Methods and compositions for diagnosis, stratification, and monitoring of alzheimer's disease and other neurological disorders in body fluids

• US 20050221348A1
• Filed: 11/19/2004
• Published: 10/06/2005
• Est. Priority Date: 11/19/2003
• Status: Active Grant

• Current Assignee: Rules-Based Medicine, Inc., Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.), U.S. Government Represented By The Department Of Veterans Affairs
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.), U.S. Government Represented By The Department Of Veterans Affairs
• Inventors: Wyss-Coray, Anton, Ray, Sandip
• Granted Patent: US 7,598,049 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: G01N 2333/4745 Insulin-like growth factor binding protein
• CPC Class Codes: G01N 2800/2821 Alzheimer
• CPC Class Codes: G01N 33/6896 Neurological disorders, e.g. Alzheimer's disease

Abstract

The inventors have discovered a collection of proteinaceous biomarkers (“AD biomarkers) which can be measured in peripheral biological fluid samples to aid in the diagnosis of neurodegenerative disorders, particularly Alzheimer'"'"'s disease and mild cognitive impairment (MCI). The invention further provides methods of identifying candidate agents for the treatment of Alzheimer'"'"'s disease by testing prospective agents for activity in modulating AD biomarker levels.

Claims

1. A method of aiding diagnosis of Alzheimer'"'"'s disease (“

AD”

), comprising comparing a measured level of at least one AD diagnosis biomarker in a biological fluid sample from an individual to a reference level for the biomarker, wherein the AD diagnosis biomarker is selected from the group consisting of GCSF;

IFN-g;

IGFBP-1;

BMP-6;

BMP-4;

Eotaxin-2;

IGFBP-2;

TARC;

RANTES;

ANG;

PARC;

Acrp30;

AgRP(ART);

TIMP-1;

TIMP-2;

ICAM-1;

TRAIL R3;

uPAR;

IGFBP-4;

LEPTIN(OB);

PDGF-BB;

EGF;

BDNF;

NT-3;

NAP-2;

IL-1ra;

MSP-a;

SCF;

TGF-b3;

TNF-b;

MIP-1d;

IL-3;

FGF-6;

IL-6 R;

sTNF RII;

AXL;

bFGF;

FGF-4;

CNTF;

MCP-1;

MIP-1b;

TPO;

VEGF-B;

IL-8;

FAS;

EGF-R.

2. The method of claim 1 wherein said AD diagnosis biomarker is selected from the group consisting of basic fibroblast growth factor (bFGF);

BB homodimeric platelet derived growth factor (PDGF-BB);

brain derived neurotrophic factor (BDNF);

epidermal growth factor (EGF), fibroblast growth factor 6 (FGF-6), interleukin-3 (IL-3), soluble interleukin-6 receptor (sIL-6R), leptin (also known as ob), macrophage inflammatory protein-1 delta (MIP-1δ

), macrophage stimulating protein alpha chain (MSP-α

), neurotrophin-3 (NT-3), neutrophil activating peptide-2 (NAP-2), RANTES, soluble tumor necrosis factor receptor-2 (sTNF RII), stem cell factor (SCF), thrombopoietin (TPO), tissue inhibitor of metalloproteases-1 (TIMP-1), tissue inhibitor of metalloproteases-2 (TIMP-2), transforming growth factor-beta 3 (TGF-β

3), and tumor necrosis factor beta (TNF-β

).

3. The method of claim 1, wherein said AD diagnosis marker is selected from the group consisting of BDNF, sIL-6R, IL-8, leptin, MIP-1δ

, PDGF-BB, and TIMP-1.

4. The method of claim 3, wherein said AD diagnosis marker is selected from the group consisting of sIL-6R, IL-8, and TIMP-1.

5. The method of claim 3, wherein said AD diagnosis marker is selected from the group consisting of BDNF, MIP-1δ

, and TIMP-1.

6. The method of claim 1 wherein said AD diagnosis marker is selected from the group consisting of BDNF, PDGF-BB, leptin and RANTES.

7. The method of claim 1, comprising comparing the measuring level of at least two AD diagnosis biomarkers to a reference level for the biomarkers.

