WO1998054318B1 - TUMOUR SUPPRESSOR GENE DBCCR1 AT 9q32-33 - Google Patents
TUMOUR SUPPRESSOR GENE DBCCR1 AT 9q32-33Info
- Publication number
- WO1998054318B1 WO1998054318B1 PCT/GB1998/001515 GB9801515W WO9854318B1 WO 1998054318 B1 WO1998054318 B1 WO 1998054318B1 GB 9801515 W GB9801515 W GB 9801515W WO 9854318 B1 WO9854318 B1 WO 9854318B1
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- nucleic acid
- dbccrl
- polypeptide
- cancer
- gene
- Prior art date
Links
- 230000001629 suppression Effects 0.000 title claims abstract 3
- 102100009626 BRINP1 Human genes 0.000 title abstract 4
- 101710040841 BRINP1 Proteins 0.000 title abstract 4
- 201000011510 cancer Diseases 0.000 claims abstract 13
- 206010005003 Bladder cancer Diseases 0.000 claims abstract 5
- 201000005112 urinary bladder cancer Diseases 0.000 claims abstract 5
- 150000007523 nucleic acids Chemical class 0.000 claims 43
- 108020004707 nucleic acids Proteins 0.000 claims 36
- 229920001184 polypeptide Polymers 0.000 claims 28
- 229920001850 Nucleic acid sequence Polymers 0.000 claims 13
- 230000011987 methylation Effects 0.000 claims 11
- 238000007069 methylation reaction Methods 0.000 claims 11
- 239000000523 sample Substances 0.000 claims 10
- 125000003275 alpha amino acid group Chemical group 0.000 claims 8
- 239000000126 substance Substances 0.000 claims 8
- 210000004027 cells Anatomy 0.000 claims 6
- 206010041823 Squamous cell carcinoma Diseases 0.000 claims 5
- 230000002779 inactivation Effects 0.000 claims 5
- 239000003814 drug Substances 0.000 claims 4
- 230000002401 inhibitory effect Effects 0.000 claims 4
- 238000002360 preparation method Methods 0.000 claims 4
- 108091007521 restriction endonucleases Proteins 0.000 claims 4
- 206010033128 Ovarian cancer Diseases 0.000 claims 3
- 208000006265 Renal Cell Carcinoma Diseases 0.000 claims 3
- 102000004965 antibodies Human genes 0.000 claims 3
- 108090001123 antibodies Proteins 0.000 claims 3
- 239000003112 inhibitor Substances 0.000 claims 3
- 230000035772 mutation Effects 0.000 claims 3
- 201000000849 skin cancer Diseases 0.000 claims 3
- ISAKRJDGNUQOIC-UHFFFAOYSA-N Uracil Chemical compound O=C1C=CNC(=O)N1 ISAKRJDGNUQOIC-UHFFFAOYSA-N 0.000 claims 2
- 239000012472 biological sample Substances 0.000 claims 2
- LSNNMFCWUKXFEE-UHFFFAOYSA-M bisulfite Chemical compound OS([O-])=O LSNNMFCWUKXFEE-UHFFFAOYSA-M 0.000 claims 2
- 150000001875 compounds Chemical class 0.000 claims 2
- 239000007819 coupling partner Substances 0.000 claims 2
- 230000001809 detectable Effects 0.000 claims 2
- 230000029087 digestion Effects 0.000 claims 2
- 239000003937 drug carrier Substances 0.000 claims 2
- 239000000203 mixture Substances 0.000 claims 2
- 239000002773 nucleotide Substances 0.000 claims 2
- 125000003729 nucleotide group Chemical group 0.000 claims 2
- 239000008194 pharmaceutical composition Substances 0.000 claims 2
- 230000003612 virological Effects 0.000 claims 2
- 210000004369 Blood Anatomy 0.000 claims 1
- 210000000349 Chromosomes Anatomy 0.000 claims 1
- OPTASPLRGRRNAP-UHFFFAOYSA-N Cytosine Chemical class NC=1C=CNC(=O)N=1 OPTASPLRGRRNAP-UHFFFAOYSA-N 0.000 claims 1
- XAUDJQYHKZQPEU-KVQBGUIXSA-N Decitabine Chemical compound O=C1N=C(N)N=CN1[C@@H]1O[C@H](CO)[C@@H](O)C1 XAUDJQYHKZQPEU-KVQBGUIXSA-N 0.000 claims 1
- 206010030155 Oesophageal carcinoma Diseases 0.000 claims 1
- 210000002381 Plasma Anatomy 0.000 claims 1
- 210000003296 Saliva Anatomy 0.000 claims 1
- 210000002966 Serum Anatomy 0.000 claims 1
- 238000002105 Southern blotting Methods 0.000 claims 1
- 231100000765 Toxin Toxicity 0.000 claims 1
- 229940035893 Uracil Drugs 0.000 claims 1
- 210000002700 Urine Anatomy 0.000 claims 1
- 230000003213 activating Effects 0.000 claims 1
