Integrating living analytics into biomanufacturing processes

Lead Research Organisation: Imperial College London
Department Name: Chemical Engineering


Cells are increasingly being used to manufacture a wide variety medicines, renewable plastics, chemicals, and other consumer products. Understanding the behaviour of cells during the manufacturing process is necessary to optimise production and to make sure that product yield and quality are high. Currently, this is done by measuring a few factors using established technologies based on chemistry. However, living systems have naturally have the ability to sense their environment and respond to changes accordingly. These mechanisms have better sensitivity and specificity than the chemical methods currently used. In the past few years, scientists have begun to harness these natural systems to develop analytical technology called biosensors. Biosensors can be used to detect the presence or absence of a molecule of interest in the environment. They also can be used to estimate the concentration of a molecule of interest (analyte). It is the latter type of biosensor that is interesting for biological manufacturing processes because it allows the accurate measurement of concentrations of key factors that are important for maximising the yield and productivity of cell-based manufacturing systems.

The aim of this proposal is to develop a framework for using living biosensors in biomanufacturing processes. The focus in on identifying the best way to grow the biosensor and the producing cell together in such away that both types of cells survive and function correctly. For this, we will try a number of different physical separation methods including membrane separation, trapping the biosensor in a polymer, or trapping the biosensor in a bubble of lipid. We will also try to genetically modify the biosensor cell to cause it to stick to the wall of the culture vessel or to bud off non-living particles that can still behave as biosensors, but can no longer grow.

Each of these strategies will be tested using a biosensor we have already developed to measure the concentration of an analyte coming from mammalian cells that are also producing a protein drug. We want to find conditions where the biosensor does not overgrow the mammalian cell, but still can sense and respond to changes in analyte concentration. Once the basic principle of a living analytic has been demonstrated, we hope that this will change the way that measurements of cellular behaviour are done in the future and lead to better understanding of cells during the manufacturing process. Hopefully one day this will lead to higher yields of products from biological manufacturing systems, which ultimately will decrease the costs to consumers.

Planned Impact

Manufacturers in the bioprocessing industry will benefit from this research as it will open up a new methodology for analysis of cells during production. Living biosensors can sense a wider array of compounds that correlate with product yield and can detect analytes at extremely low concentrations giving them advantages over current technology. Engagement of both existing manufacturers and startups/SMEs in the synthetic biology space will allow the technology to be broadly adopted to have the most impact.

Adoption of this technology by industry will result in benefits to consumers of products made using biomanufacturing processes. Improved analytics will result in greater process understanding, allow manufacturers to develop processes with increased yields and product quality, driving down costs. In particular, in the recombinant protein therapeutic industry, the cost of these medicines to consumers is of concern as it places increased burden on the bodies that fund healthcare (e.g. the NHS). Therefore, measures that can improve productivity and decrease the costs of manufacturing would help to reduce the costs of these therapies and should also lead to increased access to a broader range of therapies (e.g. those currently considered too expensive).

Those engaging in synthetic biology and manufacturing research will benefit from the work as the first demonstration of the full potential of biosensors applied to bioprocessing. Synthetic biology has been discussed as a disruptive technology with the potential to change the way biological systems are engineered. Using synthetic biology to develop biosensors has already been demonstrated to have benefits, but the practical application of these to industrial processes has not yet been attempted. This project would be a tangible demonstration of the benefits of using synthetic biology in manufacturing in a creative and novel way. Thus, it could serve as a talking point for researchers to illustrate the benefits of synthetic biology for industrial applications.