8. The method of claim 7, wherein one of said at least two AD diagnosis biomarkers is leptin.

9. The method of claim 7, wherein one of said at least two AD diagnosis biomarkers is BDNF.

10. The method of claim 7 wherein the AD diagnosis biomarkers are selected from the group consisting of BDNF, PDGF-BB, leptin and RANTES.

11. The method of claim 1, comprising comparing the measured level of at least three AD diagnosis biomarkers to a reference level for the biomarkers.

12. The method of claim 1, comprising comparing the measured level of at least four AD diagnosis biomarkers to a reference level for the biomarkers.

13. The method of claim 12, comprising comparing the measured level of at least BDNF, PDGF-BB, leptin and RANTES to a reference level for the biomarkers.

14. The method of claim 1, wherein comparing the measured value to a reference value for each AD diagnosis biomarker measured comprises calculating the fold difference between the measured value and the reference value.

15. The method of claim 14, further comprising comparing the fold difference for each AD diagnosis biomarker measured with a minimum fold difference value.

21. The method of claim 1, wherein said biological fluid sample is a peripheral biological fluid sample.

23. The method of claim 1 or 16, further comprising obtaining a measured level of said AD biomarker in said biological fluid sample.

39. A kit comprising:

at least one reagent specific for at least one AD diagnosis marker, said at least one AD diagnosis biomarker selected from the group consisting of GCSF;

IFN-g;

IGFBP-1;

BMP-6;

BMP-4;

Eotaxin-2;

IGFBP-2;

TARC;

RANTES;

ANG;

PARC;

Acrp30;

AgRP(ART);

TIMP-1;

TIMP-2;

ICAM-1;

TRAIL R3;

uPAR;

IGFBP-4;

LEPTIN(OB);

PDGF-BB;

EGF;

BDNF;

NT-3;

NAP-2;

IL-1ra;

MSP-a;

SCF;

TGF-b3;

TNF-b;

MIP-1d;

IL-3;

FGF-6;

IL-6 R;

sTNF RII;

AXL;

bFGF;

FGF-4;

CNTF;

MCP-1;

MIP-1b;

TPO;

VEGF-B;

IL-8;

FAS;

EGF-R and instructions for carrying out the method of claim 1.

40. The kit of claim 39 wherein said AD diagnosis biomarker is selected from the group consisting of basic fibroblast growth factor (bFGF), BB homodimeric platelet derived growth factor (PDGF-BB), brain derived neurotrophic factor (BDNF), epidermal growth factor (EGF), fibroblast growth factor 6 (FGF-6), interleukin-3 (IL-3), soluble interleukin-6 receptor (sIL-6R), leptin (also known as ob), macrophage inflammatory protein-1 delta (MIP-1δ

), macrophage stimulating protein alpha chain (MSP-α

), neurotrophin-3 (NT-3), neutrophil activating peptide-2 (NAP-2), RANTES, soluble tumor necrosis factor receptor-2 (sTNF RII), stem cell factor (SCF), thrombopoietin (TPO), tissue inhibitor of metalloproteases-1 (TIMP-1), tissue inhibitor of metalloproteases-2 (TIMP-2), transforming growth factor-beta 3 (TGF-#3), tumor necrosis factor beta (TNF-β

).

41. The kit of claim 39 comprising at least one reagent specific for each of at least two AD diagnosis markers.

42. The kit of claim 39 comprising at least one reagent specific for each of at least three AD diagnosis markers.

43. The kit of claim 39 comprising at least one reagent specific for each of at least four AD diagnosis markers.

44. The kit of any one of claim 41, 42 or 43 wherein the AD diagnosis markers are selected from the group consisting of BDNF, PDGF-BB, leptin and RANTES.

45. The kit of claim 44 wherein the reagent specific for the AD diagnosis biomarker is an antibody, or fragment thereof, that is specific for said AD diagnosis biomarker.

46. The kit of claim 39 further comprising at least one reagent specific for a biomarker that measures sample characteristics.

52. The method of claim 1 further comprising the step of obtaining a value for the comparison of the measured level to the reference level.

53. The method of claim 13 further comprising the step of obtaining a value for the comparison of the measured level to the reference level.

