Compounds and Methods for Modulating an Immune Response

• US 20120039806A1
• Filed: 03/22/2010
• Published: 02/16/2012
• Est. Priority Date: 03/23/2009
• Status: Abandoned Application

• Current Assignee: The Burnet Institute, The Walter & Eliza Hall Institute Of Medical Research
• Original Assignee: The Burnet Institute
• Inventors: Caminschi, Irina, Huang, David Ching Siang, Cowman, Alan, Lahoud, Mireille Hanna, Zhang, Jian-Guo, Van Delft, Mark Francis, NIcola, Nicos Anthony, Wright, Mark Dexter
• Application Number:
  US13/203,682
• Publication Number:
  US 20120039806A1
• Time in Patent Office: Days
• US Class Current: 424/9.1
• CPC Class Codes: A61K 2039/505 comprising antibodies
• CPC Class Codes: A61K 2039/6031 Proteins
• CPC Class Codes: A61K 39/385 Haptens or antigens, bound to carriers
• CPC Class Codes: A61K 47/64 Drug-peptide, drug-protein or drug-polyamino acid conjugates, i.e. the modifying agent being a peptide, protein or polyamino acid which is covalently bonded or complexed to a therapeutically active agent peptidic linkers A61K47/65
• CPC Class Codes: A61K 47/6801 Drug-antibody or immunoglobulin conjugates defined by the pharmacologically or therapeutically active agent
• CPC Class Codes: A61P 29/00 Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
• CPC Class Codes: A61P 31/00 Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
• CPC Class Codes: A61P 33/02 Antiprotozoals, e.g. for leishmaniasis, trichomoniasis, toxoplasmosis
• CPC Class Codes: A61P 33/06 Antimalarials
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 37/00 Drugs for immunological or allergic disorders
• CPC Class Codes: A61P 37/02 Immunomodulators
• CPC Class Codes: A61P 37/06 Immunosuppressants, e.g. drugs for graft rejection
• CPC Class Codes: A61P 37/08 Antiallergic agents antiasthmatic agents A61P11/06; ophthalmic antiallergics A61P27/14
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C07K 14/47 from mammals
• CPC Class Codes: C07K 16/2851 against the lectin superfamily, e.g. CD23, CD72
• CPC Class Codes: C07K 2317/24 containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
• CPC Class Codes: C07K 2317/34 Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
• CPC Class Codes: C07K 2317/622 Single chain antibody (scFv)
• CPC Class Codes: C07K 2317/626 : Diabody or triabody
• CPC Class Codes: G01N 2333/4724 : Lectins
• CPC Class Codes: G01N 2333/9015 : Ligases (6)
• CPC Class Codes: G01N 2800/52 : Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
• CPC Class Codes: G01N 2800/56 : Staging of a disease; Further complications associated with the disease
• CPC Class Codes: G01N 33/573 : for enzymes or isoenzymes
• CPC Class Codes: Y02A 50/30 : Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Abstract

The present invention relates to the identification of proteins which bind the dendritic cell marker known as Clec9A. The present invention provides new compounds for targeting therapeutic agents such as antigens to dendritic cells. Also provided are methods of modulating a humoral and/or T cell mediated immune response to the antigen, methods of delivery of a cytotoxic agent to dendritic cells thereof involved in diseased states, methods of modulating the uptake and/or clearance of cells with a disrupted cell membrane, cells infected with a pathogen, dying cells or dead cells, or a portion thereof, and methods of modulating antigen recognition, processing and/or presentation, as well as immune responses to material derived from cells with a disrupted cell membrane, cells infected with a pathogen, dying cells or dead cells, or a portion thereof.

Claims

1. A composition comprising compound comprising a polypeptide conjugate, wherein the polypeptide of the polypeptide conjugate comprises:

i) an amino acid sequence as provided in any one of SEQ ID NO'"'"'s 48 to 80;

ii) an amino acid sequence which is at least 50% identical to any one or more of SEQ ID NO'"'"'s 48 to 80; and

/or

iii) a biologically active fragment of i) or ii),

and wherein the polypeptide of the compound binds a second polypeptide comprising

a) an amino acid sequence as provided in any one of SEQ ID NO'"'"'s 1 to 8; and

/or

b) an amino acid sequence which is at least 50% identical to any one or more of SEQ ID NO'"'"'s 1 to 8.

