Gene expression analysis of pluri-differentiated mesenchymal progenitor cells and methods for diagnosing a leukemic disease state

• US 7,049,072 B2
• Filed: 10/03/2002
• Issued: 05/23/2006
• Est. Priority Date: 06/05/2000
• Status: Expired due to Term

• Current Assignee: University of South Florida (State University System of Florida)
• Original Assignee: University of South Florida (State University System of Florida)
• Inventors: Seshi, Beerelli
• Primary Examiner(s): Myers, Carla J.
• Application Number:
  US10/263,419
• Publication Number:
  US 20030203483A1
• Time in Patent Office: 1,328 Days
• Field of Search: 435/6, 435/91.2, 435/7.2, 435/372, 435/372.1
• US Class Current: 435/6.13
• CPC Class Codes: A61K 2035/122 for inducing tolerance or supression of immune responses
• CPC Class Codes: A61K 2035/124 the cells being hematopoietic, bone marrow derived or blood cells
• CPC Class Codes: A61K 2239/31 characterized by the route of administration
• CPC Class Codes: A61K 2239/38 characterised by the dose, timing or administration schedule
• CPC Class Codes: A61K 2239/49 Breast
• CPC Class Codes: A61K 39/461 characterised by the cell type used
• CPC Class Codes: A61K 39/4621 immunosuppressive or immunotolerising
• CPC Class Codes: A61K 39/46434 Antigens related to induction of tolerance to non-self
• CPC Class Codes: A61K 39/4644 Cancer antigens
• CPC Class Codes: C12N 2501/39 Steroid hormones
• CPC Class Codes: C12N 5/0635 B lymphocytes
• CPC Class Codes: C12N 5/0663 Bone marrow mesenchymal stem cells (BM-MSC)
• CPC Class Codes: C12Q 1/6881 for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: G01N 33/5073 Stem cells
• CPC Class Codes: G01N 33/5091 for testing the pathological state of an organism
• CPC Class Codes: G01N 33/56972 White blood cells
• CPC Class Codes: G01N 33/57426 leukemia

Abstract

Pluri-differentiated human mesenchymal progenitor cells (MPCs) are isolated. A method isolates and purifies human mesenchymal progenitor cells from Dexter-type cultures for characterization of and uses, particularly therapeutic uses for such cells. Specifically, isolated MPCs can be used for diagnostic purposes, to enhance the engraftment of hematopoietic progenitor cells, enhance bone marrow transplantation, or aid in the treatment or prevention of graft versus host disease.

Claims

1. A method for diagnosing a leukemic disease state in a patient, the method comprising:

(a) providing a gene expression profile of a patient'"'"'s bone marrow derived isolated pluri-differentiated mesenchymal progenitor cell of unknown state, wherein the isolated pluri-differentiated mesenchymal progenitor cell simultaneously expresses a plurality of genes at the protein level that are markers for multiple cell lineages, wherein the multiple cell lineages comprise at least four different mesenchymal cell lineages, and wherein each of the markers is specific for a single cell lineage; and

(b) comparing the patient'"'"'s gene expression profile to a reference gene expression profile obtained from a normal bone marrow derived pluri-differentiated mesenchymal progenitor cell, wherein the reference gene expression profile comprises an expression value of a target gene selected from the group consisting of human mRNA for cartilage specific proteoglycan, Homo sapiens tyrosine phosphatase, X-linked mental retardation candidate gene, human interleukin-10 receptor mRNA, H-interferon inducible peptide (6-16), interferon-inducible 56 kD protein, human insulin-like growth factor binding protein 5 (IGFBP5), winged helix transcription factor, interferon gamma, human mRNA for zinc finger protein (clone

     431), apolipoprotein D precursor, p53 tumor antigen, Homo sapiens Kueppel family zinc finger protein, major group rhinovirus receptor precursor, ICE like protease, caspase-10/b, human transcription factor SIM2, CMP-N-acetylneuraminic acid hydroxylase, Homo sapiens cDNA clone DKFZp586G0421 (symptom;

hute

     1), human mRNA for histone H1x, putative monocarboxylate transporter Homo sapiens gene for LD78 alpha precursor, wg82b12.x1 Soares Homo sapiens cDNA clone, human atrial natriuretic peptide clearance receptor (ANP C-receptor), human 71 kDa 2′