Finally, the proposed project has potential for public engagement with research in manufacturing. The proposed project would lead to physical output such as new bioreactor probes that can be used to explain the concepts behind the research in a visual and attractive way. Thus, it could serve as a nice demonstration platform for public engagement activities at science fairs, festivals, or in school outreach activities.
Description The aim of the project was to develop ways to practically use whole-cell biosensors for bioprocess monitoring. After discussions with the National Centre for Biologics Manufacturing (CPI), we focused on two strategies for creating biosensors that could be integrated into biomanufacturing processes without disrupting the physical properties of the system, such as mixing and aeration. These were: i) the encapsulation of the cells in reasonably small, round polymer beads that can be added and removed from the culture and ii) the creation of non-living, cell-like vesicles (mini-cells) from the asymmetric division of the biosensors.

For strategy i, we tested a variety of polymer types and developed a multi-layer encapsulation strategy that prevents biosensor cell escape, but allows the cells to remain functional for detection. The beads can be made, frozen, and stored up to 4 weeks without loss of functionality. Furthermore, the beads were used to monitor metabolite production in a co-culture with a Chinese Hamster Ovary (CHO) cell line producing a monoclonal antibody. The CHO cell viability and productivity were maintained and the biosensor beads were able to accurately reflect the increasing metabolite concentrations over time. This work was published in ACS Synthetic Biology in March 2022 and we have presented it at several international conferences including the Mammalian Synthetic Biology Workshop (2021), the American Institute of Chemical Engineers Annual Meeting (2021), and PEGS (2022). The work led to discussions with new collaborators both in academia and industry and to a follow-on project sponsored by the EPSRC.

For strategy ii, we have been able to successfully create mini-cells containing the machinery to sense metabolites, but the response to metabolites is very weak. We identified a low level of RNA production machinery (the first step in the cascade to produce a biosensor response) due to poor partitioning during the mini-cell creation as a likely source of the issue. To tackle this, we first attempted to redesign the genetic sensing component to use a different, more abundant type of RNA production machinery. This did not work well due to cell stress responses. We then tested a second way of tackling this issue, which is to tether some of the transcriptional machinery to the membrane during mini-cell formation. This would, in effect, force better partitioning, but the sensors still do not respond well.

In addition, the PDRA contributed to work towards the development of a biosensor for RNA vaccines, which was not planned as part of the initial work package, but the need arose due to the covid-19 pandemic. This work resulted in a follow on project sponsored by BBSRC and is being further developed.
Exploitation Route The polymer encapsulation strategy we have focused on are independent of the type of whole-cell biosensor used, which means it is analyte independent. Thus, we believe it could be widely adopted in the biosensor field for use with other manufacturing processes. We have received follow on funding to see how generalisable the concept is from the EPSRC (EP/W00979X/1). In addition, we are part of a multi-investigator project to develop new instrumentation that would allow the use of the encapsulated biosensors in situ, which would increase their utility (EP/W024969/1).
Sectors Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

Description Adventurous Manufacturing Follow On: Integrating Living Analytics into Biomanufacturing Processes
Amount £870,445 (GBP)
Funding ID EP/W00979X/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 03/2022 
End 11/2025
Description EP/W024969/1, BioSMART: BIOreactor Spatial Mapping and Actuation in Real Time
Amount £1,011,859 (GBP)
Funding ID EP/W024969/1, 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 02/2023 
End 02/2025
Description Collaboration with the National Biologics Manufacturing Centre (Centre for Process Innovation) 
Organisation Centre for Process Innovation (CPI)
Country United Kingdom 
Sector Private 
PI Contribution We have proposed various strategies for implementing biosensors within bioreactors to better understand what would work within the manufacturing workflows used at CPI.
Collaborator Contribution The team has considerable experience in manufacturing processes and has advised us on which strategies for encapsulation/physical containment may be more suitable and acceptable to manufacturers. This has helped us identify which strategies to focus on.
Impact No outputs as yet, but the discussions led us to focus our efforts on two strategies: one involving polymer encapsulation of the biosensors and the other involving development of mini-cell based non-living vesicles. These have the commonality that they are round and would not affect the hydrodynamics or mixing within the bioreactor, which was highlighted by the CPI team in the discussions.
Start Year 2020