Factors for angiogenesis, vasculogenesis, cartilage formation, bone formation, and methods of use thereof

• US 20030220249A1
• Filed: 02/07/2003
• Published: 11/27/2003
• Est. Priority Date: 02/07/2002
• Status: Abandoned Application

• Current Assignee: Discovery Genomics, Inc (Immusoft Corporation)
• Original Assignee: Discovery Genomics, Inc (Immusoft Corporation)
• Inventors: Nasevicius, Aidas, Larson, Jon, Roberg-Perez, Sharon, Wadman, Shannon, Hackett, Perry B., Essner, Jeffrey, Ekker, Stephen C., Clark, Karl J.
• Application Number:
  US10/360,849
• Publication Number:
  US 20030220249A1
• Time in Patent Office: Days
• US Class Current: 514/12
• CPC Class Codes: A01K 2217/05 Animals comprising random inserted nucleic acids (transgenic)
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: C07K 14/515 Angiogenesic factors; Angiogenin
• CPC Class Codes: C07K 14/705 Receptors; Cell surface antigens; Cell surface determinants tumour specific antigens C07K14/4748
• CPC Class Codes: C12N 2799/021 for the expression of a heterologous nucleic acid

Abstract

The application is related to the field of nucleic acids with identified utility, and more particularly, to genes, related nucleic acids, their complements, polypeptides, and methods of using the same for blood vessel, cartilage, and bone formation, as well as inhibition thereof. The application describes discoveries made using the zebrafish embryo technique, as well as other techniques that are described herein. The discoveries include genes, related nucleic acids, and their complements, as well as sequences, polypeptides, other molecules, and methods for using them, e.g., TDE1, PTV, MOESIN, and HKE4. Also described are polypeptide products, inhibition of expression, administration of materials and products, screening procedures, and techniques for making drugs. Moreover, uses of these discoveries in appropriate contexts are set forth.

Claims

1. An isolated nucleic acid comprising a sequence that hybridizes under stringent conditions to a hybridization probe, wherein the probe is a member of the group consisting of SEQ ID NO 7, SEQ ID NO 16, and SEQ ID NO 34;

or wherein the probe is a member of the group consisting of complements of SEQ ID NO 7, SEQ ID NO 16, and SEQ ID NO 34.

2. The nucleic acid sequence of claim 1 wherein the hybridization probe is SEQ ID NO 7 or a complement thereof.

3. The nucleic acid sequence of claim 1 wherein the hybridization probe is SEQ ID NO 16 or a complement thereof.

4. The nucleic acid sequence of claim 1 wherein the hybridization probe is SEQ ID NO 34 or a complement thereof.

5. The nucleic acid sequence of claim 1 wherein the hybridization probe is DNA, RNA, a nucleic acid analogue, or a combination of DNA and RNA.

6. The nucleic acid analogue sequence of claim 5 wherein the nucleic acid analogue sequence comprises phosphorothioate and morpholino phosphorodiamidate components.

7. The nucleic acid analogue sequence of claim 5 wherein the nucleic acid analogue sequence comprises peptide nucleic acid sequences.

8. The nucleic acid analogue sequence of claim 5 wherein the nucleic acid analogue sequence comprises locked nucleic acid sequences.

9. The nucleic acid sequence of claim 1 wherein the isolated nucleic acid sequence is at least 18 residues in length.

10. The nucleic acid sequence of claim 1 wherein the isolated nucleic acid sequence is from 15 to 100 residues in length.

11. The nucleic acid sequence of claim 1 wherein the isolated nucleic acid sequence comprises nonhybridizing portions that do not hybridize to the hybridization probe.

12. An isolated nucleic acid comprising a sequence that is at least 90% identical to a member of the group consisting of SEQ ID NO 7, SEQ ID NO 16, SEQ ID NO 34, and complements thereof.

13. The isolated nucleic acid of claim 12 wherein the isolated nucleic acid sequence is at least 90% identical to SEQ ID NO 7 and encodes a polypeptide that is a member of the TDE family, wherein the percent identity of the polypeptide sequence is closer to TDE1 than to other members of the TDE family.

14. The isolated nucleic acid of claim 12 wherein the isolated nucleic acid sequence is at least 90% identical to SEQ ID NO 16 and encodes a polypeptide that is a member of the PTV family, wherein the percent identity of the polypeptide sequence is closer to PTV than to other members of the PTV family.

15. The isolated nucleic acid of claim 12 wherein the isolated nucleic acid sequence is at least 90% identical to SEQ ID NO 34 and encodes a polypeptide that is a member of the HKE family, wherein the percent identity of the polypeptide sequence is closer to HKE4 than to other members of the HKE family

16. The isolated nucleic acid of claim 12 wherein the isolated nucleic acid sequence is at least 90% identical to SEQ ID NO 7 and encodes a polypeptide having vascular formation activity.