5′

oligoadenylate synthetase (p69 2-5A synthetase), Homo sapiens hMmTRA1b, human GOS2 protein gene, preproenkephalin, human guanylate binding protein isoform I (GBP-2), human gene for hepatitis C associated microtubular aggregate protein p44, GS3686, human monoamine oxidase B (MAOB), insulin-like growth factor II precursor, cDNA DKFZp434A202, beta-tropomyosin, Homo sapiens clone 24659, human DNA helicase Q1, OSF, ym22b12.r1, Soares infant brain 1NIB Homo sapiens cDNA clone, human mRNA for pre-mRNA splicing factor SRp20, human golgi alpha-mannosidasell, OSF-2os, Homo sapiens proline synthetase, hk02952 cDNA clone for KIAA0683, wi24g10.x1 Homo sapiens, Lysosomal enzyme deficient in Sanfilippo B syndrome, CTP synthetase (AA 1-591), human 5′

-terminal region of UMK, Homo sapiens chemokine exodus-1, human GPI-H, Homo sapiens RAMP1, transforming growth factor-beta-2 precursor, and Homo sapiens KIAA0763 protein, wherein differential expression of the target gene is indicative of a leukemic disease state, and wherein the leukemic disease state is selected from the group consisting of acute myeloid leukemia (AML), chronic myeloid leukemia (CML), and multiple myeloma (MM).

2. The method of claim 1, wherein the reference gene expression profile is contained within a database.

3. The method of claim 1, wherein said comparing is carried out using a computer algorithm.

4. The method of claim 1, wherein said method further comprises isolating the bone marrow derived isolated pluri-differentiated mesenchymal progenitor cell of unknown state from the patient.

5. The method of claim 1, wherein said method further comprises preparing the patient'"'"'s gene expression profile.

6. The method of claim 1, wherein said method further comprises:

(c) providing a gene expression profile of a bone marrow derived isolated pluri-differentiated mesenchymal progenitor cell from the patient after the patient has undergone a treatment regimen for a leukemic disease state; and

(d) comparing the post-treatment patient gene expression profile to the reference gene expression profile, to monitor the patient'"'"'s response to the treatment regimen.

7. The method of claim 1, wherein said method further comprises:

(c) providing a leukemic disease state diagnosis to the patient.

8. The method of claim 1, wherein the bone marrow derived isolated pluri-differentiated mesenchymal progenitor cell of unknown state comprises a single cell.

9. The method of claim 1, wherein the patient'"'"'s bone marrow derived isolated pluri-differentiated mesenchymal progenitor cell of unknown state comprises a plurality of cells.

10. The method of claim 1, wherein the patient'"'"'s isolated pluri-differentiated mesenchymal progenitor cells have been obtained by providing a cell culture preparation by the Dexter method, treating the cells of the cell culture preparation to obtain a cell suspension, removing macrophages from the cell suspension, fractionating the remaining cells, and collecting the fraction of cells containing the normal state pluri-differentiated mesenchymal progenitor cells.

11. The method of claim 1, wherein the at least four different mesenchymal cell lineages comprise adipocyte, osteoblast, fibroblast, and muscle cell.

12. The method of claim 1, wherein the markers specific for a single cell lineage are selected from the group consisting of Nile Red, Oil Red O, adipsin, alkaline phosphatase, cadherin-11, chondroitin sulfate, collagen type I, decorin, fibronectin, prolyl-4-hydroxylase, actin, caldesmon, and transgelin.

13. The method of claim 1, wherein the target gene is human mRNA for cartilage specific proteoglycan, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

14. The method of claim 1, wherein the target gene is Homo sapiens tyrosine phosphatase, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

15. The method of claim 1, wherein the target gene is X-linked mental retardation candidate gene, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

16. The method of claim 1, wherein the target gene is human interleukin-10 receptor mRNA, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

17. The method of claim 1, wherein the target gene is H-interferon inducible peptide (6-16), and wherein down-regulation of the target gene is indicative of a leukemic disease state.

18. The method of claim 1, wherein the target gene is interferon-inducible 56 kD protein, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

19. The method of claim 1, wherein the target gene is insulin-like growth factor binding protein 5, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

20. The method of claim 1, wherein the target gene is winged helix transcription factor, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

21. The method of claim 1, wherein the target gene is interferon-gamma, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

22. The method of claim 1, wherein the target gene is human mRNA for zinc finger protein (clone 431), and wherein up-regulation of the target gene is indicative of a leukemic disease state.

23. The method of claim 1, wherein the target gene is apolipoprotein D precursor, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

24. The method of claim 1, wherein the target gene is p53 tumor antigen, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

25. The method of claim 1, wherein the target gene is Homo sapiens Kueppel family zinc finger protein, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

26. The method of claim 1, wherein the target gene is major group rhinovirus receptor precursor, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

27. The method of claim 1, wherein the target gene is ICE like protease, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

28. The method of claim 1, wherein the target gene is caspase-10/b and wherein up-regulation of the target gene is indicative of a leukemic disease state.