2. The composition of claim 1, wherein the polypeptide comprises an amino acid sequence which is at least 90% identical to any one or more of SEQ ID NO'"'"'s 48 to 80.

3. The composition of claim 1, wherein the polypeptide is conjugated to a therapeutic agent.

4. The composition of claim 3, wherein the therapeutic agent is an antigen.

5. The composition of claim 3, wherein the therapeutic agent is selected from the group consisting of a cytotoxic agent, a cancer antigen, a self antigen, an allergen, or an antigen from an infectious organism.

6. The composition of claim 3, wherein the therapeutic agent is a drug and/or pharmacological agent.

7. The composition of claim 1, wherein the polypeptide is conjugated to a detectable label.

19. The composition according to claim 1 wherein the composition comprises a pharmaceutically acceptable carrier.

20. The composition of claim 19 which comprises an adjuvant.

21. The composition of claim 19, wherein the compound is encapsulated in, or exposed on the surface of, a liposome.

22. A method of modulating an immune response in a subject, the method comprising administering to the subject a composition according to claim 1.

23. The method of claim 22, wherein an immune response to an antigen is induced and/or enhanced.

24. The method of claim 22, wherein an immune response to a self antigen or allergen is reduced.

25. A method of modulating an immune response to an antigen in a subject, the method comprising exposing dendritic cells or precursors thereof in vitro to a composition according to claim 3, and administering said cells to the subject.

26. The method of claim 25, wherein the cells have been isolated from the subject.

29. A method of treating and/or preventing a disease involving dendritic cells or precursors thereof, the method comprising administering to the subject a composition according to claim 3, wherein.

33. The method according to claim 29, wherein the disease involving dendritic cells or precursors thereof is cancer, an infection, an autoimmune disease or an allergy.

34. The method of claim 33, wherein the autoimmune disease is lupus erythematosus.

35. The method of claim 33, wherein the infection is a Plasmodium sp. infection.

36. A method of modulating the uptake and/or clearance of cells with a disrupted cell membrane, cells infected with a pathogen, dying cells or dead cells, or a portion thereof, in a subject, the method comprising administering

i) a polypeptide comprising

a) an amino acid sequence as provided in any one of SEQ ID NO'"'"'s 48 to 80;

b) an amino acid sequence which is at least 50% identical to any one or more of SEQ ID NO'"'"'s 48 to 80; and

/or

c) a biologically active fragment of a) or b),

ii) a composition according to claim 1.

37. A method of modulating the antigen recognition, processing and/or presentation of material derived from cells with a disrupted cell membrane, cells infected with a pathogen, dying cells or dead cells, or a portion thereof, or surrounding cells, in a subject, the method comprising administering

i) a polypeptide comprising

a) an amino acid sequence as provided in any one of SEQ ID NO'"'"'s 48 to 80;

b) an amino acid sequence which is at least 50% identical to any one or more of SEQ ID NO'"'"'s 48 to 80; and

/or

c) a biologically active fragment of a) or b),

ii) a composition according to claim 1.

38. A method of modulating an immune response to material derived from cells with a disrupted cell membrane, cells infected with a pathogen, dying cells or dead cells, or a portion thereof, or surrounding cells, in a subject, the method comprising administering a

i) a polypeptide comprising

a) an amino acid sequence as provided in any one of SEQ ID NO'"'"'s 48 to 80;

b) an amino acid sequence which is at least 50% identical to any one or more of SEQ ID NO'"'"'s 48 to 80; and

/or

c) a biologically active fragment of a) or b),

ii) a composition according to claim 1.

47. The method of claim 36, wherein the uptake and/or clearance of cells with a disrupted cell membrane, cells infected with a pathogen, dying cells or dead cells, or a portion thereof, is increased.

48. The method of claim 36, wherein the uptake and/or clearance of cells with a disrupted cell membrane, cells infected with a pathogen, dying cells or dead cells, or a portion thereof, is decreased.

