Engineering novel bacterial therapies for targeting microbes associated with chemotherapy response and toxicity

Colorectal cancer (CRC) is the second leading cause of cancer related deaths world-wide. The gut microbiome is increasingly linked in the causation of this disease and strong stage-dependent correlations with the abundance of oral pathobionts and anti-correlations with mucosal commensal bacteria have been identified. There is emerging evidence that the microbiome is also able to influence therapeutic efficacy and toxicity in many established cytotoxic therapies. The implication of this is that the gut microbiome can be modulated to abrogate the toxicity of both immuno- and chemotherapy or improve its efficacy, and that it may even serve as a novel therapeutic target. However, current strategies for microbiome modification such as pre- and probiotic therapy, antibiotic therapy, faecal microbiota transplantation and microbial engineering have yet to be widely explored for therapeutic potential.

Synthetic biology applies engineering principles and mathematical modelling to the development of new biotherapeutics. Bacteriocins are small antimicrobial peptides that are naturally produced by certain species of bacteria to target competitors and allow for the establishment of colonies. Nisin is the amongst the most studied and is used as a food preservative (E234). Bacteriocins can be highly specific or have a broad spectrum and can be combined in a modular fashion to create unique antimicrobial agents. Our hypothesis is that bacteriocins can be used for precision engineering of the CRC mucosal microbiome to influence the efficacy and toxicity of cytotoxic chemotherapy. The tools of synthetic biology will enable the rapid engineering of strains to target specific bacterial species. We deploy these therapies in a number of model systems with an aim to providing the foundation for future clinical trials. This engineering approach will facilitate the development of interventions that can be co-delivered with chemotherapy agents, allowing for a reduction in toxicity, a safe increase in dose, and ultimately improve efficacy.

The 2016 UK Roadmap Bio-design for the Bio-economy highlighted the substantial impact that synthetic biology can bring to the UK and global economies by developing: frontier science and technology; establishing a healthy innovation pipeline; a highly skilled workforce and an environment in which innovative science and businesses can thrive. Synthetic biology promises to transform the UK Bio-economy landscape, bringing bio-sustainable and affordable manufacturing routes to all industrial sectors and will ensure society can tackle many contemporary global Grand Challenges including: Sustainable Manufacturing, Environmental Sustainability Energy, Global Healthcare, and Urban Development. Whilst synthetic biology is burgeoning in the UK, we now need to build on the investments made and take a further lead in training next generation scientists to ensure sustained growth of a capable workforce to underpin the science base development and growth in an advanced UK bio-economy.
This training provided by this CDT will give students from diverse backgrounds a unique synthesis of computational, biomolecular and cellular engineering skills, a peer-to-peer and industrial network, and unique entrepreneurial insight. In so doing, it will address key EPSRC priority areas and Bioeconomy strategic priorities including: Next-generation therapeutics; Engineered biomaterials; Renewable alternatives for fuels, chemicals and other small molecules; Reliable, predictable, and scalable bioprocesses; Sustainable future; Lifelong health & wellbeing.
Advances created by our BioDesign Engineering approach will address major societal challenges by delivering new routes for chemical/pharma/materials manufacture through to sustainable energy, whilst providing clean growth and reductions in energy use, greenhouse gas emissions and carbon footprints. Increased industry awareness of bio-options with better civic understanding will drive end-user demand to create market pull for products. The CDT benefits from unrivalled existing academic-industry frameworks at the host institutions, which will provide direct links to industrial partners and a direct pathway to early economic and industrial impact.

This CDT will develop 80-100 next-generation scientists and technologists (via the funded cohort and wider integration of aligned students at the three institutions) as adept scientists and engineers, instilled with technical leadership, who as broadly trained individuals will fill key skills gaps and could be expected to impact internationally through leadership roles in the medium term. Importantly the CDT addresses key skill-gaps identified with industry, which are urgently required to create and support high value jobs that will enable the UK to compete in global markets. Commercialisation and entrepreneurship training will equip the next generation of visionaries and leaders needed to accelerate and support the creation of new innovative companies to exploit these new technologies and opportunities.

The UK government identified Synthetic Biology as one of the "Eight Great Technologies" that could be a key enabler to economic and societal development. This CDT will be at the forefront of research that will accelerate the clean growth agenda and the development of a resilient circular bioeconomy, and will align with key EPSRC prosperity outcomes including a productive, healthy and resilient nation. To foster wider societal impact, the CDT will expect all students to contribute to public outreach and engagement activities including: open days, schools visits, and science festival events: students will participate in an outreach programme, with special focus on widening participation.

This CDT will contribute to the development of industrial strategy through the Synthetic Biology Leadership Council (SBLC), Industrial Biotechnology Leadership Forum (IBLF), and wider Networks in Industrial Biotechnology and Bioenergy and Professional Institutes.