Engineering probiotic yeast micro-factories for gastrointestinal biologic delivery

Inflammatory bowel disease (IBD) affects millions of people worldwide and causes significant intestinal mucosal injury, leading to debilitating symptoms including abdominal pain, fatigue, weight loss and severe diarrhoea. In the late 1990s, the introduction of anti-TNF therapies transformed treatment of severe or refractory IBD by targeting a key molecular driver of inflammation. However, anti-TNF biologics are typically administered systemically via intravenous infusion or subcutaneous injection. The circulation of the drug throughout the entire body leads to significant issues, including off-target immune suppression, increased infection risk and staggering healthcare costs. To address these limitations, there is a critical need for localised treatment that concentrates anti-inflammatory effects within the gut, while sparing the rest of the body.In their study, Palou, Tyers and colleagues address this limitation by engineering the probiotic yeast Saccharomyces boulardii into a high-tech ‘micro-factory’ for in situ drug delivery of anti-TNF nanobodies. Unlike many bacterial species that perish in the harsh acidic environment of the stomach, S. boulardii is naturally acid tolerant, making it an ideal vehicle for oral delivery. Nanobodies are tiny, ultra-stable antibody fragments that are small enough to be produced in bacteria or yeast. The authors found that nanobodies based on a camelid heavy chain-single variable (VHH) scaffold yielded far higher levels of secretion than conventional antibodies and other variants tested. The authors then assessed different promoters to drive expression of the VHH nanobody scaffold within S. boulardii. The ADH2 promoter achieved higher yields of anti-murine TNF (mTNF) and anti-human TNF (hTNF) nanobodies over other promoters tested. ADH2 was, therefore, selected to drive production of anti-mTNF nanobodies for in vivo studies as it is known to be active in low glucose and hypoxic conditions found within the distal intestine. Importantly, the oral administration of S. boulardii engineered to express ADH2-driven anti-mTNF VHH in a dextran sodium sulphate mouse model of colitis led to a 60% improvement in survival and significantly reduced disease severity compared to that in colitic mice treated with saline alone. This genetically modified probiotic was also shown to neutralise inflammation without disrupting the delicate balance of the endogenous microbiome.This innovative model system paves the way for future novel therapeutic strategies by positioning engineered yeast as a cost-effective, site-specific alternative to systemic injections. As S. boulardii is already a ‘generally recognised as safe’ organism, this platform is a prime candidate for human clinical trials. Furthermore, its adaptability suggests future applications in delivering a range of biologics to the intestine to locally treat intestinal diseases, thus having the potential to revolutionise human and veterinary medicine.