Companion diagnostic for anti-hyaluronan agent therapy and methods of use thereof

• US 8,846,034 B2
• Filed: 10/24/2012
• Issued: 09/30/2014
• Est. Priority Date: 10/24/2011
• Status: Active Grant

• Current Assignee: Halozyme, Inc. (Halozyme Therapeutics, Inc.)
• Original Assignee: Halozyme, Inc. (Halozyme Therapeutics, Inc.)
• Inventors: Jiang, Ping, Shepard, H. Michael, Huang, Lei
• Primary Examiner(s): Cochrane Carlson, Karen
• Application Number:
  US13/694,071
• Publication Number:
  US 20130202583A1
• Time in Patent Office: 706 Days
• Field of Search: 424/94.62
• US Class Current: 424/94.62
• CPC Class Codes: A61K 38/47 acting on glycosyl compounds (3.2), e.g. cellulases, lactases
• CPC Class Codes: A61K 47/10 Alcohols; Phenols; Salts thereof, e.g. glycerol; Polyethylene glycols [PEG]; Poloxamers; PEG/POE alkyl ethers
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C07K 14/47 from mammals
• CPC Class Codes: C07K 2319/00 Fusion polypeptide
• CPC Class Codes: C07K 2319/30 Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto
• CPC Class Codes: C07K 2319/735 containing a domain for self-assembly, e.g. a viral coat protein (includes phage display)
• CPC Class Codes: C12N 9/2474 Hyaluronoglucosaminidase (3.2.1.35), i.e. hyaluronidase
• CPC Class Codes: G01N 2333/705 Assays involving receptors, cell surface antigens or cell surface determinants
• CPC Class Codes: G01N 2400/40 Glycosaminoglycans, i.e. GAG or mucopolysaccharides, e.g. chondroitin sulfate, dermatan sulfate, hyaluronic acid, heparin, heparan sulfate, and related sulfated polysaccharides
• 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 33/566 using specific carrier or receptor proteins as ligand binding reagents where possible specific carrier or receptor proteins are classified with their target compounds
• CPC Class Codes: G01N 33/574 for cancer
• CPC Class Codes: G01N 33/57488 involving compounds identifable in body fluids
• CPC Class Codes: G01N 33/6893 related to diseases not provided for elsewhere

Abstract

Methods and diagnostic agents for identification of subjects for cancer treatment with an anti-hyaluronan agent, such as a hyaluronan-degrading enzyme, are provided. Diagnostic agents for the detection and quantification of hyaluronan in a biological sample and monitoring cancer treatment with an anti-hyaluronan agent, for example a hyaluronan-degrading enzyme, are provided. Combinations and kits for use in practicing the methods also are provided.

Claims

1. A TSG-6-LM multimer, comprising:

a first polypeptide containing a TSG-6 link module linked directly or indirectly via a linker to a first multimerization domain; and

a second polypeptide containing a TSG-6 link module linked directly or indirectly via a linker to a second multimerization domain, wherein;

the first and second multimerization domains interact to form a multimer containing two or more TSG-6 link modules; and

the first and second polypeptide do not comprise the full-length sequence of TSG-6.

2. The TSG-6-LM multimer of claim 1, wherein the full-length sequence of TSG-6 is set forth in SEQ ID NO:

206 or SEQ ID NO;

222.

3. The TSG-6-LM multimer of claim 1, wherein the link module is the only TSG-6 portion of the first polypeptide and the second polypeptide.

4. The TSG-6 multimer of claim 1, wherein the first and second link module are the same or different.

5. The TSG-6 multimer of claim 1, wherein the link module comprises the sequence of amino acids set forth in SEQ ID NO:

207, 360, 417 or 418 or a sequence of amino acids comprising at least 85% amino acid sequence identity to the sequence of amino acids set forth in SEQ ID NO;

207, 360, 417 or 418 that specifically binds HA.

