Engineering 'Living Therapeutics'
Lead Research Organisation:
University College London
Department Name: Structural Molecular Biology
Abstract
Within the human body, host cells are vastly outnumbered by the symbiotic bacteria which constitute the 'microbiota'. Estimates currently suggest that the microbiota may be made up of over 100 trillion individual cells. In recent years, this population has aroused considerable excitement due to new insights which have shown that it has fundamental impacts on host health and wellbeing. These impacts range from aiding digestion, to suppressing inflammation and regulating the host immune system and metabolism. Therefore, the microbiota offers a wide array of cells which may be engineered and redesigned to offer new methods of improving patient health and well-being around the globe. However, despite increasing awareness of the importance of the microbiota, the potential it presents has remained relatively untapped. It is hoped that by using techniques from the field of synthetic biology this may be resolved.[1]
Synthetic Biology is a rapidly developing, multidisciplinary field found at the intersection of engineering and biology. This field aims to employ rational design and quantitative engineering principles to all aspects of biology. As such it has the potential to open many new avenues of research. It is hoped that these principles can be used to lay the foundations for the creation of engineered 'living therapeutics' or 'designer probiotics' in the future. These living therapeutics will reengineer the microbiota of a host individual, providing them with novel functions. These functions may primarily be designed to detect, diagnose and treat disease in-vivo. Living therapeutics may therefore, offer an alternative category of treatments for disorders which currently lack suitable options. This could include diseases such as diabetes, cancers and other metabolic/genetic disorders. In addition, the design process will greatly add to our understanding of the relationship and interactions between the host and resident microbiota.[2]
As a proof-of-concept for living therapeutic design, the E. coli Nissle strain is an ideal candidate. This strain has a proven track-record of being a safe probiotic (approved for use within the EU) and many genetic manipulation techniques for E. coli have previously been reported within the literature. Initially, metabolic engineering will be used to create a Nissle strain capable of producing butyrate. A molecule which has been shown to have anti-inflammatory and anti-carcinogenic properties. In addition, it should be noted that butyrate has numerous industrial applications; therefore, novel butyrate producing strains may also be utilised in non-medical applications. Subsequently, the strain may be engineered for its ability to detect specific markers of disease, allowing for predictable control of the butyrate production.[3]
This project will therefore employ a range of experimental techniques, drawing on principles from both engineering and biology. Initially, the techniques employed will include cell transformation, plasmid construction and cloning. Amongst others, High Performance Liquid Chromatography (HPLC) will also be used for the detection of butyrate production and Flux Balance Analysis (FBA) modelling for the rational design of novel Nissle strains.
Overall, it is hoped that this project will help to elucidate the fundamentals of how to design living therapeutics. Providing future studies with new tools which can be used to design living therapeutics, in turn having a positive impact upon patient health and wellbeing around the globe.
Synthetic Biology is a rapidly developing, multidisciplinary field found at the intersection of engineering and biology. This field aims to employ rational design and quantitative engineering principles to all aspects of biology. As such it has the potential to open many new avenues of research. It is hoped that these principles can be used to lay the foundations for the creation of engineered 'living therapeutics' or 'designer probiotics' in the future. These living therapeutics will reengineer the microbiota of a host individual, providing them with novel functions. These functions may primarily be designed to detect, diagnose and treat disease in-vivo. Living therapeutics may therefore, offer an alternative category of treatments for disorders which currently lack suitable options. This could include diseases such as diabetes, cancers and other metabolic/genetic disorders. In addition, the design process will greatly add to our understanding of the relationship and interactions between the host and resident microbiota.[2]
As a proof-of-concept for living therapeutic design, the E. coli Nissle strain is an ideal candidate. This strain has a proven track-record of being a safe probiotic (approved for use within the EU) and many genetic manipulation techniques for E. coli have previously been reported within the literature. Initially, metabolic engineering will be used to create a Nissle strain capable of producing butyrate. A molecule which has been shown to have anti-inflammatory and anti-carcinogenic properties. In addition, it should be noted that butyrate has numerous industrial applications; therefore, novel butyrate producing strains may also be utilised in non-medical applications. Subsequently, the strain may be engineered for its ability to detect specific markers of disease, allowing for predictable control of the butyrate production.[3]
This project will therefore employ a range of experimental techniques, drawing on principles from both engineering and biology. Initially, the techniques employed will include cell transformation, plasmid construction and cloning. Amongst others, High Performance Liquid Chromatography (HPLC) will also be used for the detection of butyrate production and Flux Balance Analysis (FBA) modelling for the rational design of novel Nissle strains.
Overall, it is hoped that this project will help to elucidate the fundamentals of how to design living therapeutics. Providing future studies with new tools which can be used to design living therapeutics, in turn having a positive impact upon patient health and wellbeing around the globe.
