CD40 splice variants, compositions for making and methods of using the same

• US 20050202531A1
• Filed: 11/03/2004
• Published: 09/15/2005
• Est. Priority Date: 11/03/2003
• Status: Abandoned Application

• Current Assignee: Compugen Ltd
• Original Assignee: Compugen Ltd
• Inventors: Toporik, Amir
• Application Number:
  US10/979,178
• Publication Number:
  US 20050202531A1
• Time in Patent Office: Days
• US Class Current: 435/69.100
• CPC Class Codes: C07K 14/70578 NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95 NGF-receptor C07K14/71, TNF-receptor C07K14/7151

Abstract

Provided are isolated CD40 splice variants that include altered internal sequences and unique tail sequences relative to previously described CD40 protein sequences. Also provided are fragments of the CD40 splice variants comprising at least 10 amino acids including at least 4 amino acids of the unique tail sequence; the unique tail sequences, and homologues thereof having at least 10 amino acids and 90% identity and antibodies which bind to an epitope on such proteins are disclosed. Pharmaceutical compositions comprising the protein, antibodies, isolated nucleic acid molecule that encode such proteins and pharmaceutical composition comprising such nucleic acid molecules are also disclosed. The present invention additionally relates to recombinant expression vectors that include the nucleic acid molecules and host cells which comprise such recombinant expression vectors are disclosed. In vitro methods of detecting in a sample the presence and/or quantity of such proteins or transcript which encodes such proteins are disclosed as are kits and reagents for performing the methods. Methods of modulating CD40-CD154 interactions in an individual are disclosed.

Claims

1. An isolated protein having the amino acid sequence selected from the group consisting of:

i) SEQ ID NO;

5;

ii) a fragment of SEQ ID NO;

5 comprising at least 10 amino acids including at least 4 amino acids of the unique tail of SEQ ID NO;

5;

iii) SEQ ID NO;

6;

iv) a fragment of SEQ ID NO;

6 comprising at least 10 amino acids including at least 4 amino acids of the unique tail of SEQ ID NO;

6;

v) SEQ ID NO;

7;

vi) an amino acid sequence having at least 10 amino acids and 90% identity with any one of the sequences of i)-v); and

vii) an amino acid sequence having at least about 95% identity with any one of the sequences of i)-v).

2. The isolated protein of claim 1 having the amino acid sequence selected from the group consisting of:

SEQ ID NO;

5;

SEQ ID NO;

6; and

SEQ ID NO;

7.

3. The isolated protein of claim 1, having the amino acid sequence of a fragment of a member of the group consisting of SEQ ID NO:

5, wherein the fragment has a length equal to any integer n equal to or between 10 and 50 amino acids, and wherein the amino acid sequence of the fragment is the amino acid sequence of a member of the respective amino acid sequence starting at any amino acid number 135−

x; and

ending at any amino acid number 136+((n−

2)−

x), wherein x is any integer between 0 and (n−

2) or the end of the respective amino acid sequence, whichever is the lower number.

4. A pharmaceutical composition comprising a protein of claim 1 and a pharmaceutically acceptable carrier.

5. An isolated nucleic acid molecule that comprises a nucleic acid sequence that encodes a protein of claim 1.

6. A pharmaceutical composition comprising a nucleic acid molecule of claim 5 and a pharmaceutically acceptable carrier.

26. A method of modulating CD40-CD154 interactions in an individual, the method comprising administering to said individual a protein of claim 1 in an amount effective to modulate CD40-CD154 interactions in said individual.

27. The method of claim 26 wherein the individual is suspected of suffering from chronic inflammatory disease.

28. The method of claim 26 wherein the individual is suspected of suffering from a condition selected from the group consisting of cancer, atherosclerosis, and acute injury.

29. A method of modulating CD40-CD154 interactions in an individual, the method comprising administering to said individual a nucleic acid molecule that comprises a coding sequence that encodes a protein of claim 1,

wherein said coding sequence is operatively linked to regulatory sequences necessary for expression in the individual, and

wherein the protein is produced by expression of the coding sequence in an amount effective to modulate CD40-CD154 interactions in the individual.

30. The method of claim 29 wherein the individual is suspected of suffering from chronic inflammatory disease.

31. The method of claim 29 wherein the individual is suspected of suffering from a condition selected from the group consisting of cancer, atherosclerosis, and acute injury.

47. An antibody or an antibody fragment being capable of specifically binding to a CD40 variant polypeptide comprising an amino acid sequence of claim 3, wherein said antibody or antibody fragment does not bind to an epitope consisting of an amino acid fragment of SEQ ID NO:

14.