17. The isolated nucleic acid of claim 12 wherein the isolated nucleic acid sequence is at least 90% identical to SEQ ID NO 16 and encodes a polypeptide having blood vessel formation activity.

18. The isolated nucleic acid of claim 12 wherein the isolated nucleic acid sequence is at least 90% identical to SEQ ID NO 34 and encodes a polypeptide having cartilage forming or bone forming activity.

19. The isolated nucleic acid of claim 12 wherein

the isolated nucleic acid sequence comprises at least one change in the group consisting of point mutations, point deletions, polymorphisms, conservative substitutions, and degenerate substitutions when the isolated nucleic acid sequence is compared to a member of the group consisting of SEQ ID NO 7, SEQ ID NO 16 and SEQ ID NO 34.

20. A composition, the composition comprising:

an isolated polypeptide comprising an amino acid sequence that is at least 8 residues in length and is at least 90% identical to a member of the group consisting of SEQ ID NO 3, SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 15, SEQ ID NO 18, SEQ ID NO 30, SEQ ID NO 33, and SEQ ID NO 36.

21. The composition of claim 20 wherein the amino acid sequence is at least 12 residues in length.

22. The composition of claim 20 wherein the amino acid sequence is at least 50 residues in length.

23. The composition of claim 20 wherein the amino acid sequence comprises at least one change in the group consisting of point mutations, point deletions, polymorphisms, conservative substitutions, and degenerate substitutions when the isolated nucleic acid sequence is compared to a member of the group consisting of SEQ ID NO 3, SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 15, SEQ ID NO 18, SEQ ID NO 30, SEQ ID NO 33, and SEQ ID NO 36.

24. The composition of claim 20 wherein the amino acid sequence is at least 90% identical to SEQ ID NO 9 and the polypeptide has an activity for blood vessel formation.

25. The composition of claim 20 wherein the amino acid sequence is at least 90% identical to SEQ ID NO 27 and the polypeptide has an activity for blood vessel formation.

26. The composition of claim 20 wherein the amino acid sequence is at least 90% identical to SEQ ID NO 36 and the polypeptide has an activity for cartilage formation or bone formation.

27. The composition of claim 20 wherein the amino acid sequence is at least 95% identical to a member of the group consisting of SEQ ID NO 3, SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 15, SEQ ID NO 18, SEQ ID NO 30, SEQ ID NO 33, SEQ ID NO 36, SEQ ID NO 39, SEQ ID NO 42, and SEQ ID NO 45.

28. The composition of claim 20 wherein the amino acid sequence

is a member of the group consisting of an amino acid sequences that are at least 90% identical to SEQ ID NO 9 and the polypeptide has an activity for blood vessel formation;

at least 90% identical to SEQ ID NO 36 and the polypeptide has an activity for cartilage formation or bone formation; and

is at least 8 residues in length.

29. The composition of claim 20 further comprising a pharmaceutically acceptable buffer.

30. The composition of claim 20 wherein the polypeptide is a pharmaceutically acceptable salt.

34. The antisense oligonucleotide of claim 30 wherein the antisense polynucleic acid has a number of residues that is at least 10.

35. The antisense oligonucleotide of claim 30 wherein the antisense polynucleic acid has a number of residues that ranges from 12 to 30.

36. A teleost comprising the antisense polynucleic acid of claim 30.

37. A Danio rerio comprising the antisense polynucleic acid of claim 30.

38. A cell comprising the antisense polynucleic acid of claim 30.

39. A cell comprising the antisense polynucleic acid of claim 34.

31. An antisense polynucleic acid comprising a sequence, wherein the antisense polynucleic acid suppresses the expression of a polypeptide encoded by a polynucleic acid sequence for the polypeptide chosen from the group consisting of SEQ ID NO 1, SEQ ID NO 2, SEQ ID NO 4, SEQ ID NO 5, SEQ ID NO 7, SEQ ID NO 8, SEQ ID NO 10, SEQ ID NO 11, SEQ ID NO 13, SEQ ID NO 14, SEQ ID NO 16, SEQ ID NO 17, SEQ ID NO 19, SEQ ID NO 20, SEQ ID NO 22, SEQ ID NO 23, SEQ ID NO 25, SEQ ID NO 26, SEQ ID NO 28, SEQ ID NO 29, SEQ ID NO 31, SEQ ID NO 32, SEQ ID NO 34, and SEQ ID NO 35.

32. The antisense polynucleic acid of claim 31 wherein the antisense polynucleic acid has a backbone chosen from the group consisting of phosphorothioate, morpholino, and peptide linkage molecules.

