Report

Teaser, summary, work performed and final results

Periodic Reporting for period 2 - PHENOSPACE (Quantifying behavioural phenotype space: chemistry-to-gene screens and combination therapies)

Teaser

A central goal of precision medicine is to tailor treatments for individuals based on their genomic sequence. However, many common diseases are associated with mutations in multiple genes and drugs often interact with multiple targets, making it difficult to go from genome...

Summary

A central goal of precision medicine is to tailor treatments for individuals based on their genomic sequence. However, many common diseases are associated with mutations in multiple genes and drugs often interact with multiple targets, making it difficult to go from genome sequence to drug selection. Spontaneous locomotion in the nematode C. elegans provides a model to address fundamental questions about the mapping between chemical and genetic perturbation and complex phenotypes. To take full advantage of this potentially powerful model system, we will develop high-throughput tracking technology, both hardware and software, and use it to measure changes in worm behaviour in response to treatment with small molecules and genome-wide RNA interference. The result will be an unprecedented view of a multidimensional phenotype space in a genetically tractable model animal that will allow us to predict targets of neuroactive compounds, discover new gene-behaviour associations, and suggest new indications for approved drugs. We will then analyse this mapping to define design principles for combination therapies and test them quantitatively in vivo. The final aim is to combine automated phenotyping and liquid handling with a genetic algorithm to evolve complex drug cocktails. The result will be a better understanding of the potential of precision medicine and progress towards quantitative methods to realise that potential with combination therapies.

Work performed

We are currently in the technology development phase of the project and we have made substantial progress towards our hardware and software goals. We have assembled the multi-camera imaging systems with a field of view and resolution large enough to imaging hundreds of individual worms simultaneously from all of the wells of a multiwell plate. We have done some preliminary imaging experiments and found that we can use 96-square-well plates for worm-tracking on agar. This means we will be able to do almost 500 simultaneous worm tracking experiments on the new setup. We have also prototyped a bright blue LED system that we can use for stimulating worm locomotion. In preliminary experiments we have found we have a high enough intensity to illicit an escape response from essentially all of the worms on the plate, which will be important for consistency. The blue light stimulation may allow us to find significant phenotypes faster than would be possible with spontaneous locomotion, thus increasing our ultimate throughput.

On the software side, we have adapted Tierpsy Tracker to work with multi-well plates including the automatic detection and segmentation of multiple wells and the automatic detection of food boundaries. We are still working on a faster and more powerful worm-segmentation and skeletonisation algorithm using convolutional neural networks that will be useful for the planned drug cocktail experiments.

Final results

Our prototype multi-camera imaging system provides an approximately 100-fold increase in throughput compared to previously published worm trackers and will be essential for some of our more ambitious aims including large scale drug screens and a genome-wide RNA interference screen for complex behavioural phenotypes.