Vectors with modified initiation codon for the translation of AAV-REP78 useful for production of AAV

• US 8,952,144 B2
• Filed: 07/18/2013
• Issued: 02/10/2015
• Est. Priority Date: 06/21/2006
• Status: Active Grant

• Current Assignee: Uniqure Ip B.V. (uniQure N.V.)
• Original Assignee: Uniqure Ip B.V. (uniQure N.V.)
• Inventors: Hermens, Wilhelmus Theodorus Johannes Maria Christiaan, Haast, Saskia Jacoba Petronella, Biesmans, Dennis Johan, Bakker, Andrew Christian
• Primary Examiner(s): Humphrey, Louise
• Application Number:
  US13/945,505
• Publication Number:
  US 20130296532A1
• Time in Patent Office: 572 Days
• US Class Current: 536/23.72
• CPC Class Codes: C07K 14/005 from viruses
• CPC Class Codes: C12N 15/86 Viral vectors
• CPC Class Codes: C12N 2710/14043 viral genome or elements thereof as genetic vectore
• CPC Class Codes: C12N 2710/14044 Chimeric viral vector comprising heterologous viral elements for production of another viral vector
• CPC Class Codes: C12N 2710/14143 viral genome or elements thereof as genetic vector
• CPC Class Codes: C12N 2710/14144 Chimeric viral vector comprising heterologous viral elements for production of another viral vector
• CPC Class Codes: C12N 2710/14152 relating to complementing cells and packaging systems for producing virus or viral particles
• CPC Class Codes: C12N 2750/14121 Viruses as such, e.g. new isolates, mutants or their genomic sequences
• CPC Class Codes: C12N 2750/14122 New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12N 2750/14143 viral genome or elements thereof as genetic vector
• CPC Class Codes: C12N 2750/14151 Methods of production or purification of viral material
• CPC Class Codes: C12N 2750/14152 relating to complementing cells and packaging systems for producing virus or viral particles
• CPC Class Codes: C12N 2800/105 for insects
• CPC Class Codes: C12N 2800/50 Vectors for producing vectors
• CPC Class Codes: C12N 7/00 Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof preparing medicinal viral antigen or antibody compositions, e.g. virus vaccines, A61K39/00

Abstract

The present invention relates nucleic acid constructs for the production of recombinant parvoviral (e.g. adeno-associated viral) vectors in insect cells, to insect cells comprising such constructs and to methods wherein the cells are used to produce recombinant parvoviral virions. The insect cells preferably comprise a first nucleotide sequence encoding the parvoviral rep proteins whereby the initiation codon for translation of the parvoviral Rep78 protein is a suboptimal initiation codon that effects partial exon skipping upon expression in insect cells. The insect cell further comprises a second nucleotide sequence comprising at least one parvoviral (AAV) inverted terminal repeat (ITR) nucleotide sequence and a third nucleotide sequence comprising a sequences coding for the parvoviral capsid proteins.

Claims

1. A nucleic acid molecule comprising:

(a) a first nucleotide sequence that comprises a single open reading frame (ORF) encoding parvoviral Rep78 and Rep52 proteins, with a translation initiation site of the Rep78 protein being a suboptimal initiation codon selected from the group consisting of ACG, TTG, CTG and GTG; and

(b) an expression control sequence that comprises nonanucleotide sequence SEQ ID NO;

7 upstream of the translation initiation site operably linked to the single ORF.

2. The nucleic acid molecule according to claim 1, wherein the parvoviral Rep proteins are AAV Rep proteins.

3. The nucleic acid molecule according to claim 1, wherein one or more false translation initiation sites between the Rep78 initiation site and the Rep52 initiation site have been deleted.

4. The nucleic acid molecule according to claim 3, wherein all false translation initiation sites between the Rep78 initiation site and the Rep52 initiation site have been deleted.

5. A nucleic acid construct comprising a first nucleotide sequence that comprises a single open reading frame (ORF) encoding parvoviral Rep78 and Rep52 proteins, with a translation initiation site of the Rep78 protein being a suboptimal initiation codon selected from the group consisting of ACG, TTG, CTG and GTG, wherein an expression control sequence for expression in an insect cell is operably linked to the ORF and includes a promoter that is active in insect cells.

6. The nucleic acid construct according to claim 5, wherein one or more false translation initiation sites between the Rep78 initiation site and the Rep52 initiation site have been deleted.

7. The nucleic acid construct according to claim 6 wherein all false translation initiation sites between the Rep78 initiation site and the Rep52 initiation site have been deleted.

8. The nucleic acid construct according to claim 6, further comprising an expression control sequence that comprises nonanucleotide sequence SEQ ID NO:

7 upstream of the translation initiation site and operably linked to the single ORF.

9. The nucleic acid construct according to claim 7, further comprising an expression control sequence that comprises nonanucleotide sequence SEQ ID NO:

7 upstream of the translation initiation site and operably linked to the single ORF.

10. The nucleic acid construct according to claim 5, wherein the expression control sequence comprises a polyhedron promoter.