49. The method of claim 37, wherein antigen recognition, processing and/or presentation of material derived from cells with a disrupted cell membrane, cells infected with a pathogen, dying cells or dead cells, or a portion thereof, or surrounding cells, is increased.

50. The method of claim 37, wherein antigen recognition, processing and/or presentation of material derived from cells with a disrupted cell membrane, cells infected with a pathogen, dying cells or dead cells, or a portion thereof, or surrounding cells, is decreased.

51. The method of claim 38, wherein the immune response to material derived from cells with a disrupted cell membrane, cells infected with a pathogen, dying cells or dead cells, or a portion thereof, or surrounding cells, is increased.

52. The method of claim 38, wherein the immune response to material derived from cells with a disrupted cell membrane, cells infected with a pathogen, dying cells or dead cells, or a portion thereof, or surrounding cells, is decreased.

53. The method according to claim 36, wherein the subject is suffering from a disease selected from:

graft versus host disease (GVHD), an autoimmune disease, an infection, a neurodegenerative disease, systemic inflammatory reaction syndrome (SIRS), cancer and injury.

75. A method of distinguishing between an early stage apoptotic cell and a late stage apoptotic cell, necrotic cell or dead cell, the method comprising

i) contacting a cell with a composition according to claim 1, and

ii) determining whether binding of the compound to the polypeptide is present or absent, wherein the compound binding to the polypeptide indicates that the cell is a late stage apoptotic cell, necrotic cell or dead cell.

80. A method of enriching dendritic cells, or a subset or precursors thereof, from a sample comprising;

i) contacting a sample comprising dendritic cells or precursors thereof with a compound according to claim 1, and

ii) isolating cells bound to the compound.

82. The method of claim 80, wherein the cells obtained from step ii) are administered to a subject.

83. The method of claim 82, wherein the cells are administered to treat and/or prevent a disease selected from cancer, an infection, an autoimmune disease or an allergy.

84. A method of detecting dendritic cells, or a subset or precursors thereof, in a sample comprising;

i) contacting a sample comprising dendritic cells or precursors thereof with a compound according to claim 1, and

ii) detecting cells bound to the compound.

86. A method of detecting dendritic cells, or a subset or precursor thereof, in a subject comprising;

i) administering to the subject a compound according to claim 1,

ii) detecting cells bound to the compound.

87. The method of claim 84, wherein the compound is detectably labelled.

89. The method according to claim 80, wherein the dendritic cells express one or more of the following markers, CD8, CD24, Necl-2, CD11c, HLADR and BDCA3.

91. An isolated and/or exogenous polynucleotide encoding a compound according to claim 1, wherein the compound is a polypeptide.

93. A vector comprising a polynucleotide of claim 91.

94. The vector of claim 93 which is an expression vector.

95. A host cell comprising at least one polynucleotide of claim 91.

96. The host cell of claim 95 which is a bacterial, yeast, insect, animal or plant cell.

97. An enriched population of dendritic cells and/or precursors thereof, obtained by a method according to any claim 80.

98. An expanded dendritic cell population, and/or precursors thereof, obtained by culturing an enriched population of dendritic cells and/or precursors thereof according to claim 97.

99. A composition comprising a polynucleotide of claim 91, and a pharmaceutically acceptable carrier.

100. A kit comprising a composition according to claim 1.

8. A composition comprising a compound that binds a polypeptide which comprises:

i) an amino acid sequence as provided in any one of SEQ ID NO'"'"'s 48 to 80;

ii) an amino acid sequence which is at least 50% identical to any one or more of SEQ ID NO'"'"'s 48 to 80; and

/or

iii) a biologically active fragment of i) or ii).

9. The composition of claim 8 which binds a polypeptide which comprises an amino acid sequence which is at least 90% identical to any one or more of SEQ ID NO'"'"'s 48 to 80.

10. The composition of claim 8 which is a polypeptide.

11. The composition of claim 10 which is an antibody or antigenic binding fragment thereof.

12. The composition of claim 11, wherein the antibody is a monoclonal antibody, humanized antibody, single chain antibody, diabody, triabody, or tetrabody.