6. The TSG-6 multimer of claim 1, wherein the TSG-6 link module is modified to reduce or eliminate binding to heparin.

7. The TSG-6 multimer of claim 6, wherein the TSG-6 link module comprises an amino acid replacement at an amino acid position corresponding to amino acid residue 20, 34, 41, 54, 56, 72 or 84 set forth in SEQ ID NO:

360, whereby a corresponding amino acid residue is identified by alignment to a TSG-6-LM set forth in SEQ ID NO;

360.

8. The TSG-6 multimer of claim 7, wherein the amino acid replacement is to a non-basic amino acid residue selected from among Asp (D), Glu (E), Ser (S), Thr (T), Asn (N), Gln (Q), Ala (A), Val (V), Ile (I), Leu (L), Met (M), Phe (F), Tyr (Y) and Trp (W).

9. The TSG-6 multimer of claim 8, wherein the TSG-6 link module comprises an amino acid replacement corresponding to amino acid replacement selected from among K20A, K34A and K41A in a TSG-6-LM set forth in SEQ ID NO:

360 or the replacement at the corresponding residue in another TSG-6-LM.

10. The TSG-6 multimer of claim 9, wherein the link module comprises the sequence of amino acids set forth in SEQ ID NO:

361 or 416 or a sequence of amino acids comprising at least 85% amino acid sequence identity to the sequence of amino acids set forth in SEQ ID NO;

361 or 416 that specifically binds HA.

11. The TSG-6 multimer of claim 1, wherein the multimerization domain is selected from among an immunoglobulin constant region (Fc), a leucine zipper, complementary hydrophobic regions, complementary hydrophilic regions, compatible protein-protein interaction domains, free thiols that form an intermolecular disulfide bond between two molecules, and a protuberance-into-cavity and a compensatory cavity of identical or similar size that form stable multimers.

12. The TSG-6 multimer of claim 11, wherein the multimerization domain is an Fc domain or a variant thereof that effects multimerization.

13. The TSG-6 multimer of claim 12, wherein the Fc domain is an IgG, IgM or an IgE Fc domain.

14. The TSG-6 multimer of claim 1, comprising the sequence of amino acids set forth as amino acids 24-349 of SEQ ID NO:

212 or 215 or a sequence of amino acids that exhibits at least 85% amino acid sequence identity to amino acids 24-349 of SEQ ID NO;

212 or 215 and specifically binds HA.

15. The TSG-6 multimer of claim 1 that has a binding affinity to HA with an association constant (Ka) of at least 1×

10⁷M<sup>−

1</sup>.

16. The TSG-6 multimer of claim 1, wherein the first and second multimerization domain are the same or different.

17. The TSG-6 multimer of claim 1, wherein the Fc domain is an IgG, IgM or an IgE Fc domain.

18. A combination, comprising:

the TSG-6 multimer of claim 1; and

an anti-hyaluronan agent.

19. The combination of claim 18, wherein the TSG-6 multimer is conjugated to a detectable moiety that is detectably labeled or that can be detected.

20. The combination of claim 18, further comprising reagents for detection of the TSG-6 multimer.

21. The combination of claim 18, wherein the anti-hyaluronan agent is a hyaluronan degrading enzyme or is an agent that inhibits hyaluronan synthesis.

22. The combination of claim 18 that is packaged as a kit.

23. A method for selecting a subject for treatment of a hyaluronan-associated disease or condition with an anti-hyaluronan agent, comprising:

a) contacting a tissue or body fluid sample from a subject with a hyaluronan-associated disease or condition with a TSG-6-LM multimer of claim 1 or a hyaluronan binding region thereof; and

b) detecting binding of the TSG-6-LM multimer or a hyaluronan-binding region thereof to the sample, thereby determining the amount of hyaluronan (HA) in the sample, wherein if the amount of hyaluronan (HA) in the sample is at or above a predetermined threshold level, selecting the subject for treatment with an anti-hyaluronan agent.

24. The method of claim 23, wherein:

the predetermined threshold level is at least or above 0.015 μ

g HA/ml;

or

the predetermined threshold is an HA score of at least +2 (HA⁺²) or at least +3 (HA⁺³);

or

the predetermined threshold level is at least a percent HA positive pixels in tumor (cells and stroma) to total stain in tumor tissue of at least 10%, 10% to 25% or greater than 25%.