54. A computer readable format comprising the values obtained by the method of claim 52 or 53.

16. A method of aiding diagnosis of Alzheimer'"'"'s disease (“

AD”

), comprising;

comparing a measured level of at least 4 AD diagnosis biomarkers, wherein said biomarkers comprise BDNF, PDGF-BB, leptin and RANTES, in a biological fluid sample from an individual to a reference level for each AD diagnosis biomarker.

17. The method of claim 16 wherein BDNF is decreased at least about 20% as compared to a reference level of BDNF.

18. The method of claim 16 wherein leptin is decreased at least about 25% as compared to a reference level of Leptin.

19. The method of claim 16 wherein RANTES is decreased at least about 16% as compared to a reference level of RANTES.

20. The method of claim 16 wherein PDGF-BB is decreased at least about 85% as compared to a reference level of PDGF-BB in a normal individual is associated with severe AD.

22. The method of claim 16 or 21, wherein said peripheral biological fluid sample is blood, serum or plasma.

24. A method for monitoring progression of Alzheimer'"'"'s disease (AD) in an AD patient, comprising:

comparing a measured level of at least one AD diagnosis biomarker in a biological fluid sample from an individual to a reference level for the biomarker, wherein the AD diagnosis biomarker is selected from the group consisting of GCSF;

IFN-g;

IGFBP-1;

BMP-6;

BMP-4;

Eotaxin-2;

IGFBP-2;

TARC;

RANTES;

ANG;

PARC;

Acrp30;

AgRP(ART);

TIMP-1;

TIMP-2;

ICAM-1;

TRAIL R3;

uPAR;

IGFBP-4;

LEPTIN(OB);

PDGF-BB;

EGF;

BDNF;

NT-3;

NAP-2;

IL-1ra;

MSP-a;

SCF;

TGF-b3;

TNF-b;

MIP-1d;

IL-3;

FGF-6;

IL-6 R;

sTNF RII;

AXL;

bFGF;

FGF-4;

CNTF;

MCP-1;

MIP-1b;

TPO;

VEGF-B;

IL-8;

FAS;

EGF-R.

25. The method of claim 24 wherein said AD diagnosis biomarker is selected from the group consisting of basic fibroblast growth factor (bFGF);

BB homodimeric platelet derived growth factor (PDGF-BB);

brain derived neurotrophic factor (BDNF);

epidermal growth factor (EGF), fibroblast growth factor 6 (FGF-6), interleukin-3 (IL-3), soluble interleukin-6 receptor (sIL-6R), leptin (also known as ob), macrophage inflammatory protein-1 delta (MIP-1δ

), macrophage stimulating protein alpha chain (MSP-α

), neurotrophin-3 (NT-3), neutrophil activating peptide-2 (NAP-2), RANTES, soluble tumor necrosis factor receptor-2 (sTNF RII), stem cell factor (SCF), thrombopoietin (TPO), tissue inhibitor of metalloproteases-1 (TIMP-1), tissue inhibitor of metalloproteases-2 (TIMP-2), transforming growth factor-beta 3 (TGF-β

3), and tumor necrosis factor beta (TNF-β

).

26. The method of claim 24 wherein the AD diagnosis marker is selected from the group consisting of BDNF, PDGF-BB, leptin and RANTES.

27. The method of claim 24 wherein the AD diagnosis marker is leptin.

28. The method of claim 27, further comprising measuring a level for leptin in said biological fluid sample, thereby producing said measured value for leptin.

29. The method of claim 24, wherein said reference value is a value obtained from a biological fluid sample from the same AD patient at an earlier point in time.

30. The method of claim 24 wherein the biological fluid sample is a peripheral biological fluid sample.

31. A method for stratifying Alzheimer'"'"'s disease (AD) in an individual, comprising:

comparing measured values for brain derived neurotrophic factor (BDNF) and BB homodimeric platelet derived growth factor (PDGF-BB) levels in a biological fluid sample from said patient with reference values for BDNF and PDGF-BB.

32. The method of claim 31 wherein said biological fluid sample is a peripheral fluid sample, including blood, serum or plasma.