- 150000001413 amino acids Chemical class 0.000 claims 1
- 230000003321 amplification Effects 0.000 claims 1
- 238000004458 analytical method Methods 0.000 claims 1
- 239000008280 blood Substances 0.000 claims 1
- 239000000969 carrier Substances 0.000 claims 1
- 230000010261 cell growth Effects 0.000 claims 1
- 229920003013 deoxyribonucleic acid Polymers 0.000 claims 1
- 229940079593 drugs Drugs 0.000 claims 1
- 230000000694 effects Effects 0.000 claims 1
- 238000001976 enzyme digestion Methods 0.000 claims 1
- 201000004101 esophageal cancer Diseases 0.000 claims 1
- 238000004519 manufacturing process Methods 0.000 claims 1
- 238000003199 nucleic acid amplification method Methods 0.000 claims 1
- 238000003752 polymerase chain reaction Methods 0.000 claims 1
- 210000001519 tissues Anatomy 0.000 claims 1
- 239000003053 toxin Substances 0.000 claims 1
- 230000035897 transcription Effects 0.000 claims 1
- 238000011144 upstream manufacturing Methods 0.000 claims 1
- 230000001743 silencing Effects 0.000 abstract 1
- 230000001225 therapeutic Effects 0.000 abstract 1
Abstract
The application relates to the identification of a tumour suppressor locus at 9q32-33, and a gene within this region is disclosed. The gene is called 'DBCCR1' for Deleted in Bladder Cancer Chromosome Region candidate 1. The application further relates to uses of these findings, in particular in the diagnostic, prophylactic and therapeutic treatment of cancer, especially bladder cancer. In particular, some forms of cancer are linked to hypermethylation based silencing of the DBCCR1 promoter or gene.
Claims
1. An isolated nucleic acid molecule comprising the nucleotide sequence as set out in figure 6, or alleles thereof.
2. An isolated nucleic acid molecule comprising a nucleotide sequence encoding a polypeptide having the amino acid sequence as set out in figure 6.
3. The nucleic acid molecule of claim 1 or claim 2 which includes one or more of the polymorphisms selected from the group consisting of T1036C, C2044A and T2642C.
4. An isolated nucleic acid molecule encoding a polypeptide having a 80% sequence identity with the polypeptide having the amino acid sequence set out in figure 6.
5. An isolated nucleic acid molecule comprising a nucleotide sequence encoding a polypeptide which is an active portion or derivative of the polypeptide having the amino acid sequence set out in figure 6.
6. An isolated nucleic acid molecule which comprises a fragment of the nucleotide sequence as set out in figure 6, or a fragment of the 1632 bp promoter directly upstream of the transcription start site of the DBCCRl gene as defined in cosmid clone 50A8 from the chromosome 9 library LL09NC01P, which fragment is greater than 20 nucleotides in length with the proviso that the nucleic acid molecule is not an EST selected from the group consisting of IB3089, R42707, T15661, T15474,
88
AA011030, Z41452, F08986, R40799, H10959, R42933, W50233 or W65061 all available from GeneBank.
7. An isolated nucleic acid molecule comprising the nucleotide sequence of the DBCCRl promoter region as defined in Claim 6.
8. The nucleic acid molecule of claim 7 wherein the DBCCRl promoter region is operably linked to a reporter gene.
9. The nucleic acid molecule of claim 7 wherein the DBCCRl promoter region is operably linked to the nucleic acid sequence of any one of claims 1 to 5.
10. An expression vector comprising the nucleic acid molecule of any one of claims 1 to 9.
11. A host cell transformed with the vector of claim 10.
12. A method of producing DBCCRl polypeptide comprising culturing host cells transformed with an expression vector comprising the nucleic acid of any one of claims 1 to 5.
