Provided herein is a dual vector transfection system for the production of recombinant adeno-associated virus (rAAV). The dual vector transfection system generally comprises: (1) a first nucleic acid vector comprising a first nucleotide sequence encoding an AAV Rep protein, a second nucleotide sequence comprising an rAAV genome comprising a transgene, and a third nucleotide sequence encoding an AAV capsid protein; and (2) a second nucleic acid vector comprising a helper virus gene.

Variant phenylalanine hydroxylase polypeptides having substitutions at selected amino acid residues are disclosed. Also disclosed are methods of using variant phenylalanine hydroxylase polypeptides, or polynucleotides encoding variant phenylalanine hydroxylase polypeptides, to treat disorders such as phenylketonuria.

The application describes ceDNA vectors having linear and continuous structure for delivery and expression of a transgene. ceDNA vectors comprise an expression cassette flanked by two ITR sequences, where the expression cassette encodes a transgene encoding PAH protein. Some ceDNA vectors further comprise cis-regulatory elements, including regulatory switches. Further provided herein are methods and cell lines for reliable gene expression of PAH protein in vitro, ex vivo and in vivo using the ceDNA vectors. Provided herein are method and compositions comprising ceDNA vectors useful for the expression of PAH protein in a cell, tissue or subject, and methods of treatment of diseases with said ceDNA vectors expressing PAH protein. Such PAH protein can be expressed for treating disease, e.g., Phenylketonuria (PKU).

Described herein are production cells, and methods for identifying, selecting, or culturing production cells comprising tyrosine auxotrophy selection marker system, based on a combination of sequence encoding a phenylalanine hydroxylase (PAH) which lacks a functional N-terminal regulatory domain, and a sequence encoding a GTP cyclohydrolase 1 (GCH1). Also described are methods of making a production cell and making a product with said production cell.

The present disclosure provides, among other things, a recombinant adeno-associated virus (rAAV) vector comprising an AAV8 capsid and a codon-optimized sequence encoding a human phenylalanine hydroxylase (PAH) enzyme. The disclosure also provides a method of treating a subject having phenylketonuria (PKU), comprising administering to the subject in need thereof a recombinant adeno-associated vims (rAAV) vector comprising an AAV8 capsid, and a promoter operably linked to a nucleic acid sequence that encodes PAH, and wherein administering results in a decrease in phenylalanine level in the subject.

The present invention provides, among other things, methods of treating phenylketonuria (PKU), including administering to a subject in need of treatment a composition comprising an mRNA encoding phenylalanine hydroxylase (PAH) at an effective dose and an administration interval such that at least one symptom or feature of PKU is reduced in intensity, severity, or frequency or has delayed in onset. In some embodiments, the mRNA is encapsulated in a liposome comprising one or more cationic lipids, one or more non-cationic lipids, one or more cholesterol-based lipids and one or more PEG-modified lipids.

The present invention concerns a method to modulate the level of or to modify a target molecule in a subject or an environment, said method comprising: administering in said subject or providing to said environment an engineered bacterial strain comprising (i) a heterologous or engineered nucleic acid involved in the expression of a molecule of interest, wherein the expression of said molecule of interest modulates directly or indirectly the level of or modify the target molecule in said subject or environment, and (ii) a heterologous or engineered gene or gene set involved in the import and/or metabolism of a rare carbohydrate, wherein said heterologous gene or gene set comes from another species than the engineered bacterial strain; and further administering to said subject, or providing to said environment, said rare carbohydrate; whereby the level of the target molecule in said subject or environment is modulated or the target molecule is modified in said subject or environment.

Provided herein are adeno-associated virus (AAV) compositions that can restore phenylalanine hydroxylase (PAH) gene function in cell. Also provided are methods of use of the AAV compositions, and packaging systems for making the AAV compositions.

The present invention provides, among other things, multimeric coding nucleic acids that exhibit superior stability for in vivo and in vitro use. In some embodiments, a multimeric coding nucleic acid (MCNA) comprises two or more encoding polynucleotides linked via 3′ ends such that the multimeric coding nucleic acid compound comprises two or more 5′ ends.

Herein are described pharmabiotic compositions and methods of treatment using genetically modified bacteria that include a portion or a variant of human cDNA sequence. Generally, the modified bacterium has a genetic modification that includes the introduction or inclusion of non-native DNA which contain a human cDNA sequence that can be propagated in the genetically altered bacterium. As an example, the non-native DNA can include one or more portions of human cDNA that encode the enzyme phenylalanine hydroxylase. In an embodiment, the modified bacterium can be provided to a patient as a treatment for a metabolic disorder. In a non-limiting example, a modified bacterium including human cDNA encoding the enzyme phenylalanine hydroxylase can be provided to a patient suffering from a deficiency in phenylalanine hydroxylase or suffering from a mutation to the native gene that results in an inactive form of the enzyme. As such, certain embodiments may provide methods for treating phenylketonuria using the modified bacterium.