29. The method of claim 1, wherein the target gene is human transcription factor SIM2, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

30. The method of claim 1, wherein the reference gene expression profile comprises expression values of human mRNA for cartilage specific proteoglycan, Homo sapiens tyrosine phosphatase, X-linked mental retardation candidate gene, human interleukin-10 receptor mRNA, H-interferon inducible peptide (6-16), interferon-inducible 56 kD protein, insulin-like growth factor binding protein 5, winged helix transcription factor, interferon gamma, human mRNA zinc finger protein (clone 431), apolipoprotein D precursor, p53 tumor antigen, Homo sapiens Kueppel family zinc finger protein, major group rhinovirus receptor precursor, ICE like protease, caspase-10/b, and human transcription factor SIM2.

31. The method of claim 1, wherein the target gene is CMP-N-acetylneuraminic acid hydroxylase, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

32. The method of claim 1, wherein the target gene is Homo sapiens cDNA clone DKFZp586G0421 (symptom:

hute

     1), and wherein down-regulation of the target gene is indicative of a leukemic disease state.

33. The method of claim 1, wherein the target gene is Human mRNA for histone H1x, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

34. The method of claim 1, wherein the target gene is putative monocarboxylate transporter Homo sapiens gene for LD78 alpha precursor, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

35. The method of claim 1, wherein the target gene is wg82b12.x1 Soares Homo sapiens cDNA clone, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

36. The method of claim 1, wherein the target gene is human atrial natriuretic peptide clearance receptor (ANP C-receptor), and wherein down-regulation of the target gene is indicative of a leukemic disease state.

37. The method of claim 1, wherein the target gene is human 71 kDa 2′

5′

oligoadenylate synthetase (p69 2-5A synthetase), and wherein down-regulation of the target gene is indicative of a leukemic disease state.

38. The method of claim 1, wherein the target gene is Homo sapiens hMmTRA1b, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

39. The method of claim 1, wherein the target gene is human GOS2 protein gene, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

40. The method of claim 1, wherein the target gene is preproenkephalin, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

41. The method of claim 1, wherein the target gene is human guanylate binding protein isoform I (GBP-2), and wherein down-regulation of the target gene is indicative of a leukemic disease state.

42. The method of claim 1, wherein the target gene is human gene for hepatitis C associated microtubular aggregate protein p44, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

43. The method of claim 1, wherein the target gene is GS3686, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

44. The method of claim 1, wherein the target gene is human monoamine oxidase B (MAOB), and wherein down-regulation of the target gene is indicative of a leukemic disease state.

45. The method of claim 1, wherein the target gene is insulin-like growth factor II precursor, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

46. The method of claim 1, wherein the target gene is cDNA DKFZp434A202, and wherein down-regulation of the target gene is indicative of a leukemic disease state.

47. The method of claim 1, wherein the target gene is beta-tropomyosin, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

48. The method of claim 1, wherein the target gene is Homo sapiens clone 24659, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

49. The method of claim 1, wherein the target gene is human DNA helicase Q1, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

50. The method of claim 1, wherein the target gene is OSF, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

51. The method of claim 1, wherein the target gene is ym22b12.r1 Soares infant brain 1NIB homo sapiens cDNA clone, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

52. The method of claim 1, wherein the target gene is human mRNA for pre-mRNA splicing factor SRp20, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

53. The method of claim 1, wherein the target gene is human golgi alpha-mannosidasell, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

54. The method of claim 1, wherein the target gene is OSF-2os, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

55. The method of claim 1, wherein the target gene is Homo sapiens proline synthetase, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

56. The method of claim 1, wherein the target gene is hk02952 cDNA clone for KIAA0683, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

57. The method of claim 1, wherein the target gene is wi24g10.x1 Homo sapiens, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

58. The method of claim 1, wherein the target gene is Lysosomal enzyme deficient in Sanfilippo B syndrome, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

59. The method of claim 1, wherein the target gene is CTP synthetase (AA 1-591), and wherein up-regulation of the target gene is indicative of a leukemic disease state.

60. The method of claim 1, wherein the target gene is human 5′

-terminal region of UMK, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

61. The method of claim 1, wherein the target gene is Homo sapiens chemokine exodus-1, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

62. The method of claim 1, wherein the target gene is human GPI-H, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

63. The method of claim 1, wherein the target gene is Homo sapiens RAMP1, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

64. The method of claim 1, wherein the target gene is transforming growth factor-beta-2 precursor, and wherein up-regulation of the target gene is indicative of a leukemic disease state.

65. The method of claim 1, wherein the target gene is Homo sapiens KIAA0763 protein, and wherein up-regulation of the target gene is indicative of a leukemic disease state.