Multigenome retroviral vector preparations and methods and systems for producing and using same

• US 10,179,919 B2
• Filed: 02/22/2017
• Issued: 01/15/2019
• Est. Priority Date: 02/23/2016
• Status: Active Grant

• Current Assignee: Immune Design Corp. (Merck & Co., Inc.)
• Original Assignee: Immune Design Corp. (Merck & Co., Inc.)
• Inventors: Ter Meulen, Jan Henrik, Berglund, Peter Lars Aksel
• Primary Examiner(s): Chestnut, Barry A
• Application Number:
  US15/439,324
• Publication Number:
  US 20170268020A1
• Time in Patent Office: 692 Days
• CPC Class Codes: A61K 2039/5256 expressing foreign proteins
• CPC Class Codes: A61K 2039/70 Multivalent vaccine
• CPC Class Codes: A61K 39/0011 Cancer antigens
• CPC Class Codes: A61K 39/001102 Receptors, cell surface antigens or cell surface determinants
• CPC Class Codes: A61K 48/005 characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 37/04 Immunostimulants
• CPC Class Codes: C07K 14/005 from viruses
• CPC Class Codes: C07K 14/4748 Tumour specific antigens; Tumour rejection antigen precursors [TRAP], e.g. MAGE
• CPC Class Codes: C12N 15/86 Viral vectors
• CPC Class Codes: C12N 2740/15043 viral genome or elements thereof as genetic vector
• CPC Class Codes: C12N 2740/15052 relating to complementing cells and packaging systems for producing virus or viral particles
• CPC Class Codes: C12N 2770/36122 New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12N 2810/609 positive strand RNA viruses

Abstract

The present invention provides novel multigenome retroviral vectors, methods and packaging systems for making such retroviral vectors and methods of use.

Claims

1. A recombinant multigenome retroviral vector preparation comprising:

a. a first retroviral particle comprising two copies of a first retroviral vector genome comprising a first sequence of interest;

b. a second retroviral particle comprising two copies of a second retroviral vector genome comprising a second sequence of interest;

c. a third retroviral particle comprising one copy of the first retroviral vector genome comprising a first sequence of interest and one copy of the second retroviral vector genome comprising a second sequence of interest;

d. a fourth retroviral particle comprising two copies of a third retroviral vector genome comprising a third sequence of interest;

e. a fifth retroviral particle comprising one copy of the first retroviral vector genome comprising a first sequence of interest and one copy of the third retroviral vector genome comprising the third sequence of interest; and

f. a sixth retroviral particle comprising one copy of the second retroviral vector genome comprising a second sequence of interest and one copy of the third retroviral vector genome comprising the third sequence of interest;

wherein the first, second and third sequences of interest are different; and

wherein the retroviral vector preparation is pseudotyped with a heterologous envelope glycoprotein.

2. The recombinant multigenome retroviral vector preparation of claim 1 wherein the third, fifth and sixth retroviral particles make up at least 50% of the total retroviral particles in the preparation.

3. The recombinant multigenome retroviral vector preparation of claim 1 wherein the third, fifth and sixth retroviral particles make up at least 60% of the total retroviral particles in the preparation.

4. The recombinant multigenome retroviral vector preparation of claim 1 wherein the third, fifth and sixth retroviral particles make up at least 75% of the total retroviral particles in the preparation.

5. The recombinant multigenome retroviral vector preparation of claim 1, wherein the heterologous envelope glycoprotein is selected from the group consisting of VSVg, measles envelope glycoprotein, an alphavirus glycoprotein, and a Sindbis envelope glycoprotein.

6. The recombinant multigenome retroviral vector preparation of claim 5, wherein the heterologous envelope glycoprotein comprises a variant alphavirus E2 glycoprotein.

7. The recombinant multigenome retroviral vector preparation of claim 6, wherein the variant alphavirus E2 glycoprotein targets the vector to dendritic cells.

8. The recombinant multigenome retroviral vector preparation of claim 1, wherein the retroviral vector preparation is a lentiviral vector preparation.

9. The recombinant multigenome retroviral vector preparation of claim 1, wherein the first sequence of interest encodes a tumor-associated antigen or one or more neoantigens and the second sequence of interest encodes an immunomodulatory molecule.

10. The recombinant multigenome retroviral vector preparation of claim 1, wherein the first sequence of interest encodes a tumor-associated antigen and the second sequence of interest encodes a different tumor-associated antigen.

11. The recombinant multigenome retroviral vector preparation of claim 1, wherein the first sequence of interest encodes a tumor-associated antigen and the second sequence of interest encodes one or more neoantigens.

12. The recombinant multigenome retroviral vector preparation of claim 11, wherein the one or more neoantigens is a neoantigen of the tumor-associated antigen of the first sequence of interest.

29. The recombinant multigenome retroviral vector preparation of claim 1 wherein the first retroviral vector genome comprises about 50% of the vector genomes in the multigenome vector preparation.

41. A method of inducing an immune response in a subject comprising administering the multigenome retroviral vector preparation of claim 1.

42. A method of treating cancer in a subject comprising administering the multigenome retroviral vector preparation of claim 1.

43. A method for delivering and expressing multiple sequences of interest to a subject in vivo comprising administering the multigenome retroviral vector preparation of claim 1.

44. A recombinant multigenome retroviral vector preparation of claim 1 for use in therapy.

45. A recombinant multigenome retroviral vector preparation of claim 1 for use in a method of treatment of a patient.

46. The recombinant multigenome retroviral vector preparation of claim 1, wherein the first sequence of interest, the second sequence of interest, and the third sequence of interest each encodes a different tumor antigen.

