Efficacy and Safety of SYNB1934 in Patients With PKU (SYNPHENY-3)

In the DEP, all enrolled participants maintained a stable diet reflecting their baseline phenylalanine (Phe) intake and received escalating doses of SYNB1934v1 from approximately 3 to 15 weeks to determine an individually titrated dose (iTD), which was defined as the highest dose the participant was able to tolerate. A participant was defined as having reached an iTD if they tolerated 3 weeks at a dose, regardless of whether other doses were tolerated.

Blood Phe level was measured at each dose level after 3 weeks at that level. A responder was defined as a participant who achieved a ≥ 20% reduction in blood Phe level compared to DEP baseline on SYNB1934v1.

Participants who completed at least 3 weeks at their iTD during the DEP entered a 4-week RWP in which they were randomized 1:1 to receive SYNB1934v1 at their iTD determined in the DEP or placebo TID. Randomization was stratified on screening Phe level. Participants remained on their assigned dose (iTD of SYNB1934v1 or matching placebo) for the duration of the RWP, unless they developed intolerance or met other discontinuation criteria, and remained on the same diet they consumed during the DEP. Blood Phe level was measured at Weeks 1, 3, and 4 of the RWP.

Participants who completed the 4-week RWP may have entered the OLE and received SYNB1934v1 for up to 36 months. During the OLE, participants completed a dose ramp to their iTD over time guided by tolerability. The iTD in the OLE may have been different from the iTD in the DEP. The investigator may have escalated the SYNB1934v1 dose up to 1 × 10\^12 live cells based on tolerability. Participants were allowed to modify their standard diet, with guidance from the investigator, if their blood Phe level was < 240 µmol/L.

• SYNB1934v1 (Drug): SYNB1934v1 consisted of powder for oral suspension packaged in sachets. During dose preparation, the powder was resuspended in water or apple juice prior to administration.
• Placebo (Drug): Placebo was manufactured using an inactive powder that was color matched to the SYNB1934v1 drug product. In order to maintain study blinding during the RWP, placebo was packaged, labeled, stored, and administered in an identical manner to SYNB1934v1.

Primary outcomes

• Mean Percent Change From DEP Baseline in Blood Phenylalanine (Phe) Level at Week 3 of iTD During the DEP [Up to 15 weeks]: Baseline for blood Phe level in the DEP was defined as the mean of the duplicate blood Phe level measurements obtained immediately prior to administration of the first dose in the DEP. If only 1 blood Phe level measurement was available, then that measure was used as baseline. The last measurement was the participant's last Week 3 blood Phe level at the iTD of SYNB1934v1.

Secondary outcomes

• Absolute Change From DEP Baseline in Blood Phe Level at Week 3 of iTD During the DEP [Up to 15 weeks]: Baseline for blood Phe level in the DEP was defined as the mean of the duplicate blood Phe level measurements obtained immediately prior to administration of the first dose in the DEP. If only 1 blood Phe level measurement was available, then that measure was used as baseline. The last measurement was the participant's last Week 3 blood Phe level at the iTD of SYNB1934v1.
• Number of Participants With a ≥ 20% Reduction From Baseline in Blood Phe Level at Any Time in the DEP [Up to 15 weeks]: Baseline for blood Phe level in the DEP was defined as the mean of the duplicate blood Phe level measurements obtained immediately prior to administration of the first dose in the DEP. If only 1 blood Phe level measurement was available, then that measure was used as baseline. Blood Phe level was measured at each dose level after 3 weeks at that level.

Sex: All, ages: 18 Years to any

Male and female participants were enrolled.