13. The method of claim 12 further comprising the step of recovering the DBCCRl polypeptide.
14. A substance which is an isolated polypeptide comprising a polypeptide having the amino acid sequence set out in figure 6.
89
15. A substance which is an isolated polypeptide having greater than 80% sequence identity with the amino acid sequence set out in figure 6.
16. A substance which is a polypeptide which is a derivative or allele of the DBCCRl polypeptide having the sequence set out in figure 6.
17. A substance which is a fragment of the DBCCRl polypeptide having greater than seven contiguous amino acids having sequence identity with the amino acid sequence set out in figure 6.
18. A substance which is an active portion of a DBCCRl polypeptide having the amino acid sequence of figure 6.
19. The substance of any one of claims 14 to 18 which is linked to a coupling partner.
20. The substance of claim 19 wherein the coupling partner is an effector molecule, a label, a drug, a toxin, a carrier or a transport molecule.
21. A nucleic acid molecule of any one of claims 1 to 9 for use in a method of medical treatment.
22. Use of a nucleic acid molecule of any one of claims 1 to 5 for the preparation of a medicament for the treatment of cancer.
23. The use of claim 22 wherein the nucleic acid is expressed in a population of cells to produce biologically active DBCCRl polypeptide.
90
24. The use of claim 22 wherein a viral vector is used to deliver the nucleic acid to the population of cells.
25. The use of claim 22 or 23 wherein the DBCCRl polypeptide has the biological activity of inhibiting cell growth.
26. The use of any one of claims 22 to 25 wherein the population of cells are tumour cells.
27. The use of any one of claims 22 to 26 wherein the cancer is a bladder cancer, squamous carcinoma, skin cancer, renal cell carcinoma, squamous cell carcinoma of the oesophagus or ovarian cancer.
28. A polypeptide of any one of claims 14 to 20 for use in a method of medical treatment.
29. Use of polypeptide of any one of claims 14 to 20 for use in the preparation of medicament for the treatment of cancer.
30. The use of claim 29 wherein the cancer is bladder cancer, squamous carcinoma, skin cancer, renal cell carcinoma, squamous cell carcinoma of the esophagus and ovarian cancer.
31. An antibody which is capable of specifically binding to a DBCCRl polypeptide of any one of claims 14 to 20.
9 1
32. Use of a polypeptide of any one of claims 14 to 20 in the preparation of an antibody which is capable of specifically binding to the polypeptide.
33. A pharmaceutical composition comprising the nucleic acid molecule of any one of claims 1 to 9 in combination with a pharmaceutically acceptable carrier.
34. A pharmaceutical composition comprising a DBCCRl polypeptide of any one of claims 14 to 20 in combination with a pharmaceutically acceptable carrier.
35. Use of a methylation inhibitor for the preparation of a medicament for increasing the expression of the DBCCRl gene having the nucleic acid sequence as set out in figure 6.
36. The use of claim 36 wherein the methylation inhibitor is methylation inhibitor 5-aza-2'-deoxycytidine.
37. A method of determining inactivation of the DBCCRl gene in a patient, the method comprising: obtaining from the patient a nucleic acid sample comprising the
DBCCRl promoter region as defined in claim 6 and/or the DBCCRl nucleic acid having the sequence set out in figure 6; and, determining the extent of methylation of the nucleic acid, wherein hypermethylation of the nucleic acid indicates inactivation of the DBCCRl gene.
92
38. The method of claim 37 wherein the method comprises the further step of correlating the inactivation of the DBCCRl gene to the presence of a tumour or a predisposition of the patient to cancer.
39. The method of claim 37 or claim 38 wherein the methylation of the nucleic acid is determined using methylation sensitive single nucleotide primer extension (Ms-SNuPE).
40. The method of claim 37 or claim 38 wherein the methylation of nucleic acid is determined by digestion with methylation sensitive restriction enzymes, followed by Southern analysis.
41. The method of claim 37 or claim 38 wherein the methylation of the nucleic acid is determined by digestion with methylation sensitive restriction enzymes followed by PCR amplification of the nucleic acid.
42. The method of claim 37 or claim 38 wherein the nucleic acid is treated with bisulphite to cause unmethylated cytosine in the nucleic acid sample to be converted to uracil and the bisulphite treated nucleic acid is amplified by PCR.
43. The method of claim 42 wherein the extent of methylation of the amplified nucleic acid is determined by restriction enzyme digestion or by sequencing of the PCR product.