25. The method of claim 23, wherein the hyaluronan-associated disease or condition is a tumor or cancer.

26. The method of claim 23, wherein the TSG-6-LM in the multimer has the sequence of amino acids set forth in SEQ ID NO:

207, 360, 417 or 418, or a sequence of amino acids comprising at least 85% amino acid sequence identity to the sequence of amino acids set forth in SEQ ID NO;

207, 360, 417 or 418 and specifically binds HA.

27. The method of claim 23, wherein the TSG-6 link module in the multimer is modified to reduce or eliminate binding to heparin.

28. The method of claim 27, wherein the TSG-6 link module in the multimer comprises an amino acid replacement at an amino acid position corresponding to amino acid residue 20, 34, 41, 54, 56, 72 or 84 set forth in SEQ ID NO:

360, whereby a corresponding amino acid residue is identified by alignment to a TSG-6-LM set forth in SEQ ID NO;

360.

29. The method of claim 28, wherein the amino acid replacement is to a non-basic amino acid residue selected from among Asp (D), Glu (E), Ser (S), Thr (T), Asn (N), Gln (Q), Ala (A), Val (V), Ile (I), Leu (L), Met (M), Phe (F), Tyr (Y) and Trp (W).

30. The method of claim 29, wherein the TSG-6 link module in the multimer comprises an amino acid replacement corresponding to an amino acid replacement selected from among K20A, K34A and K41A in a TSG-6-LM set forth in SEQ ID NO:

360 or the replacement at the corresponding residue in another TSG-6-LM.

31. The method of claim 30, wherein the TSG-6 link module in the multimer comprises a link module having the sequence of amino acids set forth in SEQ ID NO:

361 or 416 or a sequence of amino acids comprising at least 85% amino acid sequence identity to the sequence of amino acids set forth in SEQ ID NO;

361 or 416 that specifically binds HA.

32. The method of claim 23, wherein the TSG-6-LM multimer specifically binds to HA with a binding affinity that has a dissociation constant (Kd) of at least less than or less than 1×

10<sup>−

7</sup> M.

33. The method of claim 23, wherein the first and second link module in the multimer is the same or different.

34. The method of claim 23, wherein the multimerization domain in the multimer is an Fc domain or a variant thereof that effects multimerization.

35. The method of claim 23, wherein the TSG-6-LM multimer is TSG-6-LM-Fc that has the sequence of amino acids set forth as amino acids 24-349 of SEQ ID NO:

212 or 215 or a sequence of amino acids that exhibits at least 85% amino acid sequence identity to amino acids 24-349 of SEQ ID NO;

212 or 215 and specifically binds HA.

36. The method of claim 23, wherein the step of contacting the sample with a TSG-6-LM multimer or hyaluronan-binding region is effected at between or about between pH 5.6 to 6.4.

37. The method of claim 23, wherein the TSG-6-LM multimer is conjugated to a detectable moiety that is detectably labeled or that can be detected.

38. The method of claim 37, wherein the TSG-6-LM multimer is biotinylated.

39. The method of claim 23, wherein the sample is a stromal tissue sample from a tumor.

40. The method of claim 23, wherein the sample is taken from a biopsy from a solid tumor.

41. The method of claim 23, wherein the sample is a fluid sample that is a blood, serum, urine, sweat, semen, saliva, cerebral spinal fluid, or lymph sample.

42. The method of claim 23, wherein the sample is obtained from a mammal.

43. The method of claim 42, wherein the mammal is a human.

44. The method of claim 23, wherein hyaluronan is detected by a solid phase binding assay, histochemistry or in vivo imaging.

45. The method of claim 23, wherein the anti-hyaluronan agent is a hyaluronan degrading enzyme or is an agent that inhibits hyaluronan synthesis.

46. The method of claim 45, wherein the anti-hyaluronan agent is a hyaluronan-degrading enzyme that is modified by conjugation to a polymer.

