as the number of conditions is squared compared to single drug screens (e.g. combination of 10 dose responses of 100 drugs requires 10^6 conditions).
In this project, in collaboration between the LBC (Philippe Nghe, Andrew Griffiths), the LCMD (Jérôme Bibette), the Biophysics Lab (Sander Tans) at AMOLF (Netherlands) and Sanofi (Eamonn Rooney, SANOFI Strasbourg), we propose to develop a droplet microfluidics strategy to screen antibiotic combinations at a very high throughput (10^6 conditions per experiment).
The LBC has already established protocols to culture cells, combine drugs, and sort positive drug hits in picolitre droplets. However there are currently two bottlenecks: signal multiplexing and the control of small molecule exchanges. Multiplexing will be addressed by DNA bar-coding strategies and Next Generation Sequencing, by adapting technologies currently developed in the LBC for single cell analysis in droplets. The emulsion physico-chemistry will be designed in collaboration with the LCMD, in order to control the exchanges of small compounds between droplets and allow to use very large libraries of small chemicals, such as FDA approved drugs ( 1500).
We will establish a proof-of-concept of the multiplexing technology by testing the effect of antibiotic combinations in collaboration with the Dutch partner, who is expert in the evolution of complex phenotypes. Indeed, this experiment will allow to study how antibiotic interactions are modulated by the genetic background of the bacteria. This knowledge is highly relevant to the understanding of antibiotic resistance, as it is unknown which antibiotic combinations can both fight resistant strains and limit further evolution of more aggressive resistances.
These developments will provide a solid basis to develop a very-high throughput drug combination workflow in collaboration with the R&D division for screening of Sanofi, and extend it to a broader range of cellular models.

[Palmer & Kishony, Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance, Nature reviews Genetics 2013]
[Poelwijk, Tans, Empirical fitness landscapes reveal accessible evolutionary paths Nature 2007]
[Tenaillon et al., The population genetics of commensal Escherichia coli Nature Reviews Microbiology 2010]).

Keywords

drug combinations
droplet microfluidics
molecular bar-coding
emulsion physico-chemistry
antibiotics
yeast
drug resistance
evolution

Research unit

UMR8231 Chemistry, biology and innovation

Description of the research Unit/subunit

This project will be led in the UMR Chemistry Biology Innovation (CBI) 8231 (dir. Jérôme Bibette). CBI comprises teams with expertise ranging from microbial evolution, to biochemistry, physico-chemistry, microfluidics and analytical techniques.
Philippe Nghe and Andrew Griffiths are members of the Laboratory of Biochemistry (LBC), which develops droplets microfluidics technology to performed very high-throughput (1000 Hz) biochemical operations, with applications in single cell analysis (phenotyping and genotyping) and drug screening.
Jérôme Bibette is an expert in emulsion physico-chemistry, the LCMD having developed a number of droplet systems with well controlled exchange properties.

Name of the supervisor
Philippe Nghe (philippe.nghe@espci.fr)

Name of the co-supervisor
Andrew Griffiths (andrew.griffiths@espci.fr)

3i Aspects of the proposal

By combining cutting-edge microtechnology and biotechnology, this project will push the current frontier in drug discovery, by introducing a 100 to 1000 fold increase in measurement throughput compared to conventional microtiter plate robotic systems. The considerable throughput improvement proposed in this project is made possible by the combination of droplet microfluidics, molecular bar-coding, Next Generation Sequencing and bioinformatics. The combination of these technologies is critical to cross the required throughput barrier, as they altogether provide a consistent scaling up from sample preparation to data interpretation. The project will be led in collaboration with Sander Tans. Pr Tans is the PI of the Biophysics Lab at AMOLF (ND) and professor at Delft University. These visits of the PhD in the AMOLF lab will be aimed at characterizing and modelling bacteria strains showing differential response to antibiotic combinations, notably evolve experimentally antibiotic resistant, but non-pathogenic, strains.

Expected Profile of the candidate

Given the highly interdisciplinary character of the project, the PhD candidate could either:
- have a strong engineering background, including a Master degree in physics or chemistry, and be highly motivated to learn the microbiology and molecular biology aspects of the project.
- have a background in biology, with an emphasis on systems biology and quantitative approaches, and be highly motivated for engineering challenges.
An experience in droplet-based microfluidics is not required.
Flexibility, autonomy, ability to work in a highly multidisciplinary team and good interpersonal skills are essential. Sense of entrepreneurship and a motivation for industrial challenges are a highly valued.

Important dates

Call for applications : from July 16th to September 17th 2018
Eligibility check results : Late September
3i Committee evaluation results : Late October
Interviews from the shortlisted candidates with the Selection Committee : Mid-December (week of December 10th)
Final results : Late December





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