7. An isolated nucleic acid molecule comprising the nucleotide sequence selected from the group consisting of:

i) SEQ ID NO;

1;

ii) a fragment of SEQ ID NO;

1 that encodes at least 10 amino acids of SEQ ID NO;

5 including at least 4 amino acids of the unique tail of SEQ ID NO;

5;

iii) SEQ ID NO;

2;

iv) SEQ ID NO;

3;

v) a fragment of SEQ ID NO;

3 that encodes at least 10 amino acids of SEQ ID NO;

6 including at least 4 amino acids of the unique tail of SEQ ID NO;

6;

vi) SEQ ID NO;

4; and

vii) a fragment of SEQ ID NO;

4 that encodes at least 10 amino acids of SEQ ID NO;

7;

8. A recombinant expression vector comprising the nucleic acid molecule of claim 7.

9. A host cell comprising the recombinant expression vector of claim 8.

10. The nucleic acid molecule of claim 7 comprising at least 12-150 nucleotides.

11. The nucleic acid molecule of claim 7 selected from the group consisting of:

a fragment of SEQ ID NO;

1 comprising at least 12-150 nucleotides;

a fragment of SEQ ID NO;

2 comprising at least 12-150 nucleotides;

a fragment of SEQ ID NO;

3 comprising at least 12-150 nucleotides; and

a fragment of SEQ ID NO;

4 comprising at least 12-150 nucleotides.

12. The nucleic acid molecule of claim 7 comprising at least 15-50 nucleotides.

13. The nucleic acid molecule of claim 7 selected from the group consisting of:

a fragment of SEQ ID NO;

1 comprising at least 15-50 nucleotides;

a fragment of SEQ ID NO;

2 comprising at least 12-150 nucleotides;

a fragment of SEQ ID NO;

3 comprising at least 15-50 nucleotides; and

a fragment of SEQ ID NO;

4 comprising at least 15-50 nucleotides.

14. The nucleic acid molecule of claim 7 comprising at least 18-30 nucleotides.

15. The nucleic acid molecule of claim 7 selected from the group consisting of:

a fragment of SEQ ID NO;

1 comprising at least 18-30 nucleotides;

a fragment of SEQ ID NO;

2 comprising at least 12-150 nucleotides;

a fragment of SEQ ID NO;

3 comprising at least 18-30 nucleotides; and

a fragment of SEQ ID NO;

4 comprising at least 18-30 nucleotides.

16. An isolated antibody that specifically binds to an epitope on SEQ ID NOs:

5, 6 or 7

wherein the isolated antibody does not bind to an epitope consisting of an amino acid fragment of SEQ ID NO;

14.

a. The antibody of claim 16, wherein said epitope includes at least 4 amino acids from the unique tail of SEQ ID NO;

5;

or at least 4 amino acids from the unique tail of SEQ ID NO;

6.

17. The antibody of claim 16 wherein said antibody is a monoclonal antibody.

18. A method of detecting the presence of a protein in a sample, the method comprising

contacting a sample with an antibody of claim 16;

and

determining if said antibody is bound to protein in said sample,

wherein binding of said antibody to protein in said sample is indicative of the presence of a protein selected from the group consisting of SEQ ID NO;

5-7, in said sample.

19. The method of claim 18 wherein said sample is body fluid.

20. The method of claim 19 wherein said body fluid is blood.

21. A kit for detecting the presence of a protein in a sample, the protein selected from the group consisting of SEQ ID NO:

5-7, comprising a container that comprises an antibody of claim 16 and a container that comprises a positive control sample or a container that comprises a negative control sample.

22. A method of detecting whether an individual is expressing a protein, the method comprising

detecting in a sample from the individual a transcript that encodes a protein selected from the group consisting of SEQ ID NO:

5-7,

wherein detection of the transcript in a sample is indicative of expression of said protein by said individual.

23. The method of claim 22 wherein the transcript is detected using polymerase chain reaction.

24. The method of claim 22 wherein said sample is body fluid.

25. The method of claim 24 wherein said body fluid is blood.

32. An isolated chimeric polypeptide comprising a first amino acid sequence being at least 95% homologous to amino acids 1-135 of wild-type CD40 (SEQ ID NO:

14), and a second amino acid sequence being at least 95% homologous to a polypeptide having the sequence VRPKTWLCNRQAQTRLMLSVVSPGQWALEKA (SEQ ID NO;

     20), wherein the first and said second amino acid sequences are contiguous and in a sequential order.

33. A fragment of the polypeptide of claim 32, wherein the fragment has a length of any integer n equal to or between 10 and 50 amino acids, and wherein the amino acid sequence of the fragment is the amino acid sequence of SEQ ID NO:

5 wherein at least two amino acids include AV, having a structure as follows (numbering according to SEQ ID NO;

     5);

a sequence starting from any of amino acid numbers (135−

x) to 135;

ending at any of amino acid numbers 136+((n−

2)−

x), in which x varies from 0 to (n−

2), such that the fragment does not extend beyond the last amino acid of SEQ ID NO;

5.

34. The polypeptide of claim 32, wherein the second amino acid sequence is at least 95% identical to the polypeptide having the sequence VRPKTWLCNRQAQTRLMLSVVSPGQWALEKA (SEQ ID NO:

20).

35. The polypeptide of claim 32, wherein the second amino acid sequence is at least 98% identical to the polypeptide having the sequence VRPKTWLCNRQAQTRLMLSVVSPGQWALEKA (SEQ ID NO:

20).

