An engineered E. coli Nissle improves hyperammonemia and survival in mice and shows dose-dependent exposure in healthy humans

Abstract

The intestine is a major source of systemic ammonia (NH3); thus, capturing part of gut NH3 may mitigate disease symptoms in conditions of hyperammonemia such as urea cycle disorders and hepatic encephalopathy. As an approach to the lowering of blood ammonia arising from the intestine, we engineered the orally delivered probiotic Escherichia coli Nissle 1917 to create strain SYNB1020 that converts NH3 to l-arginine (l-arg). We up-regulated arginine biosynthesis in SYNB1020 by deleting a negative regulator of l-arg biosynthesis and inserting a feedback-resistant l-arg biosynthetic enzyme. SYNB1020 produced l-arg and consumed NH3 in an in vitro system. SYNB1020 reduced systemic hyperammonemia, improved survival in ornithine transcarbamylase–deficient spfash mice, and decreased hyperammonemia in the thioacetamide-induced liver injury mouse model. A phase 1 clinical study was conducted including 52 male and female healthy adult volunteers. SYNB1020 was well tolerated at daily doses of up to 1.5 × 1012 colony-forming units administered for up to 14 days. A statistically significant dose-dependent increase in urinary nitrate, plasma 15N-nitrate (highest dose versus placebo, P = 0.0015), and urinary 15N-nitrate was demonstrated, indicating in vivo SYNB1020 activity. SYNB1020 concentrations reached steady state by the second day of dosing, and excreted cells were alive and metabolically active as evidenced by fecal arginine production in response to added ammonium chloride. SYNB1020 was no longer detectable in feces 2 weeks after the last dose. These results support further clinical development of SYNB1020 for hyperammonemia disorders including urea cycle disorders and hepatic encephalopathy.

Engineered butyrate-producing bacteria prevents high fat diet-induced obesity in mice

“…Fecal metabolomics has been focused on revealing changes in metabolites and metabolic pathways in diseases [36,42,43]. Thus, we performed metabolomics analysis of fecal samples to investigate changes in metabolite levels and metabolic pathways.…”

Developing a new class of engineered live bacterial therapeutics to treat human diseases

“…Engineered bacterial therapeutics possess a potential advantage over alternative microbiota-directed therapeutic approaches, such as fecal microbiota transplants or defined consortia of naturally occurring species, in that genetic engineering can confer functions that are not expressed by the endogenous microbiota. Engineered LBPs can be designed to perform natural biological processes, such as the assimilation of ammonia into amino acids, at significantly increased rates 14 and to produce effectors that are not native to bacteria, including human proteins 16 . Functions encoded by engineered bacteria also have potential for the treatment of inborn errors of metabolism (IEMs) present in the host, such as phenylketonuria (PKU) 54 .…”

“…In the United States, recombinant LBPs are regulated by the Food and Drug Administration (FDA) through the Center for Biologics Evaluation and Research (CBER). While there have been numerous probiotics approved as nutritional supplements and some engineered bacterial strains have been studied in the clinic [14][15][16] , the FDA has not approved a live biotherapeutic product for medicinal use to date. In 2016, the FDA issued a guidance document describing the regulatory considerations for conducting clinical trials with LBPs 10 .…”

Adaptive Strategies of the Candidate Probiotic E. coli Nissle in the Mammalian Gut

“…We focus on the probiotic Escherichia coli Nissle 1917 (EcN), an E. coli clade B2 commensal ( Figure S1). EcN has a long history of use in humans (Westendorf et al, 2005), has demonstrated efficacy against inflammatory bowel disease (Scaldaferri et al, 2016), and has been gaining increased attention as a chassis for engineered function (Hwang et al, 2017;Isabella et al, 2018;Kurtz et al, 2019;Palmer et al, 2018). We expected several factors to drive adaptation of EcN in the mouse gut.…”