De-mannosylation of phosphorylated N-glycans

• US 10,344,310 B2
• Filed: 05/12/2017
• Issued: 07/09/2019
• Est. Priority Date: 09/29/2010
• Status: Active Grant

• Current Assignee: Universiteit Gent Vzw, VIB VZW
• Original Assignee: Oxyrane UK Limited
• Inventors: Piens, Kathleen Camilla Telesphore Alida Maria, Vervecken, Wouter
• Primary Examiner(s): Raghu, Ganapathirama
• Application Number:
  US15/594,256
• Publication Number:
  US 20170306379A1
• Time in Patent Office: 788 Days
• CPC Class Codes: C12N 15/80 for fungi
• CPC Class Codes: C12P 21/005 Glycopeptides, glycoproteins
• CPC Class Codes: C12Y 302/01113 Mannosyl-oligosaccharide 1,2-alpha-mannosidase (3.2.1.113), i.e. alpha-1,2-mannosidase
• CPC Class Codes: Y02P 20/52 using catalysts, e.g. selective catalysts

Abstract

Methods for demannosylating phosphorylated N-glycans on a glycoprotein are described that use a mannosidase capable of hydrolyzing a terminal alpha-1,2 mannose linkage when the underlying mannose is phosphorylated.

Claims

1. A method for demannosylating phosphorylated N-glycans on a glycoprotein, the method comprising contacting a glycoprotein comprising a terminal alpha-1,2 mannose linkage in which the underlying mannose is phosphorylated with a mannosidase, or a biologically active fragment of the mannosidase, that hydrolyzes a terminal alpha-1,2 mannose linkage when the underlying mannose is phosphorylated, wherein the contacting results in hydrolysis of the terminal alpha-1,2 mannose linkage, to produce a demannosylated glycoprotein, wherein the mannosidase is of the GH47 family or of the GH92 family.

11. The method of claim 1, wherein the contacting occurs in a fungal organism.

21. The method of claim 1, wherein said mannosidase is from Aspergillus satoi.

22. The method of claim 1, wherein said mannosidase is from Cellulosimicrobium cellulans.

23. The method of claim 1, wherein the mannosidase comprises an amino acid sequence that is at least 85% identical to SEQ ID NO:

5.

24. The method of claim 1, wherein the mannosidase comprises SEQ ID NO:

5.

25. The method of claim 1, wherein the mannosidase comprises an amino acid sequence encoded by a nucleic acid that is at least 85% identical to SEQ ID NO:

4.

26. The method of claim 1, wherein the mannosidase comprises an amino acid sequence encoded by SEQ ID NO:

4.

27. The method of claim 1, wherein the method further comprises isolating the demannosylated glycoprotein.

28. The method of claim 1, wherein the glycoprotein is a human protein.

29. The method of claim 11, wherein the fungal organism is a Yarrowia lipolytica cell or a Arxula adeninivorans cell.

30. The method of claim 11, wherein the fungal organism is a methylotrophic yeast cell.

31. The method of claim 30, wherein the methylotrophic yeast is selected from the group consisting of Pichia pastoris, Pichia methanolica, Oogataea minuta, and Hansenula polymorpha.

32. The method of claim 11, wherein the fungal organism is a filamentous fungus cell.

33. The method of claim 32, wherein the filamentous fungus is selected from the group consisting of Aspergillus caesiellus, Aspergillus candidus, Aspergillus carneus, Aspergillus clavatus, Aspergillus deflectus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus glaucus, Aspergillus nidulans, Aspergillus niger, Aspergillus ochraceus, Aspergillus oryzae, Aspergillus parasiticus, Aspergillus penicilloides, Aspergillus restrictus, Aspergillus sojae, Aspergillus sydowi, Aspergillus tamari, Aspergillus terreus, Aspergillus ustus, Aspergillus versicolor, Neurospora, Trichoderma, Fusarium, and Chrysosporium.

34. The method of claim 1, wherein the glycoprotein is selected from the group consisting of a pathogen protein, a lysosomal protein, a growth factor, a cytokine, a chemokine, an antibody or antigen-binding fragment thereof, and a fusion protein.