13. A retroviral vector packaging system for producing a pseudotyped multigenome retroviral vector preparation, comprising:

a. a first nucleic acid molecule encoding a viral envelope protein;

b. a second nucleic acid molecule encoding gag and pol proteins;

c. a third nucleic acid molecule encoding rev;

d. a fourth nucleic acid molecule comprising a first retroviral vector genome comprising a first sequence of interest;

e. a fifth nucleic acid molecule comprising a second retroviral vector genome comprising a second sequence of interest;

f. a sixth nucleic acid molecule comprising a third retroviral vector genome comprising a third sequence of interest;

g. optionally a sixth nucleic acid molecule encoding vpx; and

h. a packaging cell or cell line.

14. The retroviral vector packaging system of claim 13 wherein the retroviral vector preparation is a lentiviral vector preparation.

15. The retroviral vector packaging system of claim 13 wherein the first sequence of interest encodes a tumor-associated antigen or one or more neoantigens and the second sequence of interest encodes an immunomodulatory molecule.

16. The retroviral vector packaging system of claim 13 wherein the first sequence of interest encodes a tumor-associated antigen and the second sequence of interest encodes a different tumor-associated antigen.

17. The retroviral vector packaging system of claim 13 wherein the first sequence of interest encodes a tumor-associated antigen and the second sequence of interest encodes one or more neoantigens.

18. The retroviral vector packaging system of claim 13 wherein the viral envelope protein is selected from the group consisting of VSVg, measles envelope glycoprotein, and an alphavirus envelope glycoprotein.

19. The retroviral vector packaging system of claim 13 wherein the viral envelope protein comprises a Sindbis virus E2 glycoprotein or a variant thereof capable of targeting dendritic cells.

20. The retroviral vector packaging system of claim 13 wherein equal amounts of the fourth nucleic acid molecule, the fifth and the sixth nucleic acid molecule are used.

21. The retroviral vector packaging system of claim 13 wherein the relative input ratio of the fourth nucleic acid molecule to the fifth nucleic acid molecule used in the packaging system is 3:

2.

22. The retroviral vector packaging system of claim 13 wherein the first lentiviral vector genome, the second lentiviral vector, and the third lentiviral vector comprise a palindromic dimer initiation site (DIS) sequence.

23. The retroviral vector packaging system of claim 13 wherein the palindromic DIS sequence in the first lentiviral vector genome and the second lentiviral vector is the same.

24. The retroviral vector packaging system of claim 13 wherein the first lentiviral vector genome comprises a first palindromic DIS sequence and the second lentiviral vector comprise a second palindromic DIS sequence.

25. The retroviral vector packaging system of claim 24 wherein the retroviral vector packaging system preferentially produces homozygous retroviral vector particles.

26. The retroviral vector packaging system of claim 13 wherein the first lentiviral vector genome comprises a first DIS sequence and the second lentiviral vector comprise a second DIS sequence wherein the first and second DIS sequences are non-palindromic.

27. The retroviral vector packaging system of claim 26 wherein the first DIS sequence pairs with the second DIS sequence during packaging such that the retroviral vector packaging system preferentially produces heterozygous retroviral vector particles.

28. The retroviral vector packaging system of claim 13 wherein the pol protein has a non-functional integrase.

47. The retroviral vector packaging system of claim 13, wherein the first sequence of interest, the second sequence of interest, and the third sequence of interest each encodes a different tumor antigen.

30. A multigenome retroviral vector packaging system, comprising:

a. at least three nucleic acid molecules each comprising a retroviral vector genome comprising a unique sequence of interest;

b. one or more nucleic acid molecules encoding the components necessary to generate pseudotyped retroviral vector particles;

c. optionally a nucleic acid molecule encoding vpx; and

d. a packaging cell line.

31. The multigenome retroviral vector packaging system of claim 30, consisting of 3 to 8 nucleic acid molecules each comprising a retroviral vector genome comprising a unique sequence of interest.

32. The multigenome retroviral vector packaging system of claim 31, consisting of 5 nucleic acid molecules each comprising a retroviral vector genome comprising a unique sequence of interest.

33. The multigenome retroviral vector packaging system of claim 32, wherein the relative input ratio of the 5 nucleic acid molecules each comprising a retroviral vector genome comprising a unique sequence of interest is selected from one of the input ratios shown in Table 3.

34. The multigenome retroviral vector packaging system of claim 32, wherein the relative input ratio of the 5 nucleic acid molecules each comprising a retroviral vector genome comprising a unique sequence of interest is 4:

1;

1;

1;

1.

35. The multigenome retroviral vector packaging system of claim 30, wherein the unique sequences of interest are selected from the group consisting of the sequences encoding MAGEA1, MAGEA4, NYESO1, MAGEA3, MAGEA10, ScFvanti-PD1, IL12, IL23, CD40, ScFvanti-PDL1, and ScFvanti-CTLA4, or an immunogenic variant of any of the foregoing having at least 80%-90% identity to the wild type sequence.

36. The multigenome retroviral vector packaging system of claim 30 wherein the components necessary to generate retroviral vector particles include gag, pol, envelope, and optionally rev and/or vpx proteins.

37. The multigenome retroviral vector packaging system of claim 30 wherein the packaging cell line stably expresses one or more of the components necessary to generate retroviral vector particles.

38. The multigenome retroviral vector packaging system of claim 30 wherein the retroviral vector genome is a lentiviral vector genome.

39. A method for producing a pseudotyped multigenome retroviral vector preparation comprising culturing the packaging cell line of claim 30 transfected with the nucleic acids of (a) and (b) and optionally (c).

40. A pseudotyped multigenome retroviral vector preparation produced by the method of claim 39.