44. The method of any one of claims 37 to 42 wherein the cancer is associated with loss of heterozygosity involving 9q32-33.
45. The method of claim 44 wherein the cancer is bladder cancer, squamous carcinoma, skin cancer, renal cell carcinoma, oesophageal cancer and/or ovarian cancer.
46. A method of determining the extent of inactivation of the DBCCRl gene, the method employing a biological sample from a patient and comprising:
(a) determining the level of expression of the polypeptide encoded by the DBCCRl gene and having the amino acid sequence set out in figure 6 in a sample from a patient; and/or;
(b) determining whether the 5' end of the DBCCRl nucleic acid having the nucleotide sequence set out in figure 6 or the DBCCRl promoter region as defined in claim 6 are hypermethylated in a sample from patient; and/or, (c) determining whether all or a part of at least one of the
DBCCRl alleles is deleted in a nucleic acid sample from a patient; wherein inactivation of the DBCCRl gene indicates the presence of a tumour or a predisposition of the patient to cancer.
47. The method of claim 46 wherein the determination under (c) is assessed using Southern blotting or quantitative duplex PCR.
48. The method of claim 46 or claim 47 wherein the biological sample is blood, plasma, serum, tissue samples, tumour samples, saliva or urine.
49. A method for detecting mutations in the DCCR1 gene or the polypeptide encoded by the gene as set out in figure 6, the methods including:
94
(a) comparing the sequence of nucleic acid in the sample with the DBCCRl nucleic acid sequence to determine whether the sample from the patient contains mutations; or,
(b) determining the presence in a sample from a patient of the polypeptide encoded by the DBCCRl gene and, if present, determining whether the polypeptide is full length, and/or is mutated, and/or is expressed at the normal level; or,
(c) using DNA fingerprinting to compare the restriction pattern produced when a restriction enzyme cuts a sample of nucleic acid from the patient with the restriction pattern obtained from normal DBCCRl gene or from known mutations thereof; or,
(d) using a specific binding member capable of binding to a DBCCRl nucleic acid sequence (either a normal sequence or a known mutated sequence), the specific binding member comprising nucleic acid hybridisable with the DBCCRl sequence, or substances comprising an antibody domain with specificity for a native or mutated DBCCRl nucleic acid sequence or the polypeptide encoded by it, the specific binding member being labelled so that binding of the specific binding member to its binding partner is detectable; or, (e) using PCR involving one or more primers based on normal or mutated DBCCRl gene sequence to screen for normal or mutant DBCCRl gene in a sample from a patient.
50. A method of screening for compounds capable of activating production of DBCCRl polypeptide, the method employing a nucleic acid construct comprising a functional part of the promoter as defined in claim 6, the promoter being operably linked to a reporter gene capable of producing a detectable signal, the method comprising exposing the
construct to candidate compounds and detecting the signal produced by the reporter gene.
51. Use of the nucleic acid sequence set out in figure 6 or the promoter sequence as defined in claims 6 in the design of primers for use in the polymerase chain reaction to amplify all or part of the DBCCRl nucleic acid sequence.
52. The use of claim 51 employing the primers set out in table 3.
53. A method of suppressing the occurrence of cancer and/or reducing the size or extent of existing cancer in a patient the method comprising administering to the patient a therapeutically effective amount of a nucleic acid molecule according to any one of claims 1 to 9 or an expression vector according to claim 10.