33. The method of claim 31, further comprising comparing measured values for leptin and Rantes levels with reference values for leptin and Rantes, wherein reference values for BDNF, PDGF-BB, leptin and Rantes are for samples from individuals with MMSE scores from 25 to 28, wherein an increase in leptin and PDGF-BB levels and wherein levels of BDNF and RANTES stay substantially the same indicate mild AD as indicated by an MMSE score of 20-25.

34. The method of claim 31, further comprising comparing measured values for leptin and Rantes levels with reference values for leptin and Rantes, wherein reference values for BDNF, PDGF-BB, leptin and Rantes are for samples from individuals with MMSE scores from 20-25, wherein a decrease in Rantes, BDNF, and PDGF levels and wherein levels of Leptin stays substantially the same indicate moderate AD as indicated by an MMSE score of 10-20.

35. A method of identifying a candidate agent for treatment of Alzheimer'"'"'s Disease, comprising:

assaying a prospective candidate agent for activity in modulating an AD biomarker, said AD biomarker selected from the group consisting of GCSF;

IFN-g;

IGFBP-1;

BMP-6;

BMP-4;

Eotaxin-2;

IGFBP-2;

TARC;

RANTES;

ANG;

PARC;

Acrp30;

AgRP(ART);

TIMP-1;

TIMP-2;

ICAM-1;

TRAIL R3;

uPAR;

IGFBP-4;

LEPTIN(OB);

PDGF-BB;

EGF;

BDNF;

NT-3;

NAP-2;

IL-1ra;

MSP-a;

SCF;

TGF-b3;

TNF-b;

MIP-1d;

IL-3;

FGF-6;

IL-6 R;

sTNF RII;

AXL;

bFGF;

FGF-4;

CNTF;

MCP-1;

MIP-1b;

TPO;

VEGF-B;

IL-8;

FAS;

EGF-R.

36. The method of claim 35 wherein the AD biomarker is selected from the group consisting of basic fibroblast growth factor (bFGF), BB homodimeric platelet derived growth factor (PDGF-BB), brain derived neurotrophic factor (BDNF), epidermal growth factor (EGF), fibroblast growth factor 6 (FGF-6), interleukin-3 (IL-3), soluble interleukin-6 receptor (sIL-6R), leptin (also known as ob), macrophage inflammatory protein-1 delta (MIP-1δ

), macrophage stimulating protein alpha chain (MSP-α

), neurotrophin-3 (NT-3), neutrophil activating peptide-2 (NAP-2), RANTES, soluble tumor necrosis factor receptor-2 (sTNF RII), stem cell factor (SCF), thrombopoietin (TPO), tissue inhibitor of metalloproteases-1 (TIMP-1), tissue inhibitor of metalloproteases-2 (TIMP-2), transforming growth factor-beta 3 (TGF-β

3), tumor necrosis factor beta (TNF-β

).

37. The method of claim 35 comprising assaying a prospective candidate agent for activity in modulating a set of AD biomarkers, wherein said set comprises BDNF, PDGF-BB, leptin and RANTES.

38. The method of claim 35 wherein said assaying is performed in vivo.

47. A surface comprising attached thereto, at least one reagent specific for each AD diagnosis biomarker in a set of AD diagnosis biomarkers, wherein said set of AD diagnosis biomarkers comprises BDNF. PDGF-BB, leptin and RANTES.

49. The surface of claim 47 or 48 wherein said reagent specific for said AD diagnosis biomarker is an antibody, or fragment thereof, that is specific for said AD diagnosis biomarker.

48. A surface comprising attached thereto,

a. at least one reagent specific for each AD diagnosis biomarker in a set of AD diagnosis biomarkers, wherein said set of AD diagnosis biomarkers consists of BDNF, PDGF-BB, leptin and RANTES;

and

b. at least one reagent specific for a biomarker that measures sample characteristics.

50. A combination comprising the surface of claim 48 or 49 and a peripheral biological fluid sample from an individual.

51. The combination of claim 50 wherein said individual is at least 60, 65, 70, 75, 80, or 85.

55. A set of reference values for AD diagnosis biomarkers comprising BDNF, PDGF-BB, Leptin and RANTES.

56. A set of reagents specific for AD diagnosis biomarkers, wherein said biomarkers comprise BDNF, PDGF-BB, Leptin and RANTES.