Pharmacogenomics and identification of drug targets by reconstruction of signal transduction pathways based on sequences of accessible regions

• US 6,610,489 B2
• Filed: 04/27/2001
• Issued: 08/26/2003
• Est. Priority Date: 04/28/2000
• Status: Expired due to Term

• Current Assignee: Sangamo Biosciences, Inc.
• Original Assignee: Sangamo Biosciences, Inc.
• Inventors: Urnov, Fyodor, Collingwood, Trevor, Johnstone, Brian, Wolffe, Alan, Guschin, Dmitry, Li, Xiao-Yong
• Primary Examiner(s): Horlick, Kenneth R.
• Application Number:
  US09/844,265
• Publication Number:
  US 20020127559A1
• Time in Patent Office: 851 Days
• Field of Search: 435/6, 435/7.1
• US Class Current: 435/6.13
• CPC Class Codes: C07K 14/4702 Regulators; Modulating activity
• CPC Class Codes: C07K 2319/00 Fusion polypeptide
• CPC Class Codes: C07K 2319/02 containing a signal sequence
• CPC Class Codes: C07K 2319/09 containing a nuclear localisation signal
• CPC Class Codes: C07K 2319/24 containing a MBP (maltose binding protein)-tag
• CPC Class Codes: C07K 2319/43 containing a FLAG-tag
• CPC Class Codes: C07K 2319/71 containing domain for transcriptional activaation, e.g. VP16
• CPC Class Codes: C07K 2319/75 containing a fusion for activation of a cell surface receptor, e.g. thrombopoeitin, NPY and other peptide hormones
• CPC Class Codes: C07K 2319/81 containing a Zn-finger domain for DNA binding
• CPC Class Codes: C12N 15/102 Mutagenizing nucleic acids
• CPC Class Codes: C12N 15/1034 Isolating an individual clone by screening libraries
• CPC Class Codes: C12N 15/1072 Differential gene expression library synthesis, e.g. subtracted libraries, differential screening
• CPC Class Codes: C12N 15/62 DNA sequences coding for fusion proteins
• CPC Class Codes: C12N 15/63 Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
• CPC Class Codes: C12N 15/66 General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligation; Use of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
• CPC Class Codes: C12N 15/67 General methods for enhancing the expression
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: C12Q 2522/101 Single or double stranded nucleic acid binding proteins
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2531/113 PCR
• CPC Class Codes: G16B 30/00 : ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 : Sequence alignment; Homology search
• CPC Class Codes: G16B 50/00 : ICT programming tools or database systems specially adapted for bioinformatics

Abstract

Methods for the identification of a drug target, wherein the drug target is a component of a signal transduction pathway, are provided. The methods are based, in part, on selection of a gene of therapeutic interest and determination of regulatory DNA sequences which regulate expression of the gene in a cell of interest, followed by reconstruction of signal transduction pathways which act on molecules which bind to the regulatory sequence. Also provided are methods for assessing potential pharmacological effects and/or side effects of an agent, based on the effect of the agent on the distribution and properties of accessible regions in cellular chromatin.

Claims

1. A method for predicting the response of an individual to a drug, the method comprising:

(a) determining the location and nature of accessible regions in cellular chromatin of the individual resulting from exposure of the individual to the drug; and

(b) comparing the location and nature of accessible regions identified in step (a) to previously identified locations and natures of accessible regions associated with a known drug response;

wherein, if the location and nature of accessible regions identified in step (a) is different from the previously identified locations and natures of accessible regions associated with the known drug response, the response of the individual to the drug is predicted to be different from the known response.

2. The method of claim 1, wherein one or more of the accessible regions is associated with a gene that encodes an enzyme involved in drug metabolism.

3. The method of claim 2, wherein the gene involved in drug metabolism is a cytochrome P450 gene.

4. The method of claim 1, wherein the disease or condition is cancer.

5. The method of claim 1, wherein the disease or condition is cardiovascular disease.

6. The method of claim 1, wherein the disease or condition is osteoporosis.

7. The method of claim 1, wherein the known response is a therapeutic response.

8. The method of claim 7, wherein the known response is a side effect.

9. The method of claim 2, wherein the enzyme involved in drug metabolism is selected from the group consisting of NAD(P)H quinone oxidoreductase, N-acetyltransferase and thiopurine methyltransferase.

10. The method of claim 1, wherein one or more of the accessible regions is associated with a gene that encodes a receptor protein.

11. The method of claim 10, wherein the receptor protein is selected from the group consisting of the beta-2 adrenergic receptor and the dopamine D3 receptor.

12. The method of claim 1, wherein one or more of the accessible regions is associated with a gene that encodes a transporter protein.

13. The method of claim 12, wherein the transporter protein is encoded by the MDR-1 gene.

14. The method of claim 12, wherein the transporter protein is a multiple drug resistance protein.