54. A method according to claim 53 wherein the cancer is bladder cancer.
55. A method according to claim 52 wherein the expression vector is a viral vector.
Priority Applications (4)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CA002288235A CA2288235A1 (en) | 1997-05-28 | 1998-05-26 | Tumour suppressor gene dbccr1 at 9q32-33 |
| EP98922966A EP0983355A1 (en) | 1997-05-28 | 1998-05-26 | TUMOUR SUPPRESSOR GENE DBCCR1 AT 9q32-33 |
| AU75425/98A AU752701B2 (en) | 1997-05-28 | 1998-05-26 | Tumour suppressor gene DBCCR1 at 9q32-33 |
| JP50036199A JP2002511749A (en) | 1997-05-28 | 1998-05-26 | Tumor suppressor gene DBCCR1 at 9q32-33 |
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| GB9710995.3 | 1997-05-28 | ||
| GBGB9710995.3A GB9710995D0 (en) | 1997-05-28 | 1997-05-28 | Tumour suppressor locus and gene at 9q32-33 |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| WO1998054318A1 WO1998054318A1 (en) | 1998-12-03 |
| WO1998054318B1 true WO1998054318B1 (en) | 1999-02-11 |
Family
ID=10813172
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| PCT/GB1998/001515 WO1998054318A1 (en) | 1997-05-28 | 1998-05-26 | TUMOUR SUPPRESSOR GENE DBCCR1 AT 9q32-33 |
Country Status (6)
| Country | Link |
|---|---|
| EP (1) | EP0983355A1 (en) |
| JP (1) | JP2002511749A (en) |
| AU (1) | AU752701B2 (en) |
| CA (1) | CA2288235A1 (en) |
| GB (1) | GB9710995D0 (en) |
| WO (1) | WO1998054318A1 (en) |
Families Citing this family (15)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US6743909B2 (en) * | 2002-06-17 | 2004-06-01 | Isis Pharmaceuticals, Inc. | Antisense modulation of PTPN12 expression |
| US5871917A (en) | 1996-05-31 | 1999-02-16 | North Shore University Hospital Research Corp. | Identification of differentially methylated and mutated nucleic acids |
| US6617434B1 (en) | 1996-05-31 | 2003-09-09 | North Shore Long Island Jewish Research Institute | Identificiaton of differentially methylated and mutated nucleic acids |
| WO2000001816A1 (en) * | 1998-07-02 | 2000-01-13 | Imperial Cancer Research Technology Limited | TUMOUR SUPPRESSOR GENE DBCCR1 AT 9q32-33 |
| US6994991B1 (en) | 1998-11-18 | 2006-02-07 | North Shore - Long Island Jewish Research Institute | Identification of differentially methylated multiple drug resistance loci |
| US6982253B2 (en) | 2002-06-05 | 2006-01-03 | Supergen, Inc. | Liquid formulation of decitabine and use of the same |
| JP2008029293A (en) * | 2006-07-31 | 2008-02-14 | Hisamitsu Pharmaceut Co Inc | Method for screening cancer remedy and cancer remedy |
| EP2198042B1 (en) | 2007-09-17 | 2016-11-02 | MDxHealth SA | Novel markers for bladder cancer detection |
| US9670552B2 (en) | 2007-11-30 | 2017-06-06 | Genomictree, Inc. | Diagnosis kit and chip for bladder cancer using bladder cancer specific methylation marker gene |
| US9783857B2 (en) | 2007-11-30 | 2017-10-10 | Genomictree, Inc. | Diagnosis kit and chip for bladder cancer using bladder cancer specific methylation marker gene |
| EP2392679B1 (en) * | 2007-11-30 | 2013-09-11 | Genomictree, Inc. | Diagnosis kit and chip for bladder cancer using bladder cancer specific methylation marker gene |
| US9797017B2 (en) | 2007-11-30 | 2017-10-24 | Genomictree, Inc. | Diagnosis kit and chip for bladder cancer using bladder cancer specific methylation marker gene |
| US9670551B2 (en) | 2007-11-30 | 2017-06-06 | Genomictree, Inc. | Diagnosis kit and chip for bladder cancer using bladder cancer specific methylation marker gene |
| US10113203B2 (en) | 2007-11-30 | 2018-10-30 | Genomictree, Inc. | Diagnosis kit and chip for bladder cancer using bladder cancer specific methylation marker gene |
| WO2018050844A1 (en) | 2016-09-16 | 2018-03-22 | Qiagen Gmbh | Method for determining nucleic acid degradation in a sample in which at least two overlapping amplicons are produced and two probes are used in the method |
Family Cites Families (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US5756668A (en) * | 1994-11-15 | 1998-05-26 | The Johns Hopkins University School Of Medicine | Hypermethylated in cancer polypeptide, HIC-1 |
-
1997
- 1997-05-28 GB GBGB9710995.3A patent/GB9710995D0/en active Pending
-
1998
- 1998-05-26 EP EP98922966A patent/EP0983355A1/en not_active Withdrawn
- 1998-05-26 WO PCT/GB1998/001515 patent/WO1998054318A1/en active IP Right Grant
- 1998-05-26 JP JP50036199A patent/JP2002511749A/en active Pending
- 1998-05-26 CA CA002288235A patent/CA2288235A1/en not_active Abandoned
- 1998-05-26 AU AU75425/98A patent/AU752701B2/en not_active Ceased
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