Inclusion Criteria:

1. Age ≥ 18 years.
2. Able and willing to voluntarily complete the informed consent process.
3. Diagnosis of phenylketonuria (PKU) and failure to maintain recommended blood Phe levels on existing management (sapropterin, sepiapterin, and/or Phe-restricted diet), demonstrated by uncontrolled blood Phe level > 360 μmol/L on current therapy any time during screening and uncontrolled blood Phe level > 360 μmol/L on current therapy when taking the average of the 3 most recent Phe levels from the participant's medical history (inclusive of any screening values). All screening values must have been obtained more than 7 days apart, as determined by central or local laboratory.
4. Females of childbearing potential must have had a negative pregnancy test at screening and at the end of the DEP (in order to enter the RWP) and RWP (in order to enter the OLE) and been willing to have additional pregnancy tests during the study.
5. Sexually active female participants of childbearing potential must have been willing to use an acceptable method of contraception while participating in the study and for 2 weeks after the last dose.
6. Stable diet including stable medical formula regimen (if used) for at least 1 month prior to screening.
7. If using sapropterin or sepiapterin, must have been on a stable dose for at least 3 months.
8. Willing and able to continue current diet, sapropterin, sepiapterin, and large neutral amino acids unchanged during screening, DEP, and RWP and to engage in all study activities.

Exclusion Criteria:

1. Currently taking Palynziq® (pegvaliase-pqpz) (within 1 month of screening).
2. Acute or chronic medical, surgical, psychiatric, or social condition or laboratory abnormality that may have increased participant risk associated with study participation, compromised adherence to study procedures and requirements, and, in the judgment of the investigator, would have made the participant inappropriate for enrollment.
3. A known or suspected diagnosis of DNAJC12 deficiency, biopterin synthesis deficiency, or irritable bowel syndrome.
4. Intolerance to or allergic reaction to Escherichia coli Nissle or any of the ingredients in SYNB1934v1 formulation, or an allergy to cinnamon. Known intolerance to proton pump inhibitors and H2 blockers, since one or the other must have been used.
5. Currently taking or plans to take any type of systemic (e.g., oral or intravenous) antibiotic within 28 days prior to the first dose of SYNB1934v1 through final safety assessment in the RWP, including planned surgery, hospitalizations, dental procedures, or interventional studies that were expected to require antibiotics. Exception: topical antibiotics were allowed.
6. Pregnant, planning to become pregnant, or breastfeeding.
7. Current participation in any other investigational drug study or use of any investigational agent within 30 days or 5 half-lives (whichever was longer) prior to screening.
8. Ever received gene therapy for treatment of PKU.

Participant flow

Outcome results

• Mean Percent Change From DEP Baseline in Blood Phenylalanine (Phe) Level at Week 3 of iTD During the DEP (Primary), Median, percent change: iTD of 3 x 10^11 Live Cells ; iTD of 6 x 10^11 Live Cells -3.85 (0 to -3.85); iTD of 1 x 10^12 Live Cells 5.33 (-37.2 to 59.3); Overall DEP 3.35 (-37.2 to 59.3)
• Absolute Change From DEP Baseline in Blood Phe Level at Week 3 of iTD During the DEP (Secondary), Median, µmol/L: iTD of 3 x 10^11 Live Cells ; iTD of 6 x 10^11 Live Cells -55.00 (0 to -55.00); iTD of 1 x 10^12 Live Cells 55.25 (-227.0 to 406.5); Overall DEP 30.50 (-227.0 to 406.5)
• Number of Participants With a ≥ 20% Reduction From Baseline in Blood Phe Level at Any Time in the DEP (Secondary), Count of participants, Participants: iTD of 3 x 10^11 Live Cells 0; iTD of 6 x 10^11 Live Cells 0; iTD of 1 x 10^12 Live Cells 6; Overall DEP 6

Adverse events

Time frame: All AEs occurring from the time a participant signed the informed consent form through the safety follow-up period and at least 1 month following the last dose of IMP were documented, regardless of causal assessment to IMP.

Other adverse events by term

Limitations and caveats: Early termination leading to small numbers of participants analyzed

• Study Protocol (PDF, 2023-07-01)
• Statistical Analysis Plan (PDF, 2023-10-05)