11. The nucleic acid construct according to claim 5, wherein the nucleic acid construct is a recombinant viral vector.

12. The nucleic acid construct according to claim 11, wherein the vector is a baculoviral vector.

13. An insect cell comprising a first nucleotide sequence that comprises a single ORF encoding parvoviral Rep78 and Rep52 proteins, with a translation initiation site of the Rep78 protein being a suboptimal initiation codon selected from the group consisting of ACG, TTG, CTG and GTG,

which cell does not comprise a parvoviral Rep protein-encoding nucleotide sequence other than said first nucleotide sequence.

14. The insect cell according to claim 13, wherein the first nucleotide sequence is operably linked to an expression control sequence comprising a nonanucleotide the sequence of which is SEQ ID NO:

7 upstream of the translation initiation site.

15. The insect cell according to claim 13, wherein the parvoviral Rep proteins are AAV Rep proteins.

16. The insect cell according to claim 13, wherein the expression control sequence drives expression of said ORF in said insect cell.

17. The insect cell according to claim 16, wherein the expression control sequence comprises a polyhedron promoter.

18. The insect cell according to claim 16, wherein the nucleic acid construct is a recombinant viral vector.

19. The insect cell according to claim 18, wherein the vector is a baculoviral vector.

20. The insect cell according to claim 13, wherein one or more false translation initiation site between the Rep78 initiation site and the Rep52 initiation site has been deleted.

21. The insect cell according to claim 13, wherein all false translation initiation sites between the Rep78 initiation site and the Rep52 initiation site have been deleted.

22. The insect cell according to claim 13, that further comprises:

(a) a second nucleotide sequence comprising at least one parvoviral inverted terminal repeat (ITR) sequence; and

,

(b) a third nucleotide sequence comprising parvoviral capsid protein-coding sequences operably linked to an expression control sequence for expression of capsid proteins in said cell.

23. The insect cell according to claim 22, wherein the second nucleotide sequence further comprises a fourth nucleotide sequence encoding a gene product of interest wherein the fourth nucleotide sequence becomes incorporated into the genome of a parvoviral vector produced in the insect cell.

24. The insect cell according to claim 23, wherein the second nucleotide sequence comprises two parvoviral ITR sequences which flank the fourth nucleotide sequence.

25. The insect cell according to claim 22, wherein at least one of the first nucleotide sequence, the second nucleotide sequence or the third nucleotide sequence is stably integrated in the genome of the insect cell.

26. The insect cell according to claim 22, wherein

(i) the third nucleotide sequence encodes parvoviral VP1, VP2 and VP3 capsid proteins;

and

(ii) the initiation codon for translation of VP1 is ACG, TTG, CTG, or GTG.

27. The insect cell according to claim 26, wherein the third nucleotide sequence is operably linked to an expression control sequence comprising a nonanucleotide of SEQ ID NO:

7 upstream of the VP1 initiation codon.

28. The insect cell according to claim 26, wherein the third nucleotide sequence further comprises at least one of the following modifications of the parvoviral VP1-coding sequence:

(a) a Cat position 12,

(b) an A at position 21, and

c) a C at position 24,

wherein position 1 is the 17^th nucleotide of SEQ ID NO;

1.

29. The insect cell according to claim 13, which comprises:

(i) a first nucleic acid construct comprising;

(a) said first nucleotide sequence, and

(b) a third nucleotide sequence that encodes a parvoviral capsid protein, wherein both the first and the third nucleotide sequences are operably linked to an expression control sequence that drives expression of the capsid protein in the insect cell; and

,

(ii) a second nucleic acid construct comprises a second nucleotide sequence that includes at least one parvoviral ITR sequence.

30. The insect cell according to claim 29, wherein the first nucleic acid construct is a recombinant viral vector.

31. The insect cell according to claim 29, wherein the second nucleic acid construct is a recombinant viral vector.

32. The insect cell according to claim 30, wherein the vector is a baculoviral vector.

33. The insect cell according to claim 31, wherein the vector is a baculoviral vector.

34. The insect cell according to claim 13, comprising:

(a) a first nucleic acid construct that comprises the first nucleotide sequence, operably linked to an expression control sequence that drives expression of the ORF in the insect cell;

(b) a second nucleic acid construct that comprises a second nucleotide sequence that includes at least one parvoviral ITR sequence; and

(c) a third nucleic acid construct that comprises a third nucleotide sequence encoding a parvoviral capsid protein operably linked to an expression control sequence that drives expression of the capsid protein in the insect cell.

35. The insect cell according to claim 34, wherein each of the first, second and third nucleic acid constructs are recombinant viral vectors.

36. The insect cell according to claim 35, wherein the vectors are baculoviral vectors.

37. A recombinant AAV virion produced by:

(i) culturing the insect cell of claim 13 under conditions that permit production of the recombinant AAV virion; and

(ii) recovering the recombinant AAV virion.

38. A recombinant AAV virion produced by:

(i) culturing the insect cell of claim 22 under conditions that permit production of the recombinant AAV virion; and

(ii) recovering the recombinant AAV virion.

39. A recombinant AAV virion produced by:

(i) culturing the insect cell of claim 29 under conditions that permit production of the recombinant AAV virion; and

(ii) recovering the recombinant AAV virion.