Diagnosis of diseases associated with tumor supressor genes and oncogenes

• US 20040048254A1
• Filed: 01/21/2003
• Published: 03/11/2004
• Est. Priority Date: 03/15/2000
• Status: Abandoned Application

• Current Assignee: Epigenomics AG
• Original Assignee: Epigenomics AG
• Inventors: Olek, Alexander, Berlin, Kurt
• Application Number:
  US10/221,714
• Publication Number:
  US 20040048254A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C07K 14/4703 Inhibitors; Suppressors
• CPC Class Codes: C07K 14/82 Translation products from oncogenes
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/154 Methylation markers

Abstract

The present invention relates to the chemically modified genomic sequences of genes associated with tumor suppressor genes and oncogenes, to oligonucleotides and/or PNA-oligomers for detecting the cytosine methylation state of tumor suppressor genes and oncogenes which are directed against the sequence, as well as to a method for ascertaining genetic and/or epigenetic parameters of tumor suppressor genes and oncogenes.

Claims

1. A nucleic acid comprising a sequence at least 18 bases in length of a segment of the chemically pretreated DNA of genes associated with tumor suppressor genes and oncogenes according to one of the sequences taken from the group of Seq. ID No. 1 to Seq. ID No. 536 and sequences complementary thereto.

10. A set of oligomer probes for detecting the cytosine methylation state and/or single nucleotide polymorphisms (SNPs) in chemically pretreated genomic DNA according to claim 1 and/or a chemically pretreated DNA of a gene according to claim 2.

30. The use of a nucleic acid according to claim 1, of an oligonucleotide or PNA-oligomer according to one of the claims 3 through 5, of a kit according to claim 29, of an array according to one of the claims 12 through 15, of a set of oligonucleotides according to one of claims 6 through 9 for the diagnosis of solid tumors and cancers

31. The use of a nucleic acid according to claim 1, of an oligonucleotide or PNA-oligomer according to one of the claims 3 through 5, of a kit according to claim 29, of an array according to one of the claims 12 through 15, of a set of oligonucleotides according to one of claims 6 through 9 for the therapy of solid tumors and cancers

2. A nucleic acid comprising a sequence at least 18 bases in length of a segment of the chemically pretreated DNA of genes associated with tumor suppressor genes and oncogenes according to one of the sequences according to one of the genes BRCA2 (U43746), E2F1 (M96577), ELE1 (X71413), MN/CA9 (Z54349), PVT1 (M26714), SAC2 (AK001725), TEM8 (AK025429), TM4SF1 (X01394), TNFSF11 (AF053712), AXL (NM_—

021913&

NM_—

001699), CCND3 (NM_—

001760), CSF1R (NM_—

005211), MGMT (NM_—

002412), NOV (NM_—

002514), SFRS8 (NM_—

004592), TNFRSF6 (NM_—

000043), TPD52 (NM_—

005079), AKT1 (NM_—

005163), BCL2 (NM_—

000633&

NM_—

000657), CBL (NM_—

005188), CBLC (NM_—

012116), CRK (NM_—

005206&

NM_—

016823), DCC (NM_—

005215), EPHA1 (NM_—

005232), EPHA3 (NM_—

005233), ETS1 (NM_—

005238), ETV5 (NM_—

004454), ETV6 (NM_—

001987), FGF3 (NM_—

005247), FGF4 (NM_—

002007), FHIT (NM_—

002012), GLTSCR1 (NM_—

015711), GPS1 (NM_—

004127), GROS1(NM_—

022356), HIC1 (NM_—

006497), IGFBP7 (NM_—

001553), KISS1 (NM_—

002256), KRAS2 (NM_—

004985), LATS1 (NM_—

004690), LOC51213 (NM_—

016383), MUC1 (NM_—

002456), MUC2 (NM_—

002457), N33 (NM_—

006765), PTTG1IP (NM_—

004339), SE20-4 (NM_—

022117), SE70-2 (NM_—

022118), SFN (NM_—

006142), ST7 (NM_—

013437), SUPT3H (NM_—

003599), SUPT6H (NM_—

003170), TEM1 (NM_—

020404), TERT (NM_—

003219), THRB NM_—

000461), TIMP2 (NM_—

003255), TMEFF1 (NM_—

003692), TNFAIP6 (NM_—

007115), TNFRSF10A (NM_—

003844), TNFRSF10B (NM_—

003842), TNFRSF10C (NM_—

003841), TNFRSF11A (NM_—

003840), TNFRSF1A (NM_—

001065), TNFSF12 (NM_—

003809), TNFSF13 (NM_—

003808), TNFSF15 (NM_—

005118), TNFSF18 (NM_—

005092), TP63 (NM_—

003722), TSSC1 (NM_—

003310), VDR (NM_—

000376), YES1 (NM_—

005433), FOXG1A (NM_—

004471), GRF2 (NM_—

005312), HSPC070 (NM_—

014160), RAB3A (NM_—

002866), RAB5A (NM_—

004162), APC (NM_—

000038), BMI1 (NM_—

005180), CHES1 (NM_—

005197), SMT3H1 (NM_—

006936), TIAM1 (NM_—

003253), VAV1 (NM_—

005428), MCF2 (NM_—

005369), MSH2 (NM_—

000251), ERBB4 (NM_—

005235), FOXG1B (NM_—

005249), TACSTD1 (NM_—

002354), TRA1 (NM_—

003299), FOXG1B (NM_—

005249), TACSTD1 (NM_—

002354), FLI1 (NM_—

002017) and sequences complementary thereto.

