Method for predicting a drug transport capability by abcg2 polymorphisms

• US 20060057579A1
• Filed: 06/13/2003
• Published: 03/16/2006
• Est. Priority Date: 06/17/2002
• Status: Abandoned Application

• Current Assignee: Banyu Pharmaceutical Company Limited (Merck & Co., Inc.)
• Original Assignee: Banyu Pharmaceutical Company Limited (Merck & Co., Inc.)
• Inventors: Mizuarai, Shinji, Kotani, Hedehito
• Application Number:
  US10/517,310
• Publication Number:
  US 20060057579A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C07K 14/4748 Tumour specific antigens; Tumour rejection antigen precursors [TRAP], e.g. MAGE
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

The present invention relates to a polypeptide which excretes drugs such as cancer chemotherapeutic agents from a cell and to a gene coding therefor. More specifically, the present invention relates to a method for predicting a drug transport capability of a mammalian cell by determining a single nucleotide polymorphism(s) of ABCG2 gene and/or an amino acid polymorphism(s) of ABCG2 polypeptide and also to a polynucleotide, polypeptide, kit, and the like used for the method.

Claims

1. A method for predicting a drug transport capability of a mammalian cell, said method comprising:

collecting a sample from a mammal,

determining a polymorphism of the nucleotide sequence of ABCG2 gene or a polymorphism of the amino acid sequence of ABCG2 polypeptide.

2. The method of claim 1, wherein said ABCG2 gene comprises a DNA consisting of the nucleotide sequence of SEQ ID NO:

1, and said polymorphism of the nucleotide sequence is one or more of single nucleotide polymorphisms at positions selected from the group consisting of 34, 376 and 421 of SEQ ID NO;

1.

3. The method of claim 2, wherein said single nucleotide polymorphism is selected from the group consisting of G34A, C376T and C421A.

4. The method of claim 2, wherein said polymorphism of the nucleotide sequence is determined by any one of methods selected from the group consisting of a direct sequencing method, TaqMan method, invader method, mass spectrometry, RCA method and DNA chip method.

5. The method of claim 1, wherein said ABCG2 polypeptide comprises an amino acid sequence of SEQ ID NO:

2, and said polymorphism of the amino acid sequence is one or more of amino acid polymorphisms at positions selected from the group consisting of 12, 126, and 141 of SEQ ID NO;

2.

6. The method of claim 5, wherein said amino acid polymorphism is an amino acid substitution of Val12Met or Gln141Lys, or a deletion of the amino acid sequence downstream from the position 126 of SEQ ID NO:

2.

7. The method of claim 5, wherein said polymorphism of the amino acid sequence is determined by any one of methods selected from the group consisting of mass spectrometry, two-dimensional electrophoresis method, and protein chip method.

8. The method of claim 1, wherein said drug is a compound represented by the formula (I):

9. A polynucleotide having a single nucleotide polymorphism(s) at one or more position(s) selected from the group consisting of 34, 376 and 421 of SEQ ID NO:

1, said polynucleotide comprising any one of the positions of said single nucleotide polymorphisms and consisting of at least 10 contiguous nucleotides of SEQ ID NO;

1, or a complementary polynucleotide thereto.

10. The polynucleotide of claim 9, wherein said single nucleotide polymorphism is selected from the group consisting of G34A, C376T, C421A and single nucleotide polymorphisms complementary thereto.

11. A polynucleotide having one or more of the nucleotide polymorphisms in the polynucleotide sequence of SEQ ID NO:

1, said polymorphism selected from the group consisting of nucleotide polymorphisms by which the translated amino acid at position 12 is methionine, one at position 126 is stop codon, and one at position 141 is lysine, and consisting of at least 10 contiguous nucleotides including one or more of nucleotides located at the site of said nucleotide polymorphisms, or a complementary polynucleotide thereto.

12. A pair of PCR primers which specifically hybridize to ABCG2 gene, and amplify a DNA fragment of a portion of said gene, wherein the amplified DNA fragment comprises a nucleotide(s) at position 34, 376 or 421 of SEQ ID NO:

1

13. The pair of PCR primers of claim 12, said pair of PCR primers selected from the group of:

SEQ ID NO;

5 and SEQ ID NO;

6;

SEQ ID NO;

9 and SEQ ID NO;

10; and

SEQ ID NO;

11 and SEQ ID NO;

12.

14. A polynucleotide which specifically hybridizes to ABCG2 gene, and which is capable of detecting a polymorphism(s) of ABCG2 gene at position 34, 376 or 421 of SEQ ID NO:

1.

15. The polynucleotide of claim 14, which is capable of using in any one of methods selected from the group consisting of a direct sequencing method, TaqMan method, invader method, mass spectrometry, RCA method and DNA chip method.

16. A polypeptide having polymorphic mutation(s) to ABCG2 protein defined in the following (a) or (b), said polypeptide is a polymorphic mutant wherein one or both of amino acids at positions 12 and 141 of SEQ ID NO:

2 are substituted with other amino acid(s), a polypeptide fragment comprising said substituted amino acid and at least 10 contiguous amino acid residues of said polymorphic mutant, or a polypeptide wherein the amino acid sequence downstream from the position 126 of SEQ ID NO;

2 is deleted;

(a) a human ABCG2 polypeptide consisting of an amino acid sequence of SEQ ID No;

2,

(b) an isopolypeptide of (a) consisting of an amino acid sequence of SEQ ID NO;

2, wherein one or several amino acids except for the amino acids at positions 12, 126 and 141, are deleted, substituted or added, and having a drug transport capability.

