Nucleic acid array

• US 20050037344A1
• Filed: 10/23/2002
• Published: 02/17/2005
• Est. Priority Date: 11/09/2001
• Status: Abandoned Application

• Current Assignee: Oligene GmbH
• Original Assignee: Pathoarray GmbH
• Inventors: Haupl, Thomas, Stuhlmuller, Bruno
• Application Number:
  US10/278,698
• Publication Number:
  US 20050037344A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/158 Expression markers

Abstract

It is proposed to use selectioned monocyte macrophage genes to provide tools for diagnostic, prognostic and therapy-monitoring analysis and for performing screenings for pharmacologically active substances and substance classes of chronic inflammatory diseases, chronic inflammatory diseases induced by bacteria, arteriosclerosis, tumors, organ and tissue transplantations, and sepsis when examining blood, tissue, purified or cultivated cells.

Claims

1. Tools for diagnostic, prognostic and therapy-monitoring analysis as well as for performing screenings for pharmacologically active substances and substance classes of rheumatoid arthritis, chronic inflammatory diseases, bacteria-induced chronic inflammatory diseases, arteriosclerosis, tumors, organ and tissue transplantations, and sepsis,

characterized in that

sequences of a selection of the selective monocyte-macrophage genes listed in Table 1 and/or Table 2 or sequences of all genes listed in Table 1 and/or Table 2 are bonded to the surface of said tool or that RNA complementary to the genes listed is bonded to the surface of said tool.

2. The tools according to claim 1 wherein said genes, partial gene sequences and oligomer sequences are selectioned/subtracted genes.

3. The tools according to claims 1 or 2, characterized in that, alternatively, allels, derivatives and/or splicing variants of the genes, partial gene sequences or oligomer sequences can be present on the tool surface.

4. The tools according to at least one of claims 1 through 3, characterized in that said tools include gene sequences having at least one partial sequence identity in the protein-coding sections of mRNA.

5. The tools according to claim 4, characterized in that said tools include gene sequences having at least 80% of sequence identity in the protein-coding sections of the corresponding nucleic acid.

6. The tools according to claims 1 through 5,

characterized in that they are based on a high-throughput method of DNA array hybridization,

a high-throughput method using fluorescence cytometry (cytometric bead array)

a high-throughput method of RNA array hybridization, or

a high-throughput method using PCR for (semi-) quantification.

7. The tools according to claims 1 through 6, characterized in that the genes have a covalent bond to the surface.

8. The tools according to claims 1 through 7, characterized in that the surface consists of glass or a synthetic material that is chemically activated or modified.

9. The tools according to claim 8, characterized in that their surface is reactively coated with reactive groups that bind amino linkers, with metal compounds, or alloys.

10. The tools according to claims 8 or 9 wherein the substrate material or surface consists of a nylon membrane.

11. The tools according to any one of claims 1 through 10, characterized in that the cDNA was produced by reverse transcription from total RNA or messenger RNA of human cells of the monocyte/macrophage system.

12. The tools according to any one of claims 1 through 10, characterized in that the genes were applied using cDNA spotting methods, immobilization methods and synthesis methods of oligomers or in the form of complementary RNA.

13. The tools according to any one of claims 1 through 12, characterized in that the detection is performed using cDNA, its sequence portions, or oligo probes.

14. The tools according to claim 10, characterized in that the sequences contain deviations.

15. The tools according to claim 11, characterized in that the deviation of cDNA and oligo probes for detection is up to 20%.

16. The tools according to any one of claims 1 through 15, characterized in that the probes for detection are labeled with a fluorochrome, enzyme, protein, or are radio labeled and permit amplification.

17. The tools according to claims 1 through 16, characterized in that coupled biotin, digoxigenin, (noble) metal chelate and protein (molecules) are used for amplification.

18. The tools according to claim 17, characterized in that streptavidin, (noble) metal chelate or antibodies are used for amplification.

19. The tools according to claim 18, characterized in that detection is performed by means of a fluorochrome, radioactivity, or enzymes.

20. The tools according to any one of claims 1 through 19, wherein the tools are formed by a DNA array.

21. The tools according to any one of claims 1 through 19 wherein the tools are formed by a cytofluorescent DNA array (beads).

22. The tools according to any one of claims 1 through 19, wherein the tools are formed by an RNA array that mirrors a DNA array.

23. The tools according to claims 1 through 22, characterized in that the selective genes, their partial sequences or oligomers are used for detecting solid phase bound total RNA or messenger RNA.

24. The tools according to claims 1 through 23, characterized in that the probes are produced by reverse transcription from messenger RNA of human cells of the monocyte/macrophage system.

25. The tools according to any one of claims 1 through 24, characterized in that RNA from up to 500 tissue and/or blood samples is applied to the array.

26. The tool according to any one of claims 1 through 25, characterized in that the probe is labeled with fluorochromes, biotin, digoxigenin, peroxidase, alkaline phosphatase and radioactivity.

27. The tool according to any one of claims 1 through 26, characterized in that detection of the sequences listed is to be carried out using reverse transcription PCR (RT-PCR).

28. The tools according to any one of claims 1 through 27, characterized in that the genes or gene sequences are equipped with a labeling or reporter function so that these can be used for other detection methods.

29. Use of the tools according to any one of claims 1 through 27, characterized in that said tools are used for measuring monocyte/macrophage activation or the inflammatory activity in the blood or in cell tissue.