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EASTBIO A synthetic biology approach to design ‘intelligent’ organoids for the study of host-microbe interactions

  • Full or part time
    Dr E Cachat
    Dr Luke Boulter
  • Application Deadline
    Sunday, January 05, 2020
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description


Organoids are self-organised, 3D structures generated in vitro from adult or pluripotent stem cells, that exhibit similar functionality as their tissue of origin. Organoid-based systems are recognised in the biomedical field as a rapidly developing technology broadening the scope for developmental biology, disease modelling and drug screening. They are emerging as a complement (and maybe in the future as an alternative) to animal experiments, as they are well suited to the study of human diseases. A recent advance and promising clinical application for organoid technologies is the study of host-pathogen and host-microbiome interactions. Organoids infected with pathogens can be used to better understand the infection process and disease progression in human-like tissues. Organoid co-culture systems can also be used to dissect the complex interactions between host tissue and the commensal microbiota in a controlled in vitro environment.

Although extremely promising, organoid technologies are still in their infancy and some challenges need to be overcome before they can be widely implemented. In particular, organoid-based assays lack high-throughput screening capabilities: 3D fluorescence imaging allow the study of various processes mimicked in organoid platforms, but achieving high-throughput imaging with high spatial resolution is essential for their use as disease modelling platforms. In the case of host-microbe interaction studies, simplifying the analysis of the complex interplay between organoid cells and colonising microorganisms will greatly contribute to the establishment of these technologies as transformative research tools.

Recent advances in genome-editing tools, such as the CRISPR/Cas9 technology, have allowed the development of organoids for gene therapy. Stem cells from which organoids are derived can be modified, and the resulting organoids used to generate healthy tissues. These modified organoids have opened new possibilities for the development of ‘synthetic’ organoids. In a same way, stem cells can be engineered with synthetic gene circuits that endow derived organoids with customisable functions. This synthetic biology approach allows to program organoids with new behaviours and in particular with new reporting capabilities that can facilitate the microscopic analysis of a wide variety of organoid-based investigations (host-pathogen interaction, drug screening, etc.).

This project aims at designing ‘intelligent’ organoids that can spatially report on their interaction with microbes. As a proof-of-concept, ES cells will be programmed with synthetic gene circuits that allow reporter expression upon bacterial interaction. These engineered cells will be used to derive intestinal organoids and their 3D spatiotemporal imaging optimised. The cellular interactions between bacteria and organoid cells will be investigated to answer various questions relating to pathogen gut infection and the effect of drug treatment on different bacterial populations. Within this project, the student will receive training in scientific research skills and analytical methods (such as microscopy and flow cytometry), but also acquire specific skills in molecular and synthetic biology, as well as stem cells and organoid biology.

Funding Notes

The “Visit Website” button will take you to our Online Application checklist. Complete each step and download the checklist which will provide a list of funding options and guide you through the application process. Follow the instructions on the EASTBIO website (you will be directed here from our application checklist), ensuring you upload an EASTBIO application form and transcripts to your application, and ticking the box to request references. Your referees should upload their references using the EASTBIO reference form, in time for the 5th January deadline so please give them plenty of time to do this by applying early.

How good is research at University of Edinburgh in Biological Sciences?

FTE Category A staff submitted: 109.70

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