Characterization of an engineered live bacterial therapeutic for the treatment of phenylketonuria in a human gut-on-a-chip

M Tyler Nelson,Eric S Greenwood,Mary J Castillo,David Lubkowicz,Elaine A Merrill,Heidi G Coia,Peter J Robinson,Camilla A Mauzy,Corey Holt,Mark R Charbonneau

doi:10.1038/s41467-021-23072-5

Abstract

Engineered bacteria (synthetic biotics) represent a new class of therapeutics that leverage the tools of synthetic biology. Translational testing strategies are required to predict synthetic biotic function in the human body. Gut-on-a-chip microfluidics technology presents an opportunity to characterize strain function within a simulated human gastrointestinal tract. Here, we apply a human gut-chip model and a synthetic biotic designed for the treatment of phenylketonuria to demonstrate dose-dependent production of a strain-specific biomarker, to describe human tissue responses to the engineered strain, and to show reduced blood phenylalanine accumulation after administration of the engineered strain. Lastly, we show how in vitro gut-chip models can be used to construct mechanistic models of strain activity and recapitulate the behavior of the engineered strain in a non-human primate model. These data demonstrate that gut-chip models, together with mechanistic models, provide a framework to predict the function of candidate strains in vivo.

Highlights

Engineered bacteria represent a new class of therapeutics that leverage the tools of synthetic biology
We recently described the development of a synthetic biotic strain of E. coli Nissle 1917, called SYNB1618, designed to consume Phe in the human upper gastrointestinal tract[4]
We have previously shown that oral administration of SYNB1618 significantly lowered blood Phe concentrations in a mouse model of PKU and resulted in dosedependent production of the phenylalanine ammonia lyase (PAL)-specific urinary biomarker, hippuric acid (HA), in healthy non-human primates (NHP)

Summary

Introduction

Engineered bacteria (synthetic biotics) represent a new class of therapeutics that leverage the tools of synthetic biology. Significant advances have been made toward organ-on-a-chip (OOC) microfluidic systems that can be used to study the effects of engineered microbes and their products on human tissues, including effects on tissue viability[8] These microscale synthetic tissue surrogates enable robust cellular and molecular analysis, fine control over transport and fluid flow dynamics, and incorporation of complex mechanical stimuli that capture aspects of human gut physiology. Single bolus application of a synthetic live biotherapeutic, SYN5183, is applied to the gut-compartment resulting in dose dependent increases in the biomarker, transcinnamic acid (TCA), and a corresponding 26.9% decrease in systemic Phe. Simulations performed using a mathematical model, calibrated to in vitro gut-chip results, showed a high degree of correlation with previously published non-human primate results[4], highlighting the predictive potential of gut-chip technology to accelerate synbiotic development

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