17. An antibody which specifically binds to the mutant ABCG2 polypeptide of claim 16.

20. A method for diagnosing a drug sensitivity, said method comprising:

analyzing a biological sample from a subject, and determining the presence or absence of a polynucleotide having a single nucleotide polymorphism(s) at one or more position(s) selected from the group consisting of 34, 376 and 421 of SEQ ID NO;

1, said polynucleotide comprising any one of the positions of said single nucleotide polymorphisms and consisting of at least 10 contiguous nucleotides of SEQ ID NO;

1, or a complementary polynucleotide thereto;

or

a polynucleotide having one or more of the nucleotide polymorphisms in the polynucleotide sequence of SEQ ID NO;

1, said polymorphism selected from the group consisting of nucleotide polymorphisms by which the translated amino acid at position 12 is methionine, one at position 126 is stop codon, and one at position 141 is lysine, and consisting of at least 10 contiguous nucleotides including one or more of nucleotides located at the site of said nucleotide polymorphisms, or a complementary polynucleotide thereto;

or

a polypeptide of claim 16.

21. The method of claim 20, wherein the subject having said polynucleotide and/or said polypeptide is suggested to be sensitive to the compound represented by the formula (I):

22. A kit for diagnosing a drug sensitivity comprising one or more of the following (a) to (f):

(a) a polynucleotide having a single nucleotide polymorphism(s) at one or more position(s) selected from the group consisting of 34, 376 and 421 of SEQ ID NO;

1, said polynucleotide comprising any one of the positions of said single nucleotide polymorphisms and consisting of at least 10 contiguous nucleotides of SEQ ID NO;

1, or a complementary polynucleotide thereto;

or

a polynucleotide having one or more of the nucleotide polymorphisms in the polynucleotide sequence of SEQ ID NO;

1, said polymorphism selected from the group consisting of nucleotide polymorphisms by which the translated amino acid at position 12 is methionine, one at position 126 is stop codon, and one at position 141 is lysine and consisting of at least 10 contiguous nucleotides including one or more of nucleotides located at the site of said nucleotide polymorphisms, or a complementary polynucleotide thereto;

(b) a pair of PCR primers which specifically hybridize to ABCG2 gene, and amplify a DNA fragment of a portion of said gene, wherein the amplified DNA fragment comprises a nucleotide(s) at position 34, 376 or 421 of SEQ ID NO;

1;

(c) a polynucleotide which specifically hybridizes to ABCG2 gene, and which is capable of detecting a polymorphism(s) of ABCG2 gene at position 34, 376 or 421 of SEQ ID NO;

1;

(d) a polypeptide having polymorphic mutation(s) to ABCG2 protein defined in the following (i) or (ii), said polypeptide is a polymorphic mutant wherein one or both of amino acids at positions 12 and 141 of SEQ ID NO;

2 are substituted with other amino acid(s), a polypeptide fragment comprising said substituted amino acid and at least 10 contiguous amino acid residues of said polymorphic mutant, or a polypeptide wherein the amino acid sequence downstream from the position 126 of SEQ ID NO;

2 is deleted;

(i) a human ABCG2 polypeptide consisting of an amino acid sequence of SEQ ID No;

2,

(ii) an isopolypeptide of (i) consisting of an amino acid sequence of SEQ ID NO;

2, wherein one or several amino acids except for the amino acids at positions 12, 126 and 141, are deleted, substituted or added, and having a drug transport capability;

(e) said antibody of claim 17, and

(f) a transformed cell which expresses an polypeptide having polymorphic mutation(s) to ABCG2 protein defined in the following (i) or (ii), said polymorphic mutation(s) being one or both of amino acid substitutions Val12Met and Gln141Lys of the amino acid sequence of SEQ ID NO;

2;

(i) a human ABCG2 polypeptide consisting of an amino acid sequence of SEQ ID NO;

2,

(ii) an isopolypeptide of (i) consisting of an amino acid sequence of SEQ ID NO;

2, wherein one or several amino acids except for the amino acids at positions 12, 126 and 141, are deleted, substituted or added, and having a drug transport capability.

18. A transformed cell which expresses an polypeptide having polymorphic mutation(s) to ABCG2 protein defined in the following (a) or (b), said polymorphic mutation(s) being one or both of amino acid substitutions Val12Met and Gln141Lys of the amino acid sequence of SEQ ID NO:

2;

(a) a human ABCG2 polypeptide consisting of an amino acid sequence of SEQ ID NO;

2,

(b) an isopolypeptide of (a) consisting of an amino acid sequence of SEQ ID NO;

2, wherein one or several amino acids except for the amino acids at positions 12, 126 and 141, are deleted, substituted or added, and having a drug transport capability.

19. A method for measuring a drug transport capability using the transformed cell of claim 18.

23. A computer system for analyzing data of ABCG2 polymorphism, comprising:

(a) an input/output device,

(b) a memory comprising the polymorphism data, and

(c) a central processing unit.