Methods and materials for treatment of Pompe's disease

1. A pharmaceutical composition comprising an isolated molecular complex having acid alpha glucosidase (GAA) activity and consisting of a GAA-derived protein consisting of two polypeptides, a first polypeptide having at least 85% sequence identity to amino acids 22 to 57 of SEQ ID NO: 1, and a second polypeptide having at least 85% sequence identity to amino acids 66-896 of SEQ ID NO: 1, with the proviso that the pharmaceutical composition does not include an isolated molecular complex having GAA activity and at least three or at least four polypeptides, wherein at least one of said two polypeptides includes a phosphorylated N-glycan such that said molecular complex has:

the substantial ability to bind to a mannose-6-phosphate receptor on a mammalian cell and consequently, the ability to be transported to the interior of the mammalian cell; and

a pharmaceutically acceptable carrier.

2. The molecular complex of claim 1 , wherein said mammalian cell is a human cell.

3. The pharmaceutical composition of claim 1 , wherein:

at least one of said phosphorylated N-glycans is uncapped and demannosylated; or

at least 40% of the N-glycans are uncapped and demannosylated; or

at least 60% of the N-glycans are uncapped and demannosylated; or

at least 80% of the N-glycans are uncapped and demannosylated; or

at least 90% of the N-glycans are uncapped and demannosylated; or

said sequence identity for each polypeptide is at least 90%.

4. The pharmaceutical composition of claim 1 , wherein:

said molecular complex is lyophilized; or

said molecular complex is lyophilized and said composition is packaged as a single use vial; or

said composition is formulated for intravenous or subcutaneous administration or for intravenous infusion.

5. A method of providing enzyme replacement therapy to a subject diagnosed with Pompe's disease, said method comprising administering said composition of claim 4 , to a subject diagnosed with Pompe's disease.

6. The method of claim 5 , wherein said subject is diagnosed with infantile onset Pompe's disease or with late onset Pompe's disease.

7. A method of transporting a molecular complex having GAA activity to the interior of a cell, said method comprising:

contacting a mammalian cell with an isolated molecular complex having acid alpha glucosidase (GAA) activity and consisting of a GAA-derived protein consisting of two polypeptides, a first polypeptide having at least 85% sequence identity to amino acids 22 to 57 of SEQ ID NO: 1, and a second polypeptide having at least 85% sequence identity to amino acids 66-896 of SEQ ID NO: 1, with the proviso that the mammalian cell is not in contact with an isolated molecular complex having GAA activity and having at least three or at least four polypeptides, wherein at least one of the two polypeptides includes a phosphorylated N-glycan such that said molecular complex has:

the substantial ability to bind to a mannose-6-phosphate receptor on a mammalian cell; and

consequently, the ability to be transported to the interior of the mammalian cell.

8. The method of claim 7 , wherein:

said mammalian cell is in vitro; or

said mammalian cell is in a mammalian subject; or

said mammalian cell is a human cell.

9. An isolated fungal cell comprising a nucleic acid encoding a GAA protein having at least 85% sequence identity to the GAA amino acid sequence set forth in SEQ ID NO:1 and a nucleic acid encoding an alkaline protease having at least 85% sequence identity to the amino acid sequence set forth in SEQ ID NO:8, wherein said fungal cell produces a molecular complex having GAA activity and comprising two polypeptides, each polypeptide having at least 85% sequence identity to a segment of the amino acid sequence set forth in SEQ ID NO: 1, each segment being derived by proteolysis of the amino acid sequence set forth in SEQ ID NO: 1 at one or more sites between amino acid 50 and amino acid 74 by said alkaline protease.

10. The fungal cell of claim 9 , wherein

said fungal cell further comprises a nucleic acid encoding a mannosidase, said mannosidase being capable of (i) hydrolyzing a mannose-1-phospho-6-mannose moiety to mannose-6-phosphate and (ii) hydrolyzing a terminal alpha-1,2 mannose, alpha-1,3 mannose and/or alpha-1,6 mannose linkage; or

said fungal cell further comprises a nucleic acid encoding a mannosidase, said mannosidase being capable of hydrolyzing a mannose-1-phospho-6-mannose moiety to mannose-6-phosphate; or

said fungal cell further comprises a nucleic acid encoding a mannosidase, said mannosidase being capable of hydrolyzing a terminal alpha-1,2 mannose, alpha-1,3 mannose and/or alpha-1,6 mannose linkage; or

said fungal cell further comprises a nucleic acid encoding a mannosidase, said mannosidase being capable of (i) hydrolyzing a mannose-1-phospho-6-mannose moiety to mannose-6-phosphate and (ii) hydrolyzing a terminal alpha-1,2 mannose, alpha-1,3 mannose and/or alpha-1,6 mannose linkage and further comprises a nucleic acid encoding a polypeptide capable of promoting mannosyl phosphorylation; or

said fungal cell further comprises a nucleic acid encoding a mannosidase, said mannosidase being capable of (i) hydrolyzing a mannose-1-phospho-6-mannose moiety to mannose-6-phosphate and (ii) hydrolyzing a terminal alpha-1,2 mannose, alpha-1,3 mannose and/or alpha-1,6 mannose linkage, and said fungal cell is genetically engineered to be deficient in OCH1 activity.