Organisations
People |
ORCID iD |
| Geraint Thomas (Primary Supervisor) | |
| Jack Rutter (Student) |
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M009513/1 | 01/10/2015 | 31/03/2024 | |||
| 1763910 | Studentship | BB/M009513/1 | 01/10/2016 | 14/02/2021 | Jack Rutter |
| Title | Colonised fluorescent C. elegans images |
| Description | These are images of colonised C. elegans nematodes which were collected through fluorescent microscopy. |
| Type Of Art | Image |
| Year Produced | 2018 |
| Impact | One of these images was chosen by department staff for inclusion on the front cover of the new student handbook, given to all new post-grads in our department. |
| Description | - We have developed a novel animal model based on a nematode species (C. elegans- like a little worm). This model can be used to test bacteria which have been engineered to perform a specific function within an animal's body. This will allow us to reduce the number of mice and other vertebrates that are currently used in the research of this area. It will also allow us to more accurately predict the behaviour of the bacteria we are trying to engineer. - We are also currently exploring techniques to engineer bacteria to become sensors for diseases and changes in their environments. This is an ongoing process; however, we are currently attempting to show that some of our sensors can work in a bacterial strain known as E. coli Nissle. This strain is able to live in the human digestive tract and may be very useful for attempting to detect and treat disease in the human body. - We have developed a range of novel acetoacetate-inducible biosensors. Acetoacetate is a molecule that plays a key role in human health and biology and is measured regularly in patients suffering from diabetes. We hope that the engineered biosensors may be used to help monitor and report on acetoacetate in complex environments in future. |
| Exploitation Route | There are numerous ways this work may be built upon. Firstly, the bacterial sensors characterised within this award may be used by others, to aid in the detection of metabolites or factors involved in health, biomanufacturing or environmental samples. Secondly, the C. elegans model developed may be used by others as a replacement for mice in studies of the microbiome or microbiota- this could help reduce the scale of animal based studies of the microbiome or microbiota. In addition, it can aid in the development of bacterial strains which are designed to work within in vivo conditions. The acetoacetate biosensors may also be built upon in future. To date, these biosensors have been characterised in tightly controlled conditions within the lab, future work may explore how they operate in more complex conditions (e.g. aerobic vs anaerobic conditions). This characterisation will be vital if the biosensors are to be used for in vivo monitoring in future. |
| Sectors | Agriculture, Food and Drink,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| URL | https://pubs.acs.org/doi/10.1021/acssynbio.9b00166 |
| Title | in vivo C. elegans model of host-microbe interactions |
| Description | Using the digestive tract of C. elegans to explore host-microbe interactions and characterise the in vivo behaviour of engineered bacterial strains. |
| Type Of Material | Model of mechanisms or symptoms - non-mammalian in vivo |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | This C. elegans model and accompanying protocols have now been published in ACS Synthetic Biology: https://pubs.acs.org/doi/abs/10.1021/acssynbio.9b00166. The model protocols allow rapid characterisation of fluorescent whole-cell biosensors within an in vivo environment (the C. elegans gut). These protocols may be adapted in future to help explore host-microbe and microbe-microbe interactions within microbiota communities. |
| URL | https://pubs.acs.org/doi/abs/10.1021/acssynbio.9b00166 |
| Description | Attended Cold Spring Harbor Synthetic Biology Summer school |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Around 20-30 attended the Summer school, held on Long Island in the US. Here we were able to present our research and take part in an intensive training course. This course lasted around two and a half weeks and lead to much informal discussion on a variety of our PhD projects and has allowed me to develop some academic connections outside of my own research institute. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Attended a site visit at the GSK Stevenage site. |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | This event was a visit to the GSK site in Stevenage, there was an audience of roughly 100 people. The main focus of the visit was to present our academic research to industry professionals and researchers working at the GSK site. There were also numerous talks on how to make more effective collaborations between academia and industry. This event was of great interest to myself as it helped to show me many useful examples of how academic research may be applied to a non-academic setting. It also helped to highlight some of the alternative career paths which can be chosen, alongside the more traditional academic route. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Attended multiple meetings of the 'London Synthetic Biology Network' |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | These are regular meetings, where informal presentations are given by two or three academic researches on their current work or an area of expertise. The audience of these events is made up of researchers from a range of London Universities and includes undergraduates, post-graduates, PIs and post-docs. The events focus mainly on the fields of synthetic biology and systems biology. The events often spark discussion and interest in fields that initially may seem unrelated to your own work. However, they provide a useful opportunity to see how your own work relates to the wider field of synthetic biology. They also provide a useful place to meet with others that may have experience in a certain technique or area, which can help your own research. |
| Year(s) Of Engagement Activity | 2018,2019 |
| Description | Presented my work at the International Conference of Microbiome Engineering |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Presented my work at the International Conference of Microbiome Engineering, held in Boston, USA. Attendees included private businesses, postgraduate students, senior academics and also some policy advisors. |
| Year(s) Of Engagement Activity | 2019 |