33. The antisense polynucleic acid of claim 31 wherein the antisense polynucleic acid suppresses the expression of a polypeptide encoded by a polynucleic acid sequence for the polypeptide chosen from the group consisting of SEQ ID NO 1, SEQ ID NO 4, SEQ ID NO 7, SEQ ID NO 10, SEQ ID NO 13, SEQ ID NO 16, SEQ ID NO 19, SEQ ID NO 22, SEQ ID NO 25, SEQ ID NO 28, SEQ ID NO 31, and SEQ ID NO 34 and antisense polynucleic acid is a directed to a noncoding portion of the polynucleic acid sequence for the polypeptide.

40. A vector, the vector comprising:

a first nucleic acid sequence that hybridizes under stringent conditions to a second nucleic acid sequence, wherein the second sequence is a member of the group consisting of SEQ ID NO 1, SEQ ID NO 4, SEQ ID NO 7, SEQ ID NO 10, SEQ ID NO 13, SEQ ID NO 16, SEQ ID NO 19, SEQ ID NO 22, SEQ ID NO 25, SEQ ID NO 28, SEQ ID NO 31, SEQ ID NO 34, or wherein the second sequence is a member of the group consisting of complements of SEQ ID NO 1, SEQ ID NO 4, SEQ ID NO 7, SEQ ID NO 10, SEQ ID NO 13, SEQ ID NO 16, SEQ ID NO 19, SEQ ID NO 22, SEQ ID NO 25, SEQ ID NO 28, SEQ ID NO 31, SEQ ID NO 34;

wherein the first nucleic acid sequence is operably linked to an expression control sequence that directs production of a transcript from the first nucleic acid sequence.

41. The vector of claim 40 wherein the second nucleic acid sequence is SEQ ID NO 7 or a complement thereof.

42. The vector of claim 40 wherein second nucleic acid sequence is SEQ ID NO 16 or a complement thereof.

43. The vector of claim 40 wherein the second nucleic acid sequence is SEQ ID NO 25 or a complement thereof.

44. The vector of claim 40 wherein the second nucleic acid sequence is SEQ ID NO 34 or a complement thereof.

45. The vector of claim 40 wherein a number of residues in the first nucleic acid sequence is from 8 to 50.

46. The vector of claim 40 wherein the vector is a non-integrating vector.

47. The vector of claim 40 wherein the vector is an integrating vector.

48. The vector of claim 40 wherein the vector is an integrating non-viral vector.

49. The vector of claim 48 wherein the vector is a transposon vector.

50. The vector of claim 48 wherein the vector is a Sleeping Beauty transposon vector.

51. The vector of claim 40 wherein the vector is a member of the group consisting of lentiviruses and adenoviruses.

52. A vertebrate nonhuman animal comprising the vector of claim 49.

53. The vertebrate animal of claim 52 wherein the animal is a zebrafish.

54. The vertebrate animal of claim 52 wherein the animal is a mouse or a rat.

55. A method of using a composition, the method comprising administering a composition to an animal, the composition comprising a polypeptide having an amino acid sequence that is at least 90% identical to a member of the group consisting of SEQ ID NO 3, SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 15, SEQ ID NO 18, SEQ ID NO 30, SEQ ID NO 33, SEQ ID NO 36.

56. The method of claim 55 wherein the composition is administered by topical application.

57. The method of claim 55 wherein the polypeptide has an amino acid sequence that is at least 90% identical to a member of the group consisting of SEQ ID NO 3, SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 15, and SEQ ID NO 18, and the composition is administered to a wound by topical application or by injection.

58. The method of claim 55 wherein the composition is administered by injection.

59. The method of claim 55 wherein the polypeptide has an amino acid sequence that is at least 90% identical to a member of the group consisting of SEQ ID NO 3, SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 15, and SEQ ID NO 18, and the composition is administered to a tumor.

60. The method of claim 59 wherein the polypeptide has an amino acid sequence that is at least 90% identical to a member of the group consisting of SEQ ID NO 3, SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 15, and SEQ ID NO 18, and the composition is administered to a tumor by injection of the composition into or near the tumor.

61. The method of claim 55 wherein the polypeptide has an amino acid sequence that is at least 90% identical to a member of the group consisting of SEQ ID NO 3, SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 15, and SEQ ID NO 18, and the composition is administered to a heart by injection of the composition into or near the heart.

62. The method of claim 55 wherein the polypeptide has an amino acid sequence that is at least 90% identical to a member of the group consisting of SEQ ID NO 3, SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 15, and SEQ ID NO 18, and the composition is administered to an ischemic heart by injection of the composition into or near the heart.

63. The method of claim 55 wherein the polypeptide has an amino acid sequence that is at least 90% identical to a member of the group consisting of SEQ ID NO 3, SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 15, and SEQ ID NO 18, and the composition is administered to necrotic tissue by injection of the composition into or near the tissue.