47. The method of claim 46, wherein the polymer is PEG and the hyaluronan degrading enzyme is PEGylated.

48. The method of claim 23, wherein the anti-hyaluronan agent is a hyaluronan degrading enzyme that is a hyaluronidase.

49. The method of claim 48, wherein the hyaluronan-degrading enzyme is a PH20 hyaluronidase or truncated form thereof lacking a C-terminal glycosylphosphatidylinositol (GPI) attachment site or a portion of the GPI attachment site, whereby the truncated form exhibits hyaluronidase activity.

51. The method of claim 49, wherein the PH20 is neutral active and N-glycosylated and is selected from among:

(a) a hyaluronidase polypeptide that is a full-length PH20 or is a C-terminal truncated form of the PH20, wherein the truncated form includes at least amino acid residues 36-464 of SEQ ID NO;

1, wherein the full-length PH20 comprises the sequence of amino acids set forth in SEQ ID NO;

2;

or

(b) a hyaluronidase polypeptide comprising a sequence of amino acids having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity with the polypeptide or truncated form of sequence of amino acids set forth in SEQ ID NO;

2;

or

(c) a hyaluronidase polypeptide of (a) or (b) comprising amino acid substitutions, whereby the hyaluronidase polypeptide has a sequence of amino acids having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity with the polypeptide set forth in SEQ ID NO;

2 or the with the corresponding truncated forms thereof.

52. The method of claim 49, wherein the PH20 or truncated form thereof comprises the sequence of amino acids set forth in any of SEQ ID NOS:

4-9, 47, 48, 150-170 and 183-189 or a sequence of amino acids that exhibits at least 85% sequence identity to any of SEQ ID NOS;

4-9, 47, 48, 150-170 and 183-189.

53. The method of claim 23, comprising administering a corticosteroid prior to administration of the anti-hyaluronan agent, with administration of the anti-hyaluronan agent or after administration of the anti-hyaluronan agent, wherein the corticosteroid is administered in an amount sufficient to ameliorate an adverse effect in the subject from the administered anti-hyaluronan agent.

54. The method of claim 53, wherein the corticosteroid is a glucocorticoid.

55. The method of claim 23, further comprising:

c) administering an anti-hyaluronan agent to the selected subject, thereby treating the selected subject with an anti-hyaluronan agent.

56. A method of diagnosis of a hyaluronan-associated disease or condition, comprising:

contacting a tissue or body fluid sample from a subject with a hyaluronan-associated disease or condition with a TSG-6-LM multimer of claim 1 or a hyaluronan binding region thereof; and

detecting binding of the TSG-6-LM multimer or a hyaluronan-binding region thereof that binds to the sample, thereby determining the amount of hyaluronan in the sample, wherein the subject is diagnosed with a hyaluronan-associated disease or condition if the amount of hyaluronan is above a predetermined level or above the hyaluronan level of a reference sample.

57. A method for treating a subject with a tumor, comprising:

a) administering an anti-hyaluronan agent to a subject;

b) contacting a tissue or body fluid sample from the subject treated with the anti-hyaluronan agent with a TSG-6-LM multimer of claim 1;

c) detecting binding of the TSG-6-LM multimer to the sample, thereby determining the amount of hyaluronan in the sample;

d) comparing the level of hyaluronan to a control or reference sample to thereby determine the amount of hyaluronan in the sample relative to the control or reference sample, wherein detection of a decrease in hyaluronan compared to the control or reference sample indicates that the treatment is effective; and

e) altering treatment based on the determined amount of hyaluronan in the sample relative to the control or reference sample, wherein;

if the amount of hyaluronan in the sample is at or above the amount in the control or reference sample, continuing treatment or escalating treatment by increasing the dosage and/or dose schedule of the anti-hyaluronan agent;

or

if the amount of hyaluronan in the sample is below the amount in the control or reference sample, continuing the treatment, reducing treatment by decreasing the dosage and/or dose schedule or terminating treatment of the anti-hyaluronan agent.

58. The method of claim 57, wherein the control or reference sample is a corresponding sample from the subject before treatment with the anti-hyaluronan agent or is a corresponding sample from the subject after the previous dose of the anti-hyaluronan agent.

50. The method of 39, wherein the PH20 is selected from a human, monkey, bovine, ovine, rat, mouse or guinea pig PH20.