36. The polypeptide of claim 32, wherein the second amino acid sequence is at least 99% identical to the polypeptide having the sequence VRPKTWLCNRQAQTRLMLSVVSPGQWALEKA (SEQ ID NO:

20).

48. An antibody or an antibody fragment being capable of specifically binding to a CD40 variant polypeptide comprising an amino acid sequence of claim 32, wherein said antibody or antibody fragment does not bind to an epitope consisting of an amino acid fragment of SEQ ID NO:

14.

37. An isolated polypeptide comprising an amino acid sequence at least 95% identical to a polypeptide having the sequence VRPKTWLCNRQAQTRLMLSVVSPGQWALEKA (SEQ ID NO:

20).

49. An antibody or an antibody fragment being capable of specifically binding to a CD40 variant polypeptide comprising an amino acid sequence of claim 37, wherein said antibody or antibody fragment does not bind to an epitope consisting of an amino acid fragment of SEQ ID NO:

14.

38. An isolated chimeric polypeptide, including a first amino acid sequence being at least 95% homologous to amino acids 1-134 of WT CD40 (SEQ ID NO:

14), and a second amino acid sequence being at least 95% homologous to a polypeptide having the sequence DICQPHFPKDRGLNLLM (SEQ ID NO;

     24), wherein the first and said second amino acid sequences are contiguous and in a sequential order.

39. A fragment of the polypeptide of claim 38, wherein the fragment has a length of any integer n equal to or between 10 and 50 amino, and wherein the amino acid sequence of the fragment is the amino acid sequence of SEQ ID NO:

6 starting at any of amino acid numbers (134−

x) to 134; and

ending at any amino acid number 135+((n−

2)−

x), wherein x is any integer between 0 and (n−

2) or the end of SEQ ID NO;

6, whichever is the lower number,

and wherein at least two of the amino acids of the fragment are I and D, such that the fragment does not extend beyond the last amino acid of SEQ ID NO;

6.

40. The polypeptide of claim 39, wherein the second amino acid sequence is at least 95% identical to the polypeptide having the sequence DICQPHFPKDRGLNLLM (SEQ ID NO:

24).

41. The polypeptide of claim 39, wherein the second amino acid sequence is at least 98% identical to the polypeptide having the sequence DICQPHFPKDRGLNLLM (SEQ ID NO:

24).

42. The polypeptide of claim 39, wherein the second amino acid sequence is at least 99% identical to the polypeptide having the sequence DICQPHFPKDRGLNLLM (SEQ ID NO:

24).

43. The polypeptide of claim 39, wherein the second amino acid sequence is at least 90% identical to the polypeptide having the sequence DICQPHFPKDRGLNLLM (SEQ ID NO:

24).

50. An antibody or an antibody fragment being capable of specifically binding to a CD40 variant polypeptide comprising an amino acid sequence of claim 38, wherein said antibody or antibody fragment does not bind to an epitope consisting of an amino acid fragment of SEQ ID NO:

14.

51. An antibody or an antibody fragment being capable of specifically binding to a CD40 variant polypeptide comprising an amino acid sequence of claim 40, wherein said antibody or antibody fragment does not bind to an epitope consisting of an amino acid fragment of SEQ ID NO:

14.

44. An isolated polypeptide comprising an amino acid sequence at least 95% identical to a polypeptide having the sequence

DICQPHFPKDRGLNLLM (SEQ ID NO:

24).

45. An isolated chimeric polypeptide encoding for VAR3 (SEQ ID NO:

7), comprising a first amino acid sequence being at least 95% homologous to amino acids 1-186 of wild-type CD40 corresponding to GI;

15214587 (SEQ ID NO;

     14), which also corresponds to amino acids 1-186 of SEQ ID NO;

7 corresponding to VAR3, bridged by E and a second amino acid sequence being at least 95% homologous to amino acids 215-177 of wild-type CD40 corresponding to GI;

15214587 (SEQ ID NO;

     14), which also corresponds to amino acids 188-248 of SEQ ID NO;

7 corresponding to VAR3, wherein said first amino acid sequence is contiguous to said bridging amino acid and said second amino acid sequence is contiguous to said bridging amino acid, and wherein said first amino acid, said bridging amino acid and said second amino acid sequence are in a sequential order.

46. An isolated chimeric polypeptide encoding for an edge portion of SEQ ID NO:

7, comprising a polypeptide having a length “

n”

, wherein n is at least about 10 amino acids in length, optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise CEK (where C is the last amino acid of the WT fragment before the edge and K is the first amino acid of the WT fragment after the edge, E is the bridging amino acid), having a structure as follows (numbering according to SEQ ID NO;

7);

a sequence starting from any of amino acid numbers 186−

x to; and

ending at any of amino acid numbers 188+((n−

2)−

x), in which x varies from 0 to n−

2, such that the fragment does not extend beyond the last amino acid of SEQ ID NO;

7.