Bacteria engineered to treat disorders in which oxalate is detrimental
AssigneeSynlogic Operating Company, Inc.
InventorsVincent M. Isabella, David Lubkowicz, Michael James, Caroline Kurtz
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Abstract
The present invention provides recombinant bacterial cells comprising at least one heterologous gene encoding at least one oxalate catabolism enzyme. In another aspect, the recombinant bacterial cells further comprise at least one heterologous gene encoding an importer of oxalate. The invention further provides pharmaceutical compositions comprising the recombinant bacteria, and methods for treating disorders in which oxalate is detrimental, such as hyperoxaluria, using the pharmaceutical compositions of the invention.
Claims55
A method for reducing the levels of oxalate in a subject, the method comprising administering to the subject a pharmaceutical composition comprising a recombinant bacterium comprising:
- one or more gene sequences encoding one or more oxalate catabolism enzymes operably linked directly or indirectly to a first promoter that is not associated with the oxalate catabolism enzyme gene in nature, wherein the one or more gene sequences comprise a scaaE3 gene, an frc gene, and an oxdC gene, wherein the scaaE3 gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO:
- 3, wherein the frc gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO:
- 1, and wherein the oxdC gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO:
- 2,
- a gene encoding an oxalate importer, wherein the gene encoding the oxalate importer is an oxlT gene, and wherein the oxlT gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO:
- 11,
- a Δ thyA auxotrophy,
- a deletion in an endogenous phage,
- a modified endogenous colibactin island,
- thereby reducing the levels of oxalate in the subject.
The method of any one of the previous claims, wherein the recombinant bacterium does not comprise a gene encoding for antibiotic resistance.
The method of any one of the previous claims, wherein the recombinant bacterium has an oxalate consumption activity of about 211 mg/day under anaerobic conditions when administered to the subject three times per day.
The method of any one of the previous claims, wherein the method reduces acute levels of oxalate in the subject by about two fold.
The method of any one of the previous claims, wherein the recombinant bacterium is of the genus Escherichia.
The method of any one of the previous claims, wherein the pharmaceutical composition is administered orally.
The method of any one of the previous claims, wherein the subject is fed a meal within one hour of administering the pharmaceutical composition.
The method of any one of the previous claims, wherein the subject is a human subject.
The method of any one of the previous claims, wherein the first promoter is an inducible promoter, optionally when the inducible promoter is a FNR promoter, optionally wherein the FNR promoter comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of any one of SEQ ID NOs:
- 13-29.
The method of any one of the previous claims, wherein the subject has hyperoxaluria.
The method of any one of the previous claims, wherein the subject has urinary oxalate (Uox) levels of at least 70 mg/day prior to the administering.
The method of any one of the previous claims, wherein the subject exhibits a decrease in Uox levels of at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, or 80% after the administering.
The method of any one of the previous claims, wherein the subject has eGFR<30 mL/min/1.73 m2, requires hemodialysis, or has systemic oxalosis prior to the administering.
The method of any one of the previous claims, wherein the recombinant bacteria is administered at a dose of about 1×1011 live recombinant bacteria, about 3×1011 live recombinant bacteria, about 4.5×1011 live recombinant bacteria, about 5×1011 live recombinant bacteria, about 6×1011 live recombinant bacteria, about 1×1012 live recombinant bacteria, or about 2×1012 live recombinant bacteria.
The method of any one of the previous claims, wherein the recombinant bacteria is administered once daily, twice daily, or three times daily.
The method of any one of the previous claims, wherein the administering is about 5×1011 live recombinant bacteria with meals three times per day.
The method of any one of the previous claims, further comprising administering a proton pump inhibitor (PPI) to the subject.
The method of any one of the previous claims, wherein the pharmaceutical composition further comprises galactose.
A recombinant bacterium comprising:
- one or more gene sequences encoding one or more oxalate catabolism enzymes operably linked directly or indirectly to a first promoter that is not associated with the oxalate catabolism enzyme gene in nature, wherein the one or more gene sequences comprise a scaaE3 gene, an frc gene, and an oxdC gene, wherein the scaaE3 gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO:
- 3, wherein the frc gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO:
- 1, and wherein the oxdC gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO:
- 2,
- a gene encoding an oxalate importer, wherein the gene encoding the oxalate importer is an oxlT gene, and wherein the oxlT gene comprises a sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to, comprises, or consists of SEQ ID NO:
- 11,
- a Δ thyA auxotrophy,
- a deletion in an endogenous phage,
- a modified endogenous colibactin island.
Dependencies are inferred from the claim text.