64. The method of claim 55 wherein the polypeptide has an amino acid sequence that is at least 90% identical to a member of the group consisting of SEQ ID NO 3, SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 15, and SEQ ID NO 18, and the composition is administered to an ulcer by injection of the composition into or near the ulcer.

65. The method of claim 55 wherein the polypeptide has an amino acid sequence that is at least 90%. identical to a member of the group consisting of SEQ ID NO 3, SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 15, and SEQ ID NO 18, and the composition is administered to a venous ulcer by injection of the composition into or near the ulcer.

66. The method of claim 55 wherein the polypeptide has an amino acid sequence that is at least 90% identical to a member of the group consisting of SEQ ID NO 3, SEQ ID NO 6, SEQ ID NO 9, SEQ ID NO 12, SEQ ID NO 15, and SEQ ID NO 18, and the composition is administered to a diabetic ulcer by injection of the composition into or near the ulcer.

67. The method of claim 55 wherein the polypeptide has an amino acid sequence that is at least 90% identical to SEQ ID NO 36 and the composition is administered to bone by injection of the composition into or near the bone.

68. The method of claim 55 wherein the polypeptide has an amino acid sequence that is at least 90% identical to SEQ ID NO 36 and the composition is administered to bone by application of the composition into or near the bone in conjunction with a surgical procedure.

69. The method of claim 55 wherein the polypeptide has an amino acid sequence that is at least 90% identical to SEQ ID NO 36 and the composition is administered to cartilaginous tissue by application of the composition into or near the tissue.

70. A method, the method comprising:

administering a vector to an animal, the vector comprising;

a first nucleic acid sequence that hybridizes under stringent conditions to a second nucleic acid sequence, wherein the second sequence is a member of the group consisting of SEQ ID NO 1, SEQ ID NO 4, SEQ ID NO 7, SEQ ID NO 10, SEQ ID NO 13, SEQ ID NO 16, SEQ ID NO 19, SEQ ID NO 22, SEQ ID NO 25, SEQ ID NO 28, SEQ ID NO 31, SEQ ID NO 34;

or wherein the second sequence is a member of the group consisting of complements of SEQ ID NO 1, SEQ ID NO 4, SEQ ID NO 7, SEQ ID NO 10, SEQ ID NO 13, SEQ ID NO 16, SEQ ID NO 19, SEQ ID NO 22, SEQ ID NO 25, SEQ ID NO 28, SEQ ID NO 31, SEQ ID NO 34, SEQ ID NO 37, SEQ ID NO 40, and SEQ ID NO 43.

71. A screening method, the method comprising:

providing a polypeptide having an amino acid sequence that is at least 90% identical to a member of the group consisting of SEQ ID NO 9, SEQ ID NO 27, and SEQ ID NO 36;

exposing the polypeptide to a factor; and

determining that the factor has a specific binding affinity for the polypeptide.

72. The method of claim 71 wherein the factor is provided in isolated form by using a separations process that separates the bound factor from the polypeptide.

73. The method of claim 71 wherein the factor is isolated prior to exposure of the factor to the polypeptide.

74. The method of claim 71 wherein the polypeptide amino acid sequence is at least 95% identical to a member of the group consisting of SEQ ID NO 9, SEQ ID NO 27, and SEQ ID NO 36.

75. The method of claim 71 wherein the polypeptide amino acid sequence is at least 99% identical to a member of the group consisting of SEQ ID NO 9, SEQ ID NO 27, SEQ ID NO 36, and SEQ ID NO 45.

76. The method of claim 71 further comprising exposing the polypeptide to a cellular lysate that contains the factor.

77. The method of claim 71 wherein the factor is a small molecule that binds the polypeptide.

78. A method of administering a compound, the method comprising preparing a composition of a factor, wherein the factor is isolated by the method of claim 71.

79. A composition, the composition comprising a combination of a pharmaceutically acceptable carrier, VEGF, and at least one member of the group consisting of TDE1 and PTV.

80. The composition of claim 79 wherein the VEGF and the at least one member of the group consisting of TDE1 and PTV are packaged as a kit.

82. The method of claim 80 wherein the composition is administered by a mechanism in the group consisting of topical application or injection.

81. A method of using a composition, the method comprising administering the composition to an animal, the composition comprising a polypeptide having an amino acid sequence that is at least 90% identical to SEQ ID NO 27.

83. The method of claim 81 wherein the composition is administered according to a member of the group consisting of injection of the composition into or near a tumor, injection of the composition into or near a heart, and injection of the composition into or near a necrotic tissue.

84. The method of claim 81 wherein the composition is administered into or near a diabetic or venous ulcer.