13. The compound according to claim 8 which is conjugated to a therapeutic agent or a detectable label.

14. The composition of claim 13, wherein the compound is conjugated to a therapeutic agent.

15. The composition of claim 14, wherein the therapeutic agent is an antigen.

16. The composition of claim 13, wherein the therapeutic agent is a cytotoxic agent, a cancer antigen, a self antigen, an allergen, and/or an antigen from an infectious organism.

17. The composition of claim 13, wherein the therapeutic agent is a drug and/or pharmacological agent.

63. A method of diagnosing, prognosing and/or monitoring the status of a disease associated with cells with a disrupted cell membrane, cells infected with a pathogen, dying cells or dead cells, the method comprising

i) contacting a cell with the composition of claim 8, and

ii) determining whether the polypeptide is present or absent,

wherein the presence of the polypeptide provides a diagnosis, prognosis and/or status of the disease.

65. The method of claim 63, wherein the compound is detectably labelled.

66. The method according to claim 63 which is performed in vivo on a subject.

67. The method according to claim 63 which is performed in vitro on a sample obtained from a subject.

68. The method according to claim 63, wherein the disease is selected from:

graft versus host disease (GVHD), an autoimmune disease, an infection, a neurodegenerative disease, systemic inflammatory reaction syndrome (SIRS), cancer and injury.

69. A method of monitoring the effectiveness of a therapy for killing a cell, the method comprising;

i) exposing a cell to the therapy, and

ii) detecting a cell with a disrupted cell membrane, a dying cell or a dead cell, or a portion thereof, using a method according to claim 63,

wherein the presence of a cell with a disrupted cell membrane, a dying cell or a dead cell indicates that the therapy is effective.

70. The method of claim 69, wherein the cell in step i) is in vivo.

71. The method of claim 69, wherein the therapy is administered to a subject.

72. The method of claim 69, wherein the subject has cancer or an infection.

73. The method according to claim 69, wherein step ii) is performed on a sample obtained from a subject.

74. The method according to claim 69, wherein the therapy is drug therapy or radiotherapy.

18. (canceled)

27-28. -28. (canceled)

30. (canceled)

31. A method of treating and/or preventing a disease involving dendritic cells or precursors thereof, the method comprising administering to the subject an isolated polynucleotide and/or construct encoding said polynucleotide which, when present in a cell of the subject, modulates the level of activity of a polypeptide which comprises:

i) an amino acid sequence as provided in any one of SEQ ID NO'"'"'s 48 to 80; and

/or

ii) an amino acid sequence which is at least 50% identical to any one or more of SEQ ID NO'"'"'s 48 to 80,

in the cell when compared to a cell that lacks said polynucleotide.

32. The method of claim 31, wherein the polynucleotide down-regulates the level of activity of the polypeptide in the cell, and wherein the polynucleotide is selected from:

an antisense polynucleotide, a sense polynucleotide, a catalytic polynucleotide, a microRNA, and a double stranded RNA.

39. A method of modulating the uptake and/or clearance of cells with a disrupted cell membrane, cells infected with a pathogen, dying cells or dead cells, or a portion thereof, and/or modulating the antigen recognition, processing and/or presentation of material derived from cells with a disrupted cell membrane, cells infected with a pathogen, dying cells or dead cells, or a portion thereof, or surrounding cells and/or modulating an immune response to material derived from cells with a disrupted cell membrane, cells infected with a pathogen, dying cells or dead cells, or a portion thereof, or surrounding cells, in a subject, the method comprising:

administering to the subject a compound which modulates the production of a polypeptide which comprises;

i) an amino acid sequence as provided in any one of SEQ ID NO'"'"'s 48 to 80;

ii) an amino acid sequence which is at least 50% identical to any one or more of SEQ ID NO'"'"'s 48 to 80; and

/or

iii) a biologically active fragment of i) or ii).

42. The method according to claim 39, wherein the compound is a polynucleotide.

43. The method of claim 42, wherein the polynucleotide is operably linked to a promoter capable of directing expression of the polynucleotide in a cell of an animal.

44. The method of claim 42, wherein the polynucleotide down-regulates mRNA levels from a gene encoding the polypeptide.

45. The method of claim 44, wherein the polynucleotide is selected from:

an antisense polynucleotide, a sense polynucleotide, a catalytic polynucleotide, a microRNA, and a double stranded RNA.