35. The method of claim 34, wherein the lysosomal protein is a lysosomal enzyme.

36. The method of claim 35, wherein the lysosomal enzyme is associated with a lysosomal storage disorder (LSD).

37. The method of claim 36, wherein the LSD is selected from the group consisting of Fabry'"'"'s disease, mucopolysaccharidosis I, Farber disease, Gaucher disease, GM1-gangliosidosis, Tay-Sachs disease, Sandhoff disease, GM2 activator disease, Krabbe disease, metachromatic leukodystrophy, Niemann-Pick disease, Scheie disease, Hunter disease, Sanfilippo disease, Morquio disease, Maroteaux-Lamy disease, hyaluronidase deficiency, aspartylglucosaminuria, fucosidosis, mannosidosis, Schindler disease, sialidosis type 1, Pompe disease, pycnodysostosis, ceroid lipofuscinosis, cholesterol ester storage disease, Wolman disease, multiple sulfatase deficiency, galactosialidosis, mucolipidosis, cystinosis, sialic acid storage disorder, chylomicron retention disease with Marinesco-Sjö

gren syndrome, Hermansky-Pudlak syndrome, Chediak-Higashi syndrome, Danon disease, and geleophysic dysplasia.

2. A method of producing a glycoprotein comprising demannosylated phosphorylated N-glycans, the method comprising introducing into a fungal cell a nucleic acid encoding the glycoprotein and the glycoprotein comprises a terminal alpha-1,2 mannose linkage in which the underlying mannose is phosphorylated, wherein the fungal cell is genetically engineered to comprise a nucleic acid encoding a mannosidase, or a biologically active fragment of the mannosidase, that hydrolyzes a terminal alpha-1,2 mannose linkage when the underlying mannose is phosphorylated, to produce a demannosylated glycoprotein, wherein the mannosidase is of the GH47 family or of the GH92 family.

3. The method of claim 2, wherein the mannosidase is from Aspergillus satoi.

4. The method of claim 2, wherein the mannosidase is from Cellulosimicrobium cellulans.

5. The method of claim 2, wherein the mannosidase comprises an amino acid sequence that is at least 85% identical to SEQ ID NO:

5.

6. The method of claim 2, wherein the mannosidase comprises SEQ ID NO:

5.

7. The method of claim 2, wherein the mannosidase comprises an amino acid sequence encoded by a nucleic acid that is at least 85% identical to SEQ ID NO:

4.

8. The method of claim 2, wherein the mannosidase comprises an amino acid sequence encoded by SEQ ID NO:

4.

9. The method of claim 2, wherein the method further comprises isolating the demannosylated glycoprotein.

10. The method of claim 2, wherein the glycoprotein is a human protein.

12. The method of claim 2, wherein the fungal cell is a Yarrowia lipolytica cell or a Arxula adeninivorans cell.

13. The method of claim 2, wherein the fungal cell is a methylotrophic yeast cell.

14. The method of claim 13, wherein the methylotrophic yeast is selected from the group consisting of Pichia pastoris, Pichia methanolica, Oogataea minuta, and Hansenula polymorpha.

15. The method of claim 2, wherein the fungal cell is a filamentous fungus cell.

16. The method of claim 15, wherein the filamentous fungus is selected from the group consisting of Aspergillus caesiellus, Aspergillus candidus, Aspergillus carneus, Aspergillus clavatus, Aspergillus deflectus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus glaucus, Aspergillus nidulans, Aspergillus niger, Aspergillus ochraceus, Aspergillus oryzae, Aspergillus parasiticus, Aspergillus penicilloides, Aspergillus restrictus, Aspergillus sojae, Aspergillus sydowi, Aspergillus tamari, Aspergillus terreus, Aspergillus ustus, Aspergillus versicolor, Neurospora, Trichoderma, Fusarium, and Chrysosporium.

17. The method of claim 2, wherein the glycoprotein is selected from the group consisting of a pathogen protein, a lysosomal protein, a growth factor, a cytokine, a chemokine, an antibody or antigen-binding fragment thereof, and a fusion protein.

18. The method of claim 17, wherein the lysosomal protein is a lysosomal enzyme.

19. The method of claim 18, wherein the lysosomal enzyme is associated with a lysosomal storage disorder (LSD).

20. The method of claim 19, wherein the LSD is selected from the group consisting of Fabry'"'"'s disease, mucopolysaccharidosis I, Farber disease, Gaucher disease, GM1-gangliosidosis, Tay-Sachs disease, Sandhoff disease, GM2 activator disease, Krabbe disease, metachromatic leukodystrophy, Niemann-Pick disease, Scheie disease, Hunter disease, Sanfilippo disease, Morquio disease, Maroteaux-Lamy disease, hyaluronidase deficiency, aspartylglucosaminuria, fucosidosis, mannosidosis, Schindler disease, sialidosis type 1, Pompe disease, pycnodysostosis, ceroid lipofuscinosis, cholesterol ester storage disease, Wolman disease, multiple sulfatase deficiency, galactosialidosis, mucolipidosis, cystinosis, sialic acid storage disorder, chylomicron retention disease with Marinesco-Sjö

gren syndrome, Hermansky-Pudlak syndrome, Chediak-Higashi syndrome, Danon disease, and geleophysic dysplasia.