Abstract
Despite available treatment options, many patients with phenylketonuria (PKU) cannot achieve target plasma phenylalanine (Phe) levels1. We previously modified Escherichia coli Nissle 1917 to metabolize Phe in the gut after oral administration (SYNB1618) and designed a second strain (SYNB1934) with enhanced activity of phenylalanine ammonia lyase2,3. In a 14-day open-label dose-escalation study (Synpheny-1, NCT04534842), we test a primary endpoint of change from baseline in labeled Phe (D5-Phe AUC0−24; D5-Phe area under the curve (AUC) over 24 hours after D5-Phe administration) in plasma after D5-Phe challenge in adult participants with screening Phe of greater than 600 µM. Secondary endpoints were the change from baseline in fasting plasma Phe and the incidence of treatment-emergent adverse events. A total of 20 participants (ten male and ten female) were enrolled and 15 completed the study treatment. Here, we show that both strains lower Phe levels in participants with PKU: D5-Phe AUC0−24 was reduced by 43% from baseline with SYNB1934 and by 34% from baseline with SYNB1618. SYNB1934 led to a decrease in fasting plasma Phe of 40% (95% CI, −52, −24). There were no serious adverse events or infections. Four participants discontinued because of adverse events, and one withdrew during the baseline period. We show that synthetic biotics can metabolize Phe in the gut, lower post-prandial plasma Phe levels and lower fasting plasma Phe in patients with PKU.
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Data availability
Data in this article (and the Supplementary Information) have been presented where possible as group-level summaries. Any data presented to illustrate individual participant performance have been de-identified. The data sets generated during and/or analyzed during the current study are available from the corresponding author (N.S.) upon reasonable request including a methodologically sound proposal, although restrictions may apply owing to participant privacy and HIPAA regulations. Source data are provided with this paper.
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Acknowledgements
We thank the study participants and their families as well as the research nurses and study staff. We also acknowledge the support of the National PKU Association.
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J.V., M.P., W.S.D., K.H., C.K. and A.M.B. conceived and designed the work. J.V., M.P., G.A.D., I.G., D.K.G., C.H., H.N., J.P., S.S., J.A.T., R.Z., S.L.E., K.H. and N.M. acquired the data. J.V., N.S., W.S.D., S.L.E., N.M., C.K. and A.M.B. analyzed and interpreted the data. J.V., N.S., C.K. and A.M.B. wrote the original draft of the manuscript. All co-authors reviewed and approved the manuscript.
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N.S., M.P., W.S.D., S.L.E., K.H., N.M., C.K. and A.M.B. are current or former employees of Synlogic and hold equity in Synlogic. J.V. and G.A.D. have consulted for Synlogic. J.V., G.A.D., I.G., D.K.G., C.H., H.N., J.P., S.S., J.A.T. and R.Z. received research funding from Synlogic. Funding for this study was provided by Synlogic. The funder participated in the study design, data analysis, preparation of the manuscript and decision to publish.
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Extended data
Extended Data Fig. 1 SYNB strain design and key engineering features.
SYNB1618 (A) and SYNB1934 (B) are shown. Abbreviations; LAAD = L-amino acid deaminase from Proteus mirabilis; laad = gene for LAAD. PAL = phenylalanine ammonia lyase from Photorhabdus luminescens; pal = gene for PAL; mPAL = modified phenylalanine ammonia lyase with higher potency. mpal = gene encoding mPAL. PheP = high-affinity phenylalanine transporter; pheP = gene encoding high-affinity phenylalanine transporter; PFNR = promoter regulated by fumarate and nitrate reductase regulator; Ptac = synthetic promoter controlling PAL expression and regulated by the LacI transcriptional repressor; PBAD = promoter for laad, regulated by arabinose; ΔdapA = deletion of dapA gene leading to diaminopimelate auxotrophy; Phe = phenylalanine, PP = phenylpyruvate; TCA = trans-cinnamic acid.
Extended Data Fig. 2 D5-Phe metabolite study.
The LS mean change from baseline Day −1 in D5 Phe metabolites was determined at day 14 for SYNB1618, (navy; n = 10) and SYNB1934 (orange; n = 5). A. Plasma D5 TCA AUC change from baseline in LS mean AUC 0–24 µM*h. B. Urinary D5 HA change from baseline in amount excreted (AeT) in mmol over 6 hours.
Supplementary information
Supplementary Information
The final protocol of SYNB1618-CP-003.
Supplementary Data 1
Protocol SYNB1618-CP-003.
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Vockley, J., Sondheimer, N., Puurunen, M. et al. Efficacy and safety of a synthetic biotic for treatment of phenylketonuria: a phase 2 clinical trial. Nat Metab 5, 1685–1690 (2023). https://doi.org/10.1038/s42255-023-00897-6
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DOI: https://doi.org/10.1038/s42255-023-00897-6