46. The method of claim 42, wherein the polynucleotide up-regulates mRNA levels from a gene encoding the polypeptide.

40-41. -41. (canceled)

54-62. -62. (canceled)

64. The method of 63, wherein the compound is an antibody or antigenic binding fragment thereof.

76. A method of modulating an immune response to an antigen in a subject, the method comprising

i) obtaining a population of dendritic cells or precursors thereof,

ii) modulating the production and/or activity of a polypeptide which comprises:

a) an amino acid sequence as provided in any one of SEQ ID NO'"'"'s 48 to 80;

b) an amino acid sequence which is at least 50% identical to any one or more of SEQ ID NO'"'"'s 48 to 80; and

/or

c) a biologically active fragment of a) or b),

iii) contacting the dendritic cells or precursors thereof with the antigen, and

iv) administering the dendritic cells or precursors thereof to the subject.

77. The method of claim 76, wherein step iii) comprises contacting the dendritic cells or precursors thereof with a cell with a disrupted cell membrane, a cell infected with a pathogen, a dying cell, a dead cell, and/or a portion thereof, comprising said antigen.

78. The method of claim 76, wherein step iii) comprises

a) obtaining a cell comprising the antigen,

b) disrupting the cell membrane of the cell, and

c) contacting the product of step b) with the dendritic cells or precursors thereof.

79. The method according to claim 76 which further comprises, before step ii), enriching the population for cells expressing the polypeptide.

81. A method of enriching dendritic cells, or a subset or precursors thereof, from a sample comprising;

i) contacting a sample comprising dendritic cells or precursors thereof with a detectably labelled first polynucleotide that hybridizes to a second polynucleotide encoding a polypeptide which comprises

a) an amino acid sequence as provided in any one of SEQ ID NO'"'"'s 48 to 80; and

/or

b) an amino acid sequence which is at least 50% identical to any one or more of SEQ ID NO'"'"'s 48 to 80, and

ii) isolating the detectably labelled cells.

85. A method of detecting dendritic cells, or a subset or precursor thereof, in a sample comprising;

i) contacting a sample comprising dendritic cells or precursors thereof with a detectably labelled first polynucleotide that hybridizes to a second polynucleotide encoding a polypeptide which comprises

a) an amino acid sequence as provided in any one of SEQ ID NO'"'"'s 48 to 80; and

/or

b) an amino acid sequence which is at least 50% identical to any one or more of SEQ ID NO'"'"'s 48 to 80, and

ii) detecting the detectably labelled cells.

88. A method of detecting dendritic cells, or a subset or precursor thereof, in a subject comprising;

i) administering to the subject a detectably labelled first polynucleotide that hybridizes to a second polynucleotide encoding a polypeptide which comprises

a) an amino acid sequence as provided in any one of SEQ ID NO'"'"'s 48 to 80; and

/or

b) an amino acid sequence which is at least 50% identical to any one or more of SEQ ID NO'"'"'s 48 to 80, and,

ii) detecting the detectably labelled cells.

90. A method of detecting a cell with a disrupted cell membrane, a cell infected with a pathogen, a dying cell or a dead cell, the method comprising

i) contacting a cell with a compound that binds a polypeptide comprising

a) an amino acid sequence as provided in any one of SEQ ID NO'"'"'s 48 to 80;

b) an amino acid sequence which is at least 50% identical to any one or more of SEQ ID NO'"'"'s 48 to 80; and

/or

c) a biologically active fragment of a) or b), and

ii) determining whether binding of the compound to the polypeptide is present or absent, wherein the compound binding to the polypeptide indicates that the cell has a disrupted cell membrane, is infected with a pathogen, is dying or is dead.

92. An isolated polynucleotide which, when present in a cell of a subject, modulates the level of activity of a polypeptide in the cell when compared to a cell that lacks said polynucleotide, wherein the polypeptide comprises

i) an amino acid sequence as provided in any one of SEQ ID NO'"'"'s 48 to 80;

ii) an amino acid sequence which is at least 50% identical to any one or more of SEQ ID NO'"'"'s 48 to 80; and

/or

iii) a biologically active fragment of i) or ii).