7. A set of oligomers as recited in claim 6, comprising oligomers for detecting the methylation state of all CpG dinucleotides from one of the sequences of Seq. ID 1 through Seq. ID 536 or to a chemically pretreated DNA of a gene according to claim 2, and sequences complementary thereto.

8. A set of at least two oligonucleotides as recited in claim 3 which can be used as primer oligonucleotides for the amplification of DNA sequences of one of Seq. ID 1 through Seq. ID 536 and sequences complementary thereto and/or to a chemically pretreated DNA of a gene according to claim 2, and sequences complementary thereto, or segments thereof.

9. A set of oligonucleotides as recited in claim 8, characterized in that at least one oligonucleotide is bound to a solid phase.

11. A method for manufacturing an arrangement of different oligomers (array) fixed to a carrier material for analyzing diseases associated with the methylation state of the CpG dinucleotides of one of the Seq. ID 1 through Seq. ID 536 and sequences complementary thereto and/or a chemically pretreated DNA of a gene according to claim 2,

wherein at least one oligomer according to one of the claims 3 through 5 is coupled to a solid phase.

12. An arrangement of different oligomers (array), obtainable according to claim 11.

13. An array of different oligonucleotide- and/or PNA-oligomer sequences as recited in claim 12, characterized in that these are arranged on a plane solid phase in the form of a rectangular or hexagonal lattice.

14. The array as recited in one of the claims 12 or 13, characterized in that the solid phase surface is composed of silicon, glass, polystyrene, aluminum, steel, iron, copper, nickel, silver, or gold.

16. A method for ascertaining genetic and/or epigenetic parameters for the diagnosis and/or therapy of existing diseases or the predisposition to specific diseases by analyzing cytosine methylations, characterized in that the following steps are carried out:

a) in a genomic DNA sample, cytosine bases which are unmethylated at the 5-position are converted, by chemical treatment, to uracil or another base which is dissimilar to cytosine in terms of hybridization behavior;

b) fragments of the chemically pretreated genomic DNA are amplified using sets of primer oligonucleotides according to claim 8 or 9 and a polymerase, the amplificates carrying a detectable label;

c) Amplificates are hybridized to a set of oligonucleotides and/or PNA probes according to the claims 6 or 7, or else to an array according to one of the claims 12 through 15;

d) the hybridized amplificates are subsequently detected.

17. The method as recited in claim 16, characterized in that the chemical treatment is carried out by means of a solution of a bisulfite, hydrogen sulfite or disulfite.

18. The method as recited in one of the claims 16 or 17, characterized in that more than ten different fragments having a length of 100-2000 base pairs are amplified.

19. The method as recited in one of the claims 16 through 18, characterized in that the amplification of several DNA segments is carried out in one reaction vessel.

20. The method as recited in one of the claims 16 through 19, characterized in that the polymerase is a heat-resistant DNA polymerase.

21. The method as recited in claim 20, characterized in that the amplification is carried out by means of the polymerase chain reaction (PCR).

22. The method as recited in one of the claims 16 through 21, characterized in that the labels of the amplificates are fluorescence labels.

23. The method as recited in one of the claims 16 through 21, characterized in that the labels of the amplificates are radionuclides.

24. The method as recited in one of the claims 16 through 21, characterized in that the labels of the amplificates are detachable molecule fragments having a typical mass which are detected in a mass spectrometer.

25. The method as recited in one of the claims 16 through 21, characterized in that the amplificates or fragments of the amplificates are detected in the mass spectrometer.

26. The method as recited in any of the claims 24 or 25, characterized in that the produced fragments have a single positive or negative net charge for better detectability in the mass spectrometer

27. The method as recited in one of the claims 24 through 26, characterized in that detection is carried out and visualized by means of matrix assisted laser desorption/ionization mass spectrometry (MALDI) or using electron spray mass spectrometry (ESI).

28. The method as recited in one of the claims 16 through 27, characterized in that the genomic DNA is obtained from cells or cellular components which contain DNA, sources of DNA comprising, for example, cell lines, biopsies, blood, sputum, stool, urine, cerebral-spinal fluid, tissue embedded in paraffin such as tissue from eyes, intestine, kidney, brain, heart, prostate, lung, breast or liver, histologic object slides, and all possible combinations thereof.

3. An oligomer, in particular an oligonucleotide or peptide nucleic acid (PNA)-oligomer, said oligomer comprising in each case at least one base sequence having a length of at least 9 nucleotides which hybridizes to or is identical to a chemically pretreated DNA of genes associated with the cell cycle according to one of the Seq. ID No. 1 through Seq. ID No. 536 and sequences complementary thereto.

4. The oligomer as recited in claim 3;

wherein the base sequence comprises at least one CpG dinucleotide.

5. The oligomer as recited in claim 4;

characterized in that the cytosine of the CpG dinucleotide is located approximately in the middle third of the oligomer.

6. A set of oligomers, comprising at least two oligomers according to one of claims 3 to 5.

29. A kit comprising a bisulfite (=disulfite, hydrogen sulfite) reagent as well as oligonucleotides and/or PNA-oligomers according to one of the claims 3 through 5.

32. A kit, comprising a bisulfite (=disulfite, hydrogen sulfite) reagent as well as oligonucleotides and/or PNA-oligomers according to one of claims 3 through 5.

15. A DNA- and/or PNA-array for analyzing diseases associated with the methylation state of genes, comprising at least one nucleic acid according to one of the preceeding claims.