Surrogate genetics target characterization method

• US 6,322,973 B1
• Filed: 11/06/1998
• Issued: 11/27/2001
• Est. Priority Date: 11/07/1997
• Status: Expired due to Fees

• Current Assignee: Entelos, Inc. (SilkRoad Inc.)
• Original Assignee: Iconix Biosciences, Inc. (SilkRoad Inc.)
• Inventors: Bostian, Keith, Natsoulis, Georges
• Primary Examiner(s): Guzo, David
• Assistant Examiner(s): Leffers, Jr., Gerald G.
• Application Number:
  US09/187,918
• Time in Patent Office: 1,117 Days
• Field of Search: 435/4, 435/5, 435/6, 435/29, 435/40.5, 435/243, 435/69.1, 435/325, 435/320.1, 435/410, 435/455, 435/471, 536/23.1
• US Class Current: 435/6.14
• CPC Class Codes: C12N 15/1079 Screening libraries by altering the phenotype or phenotypic trait of the host reporter assays C12N15/1086
• CPC Class Codes: C12Q 1/025 for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics antimicrobial activity C12Q1/18
• CPC Class Codes: C12Q 1/6897 involving reporter genes operably linked to promoters

Abstract

A two-step, scalable method is described for identifying the cellular function(s) of one or more genes of unknown function, and for identifying modulators of the gene(s). The method uses the reversal or alteration of a phenotype created by the expression of the heterologous gene, e.g., a human gene, to identify modulators of that gene'"'"'s activity. That modulator is then used in an in vitro or in vivo disease model system to identify compounds which affect disease progression. The subset of compounds which influence disease in a therapeutic manner are drug leads. However, all compounds which influence disease progression are tools to at least partially characterize gene function. The inhibitor identification step of the method is preferably carried out using a plurality of microbial strains or cell lines expressing different heterologous DNA sequences in a single solution. The method is particularly useful for genes which have not been validated as good inhibitor targets.

Claims

1. A method for identifying a modulator of a function of a heterologous biomolecule, comprising:

(a) providing a mixture of host cell populations, each population comprising a different nucleic acid molecule encoding a heterologous biomolecule selected from the group consisting of an RNA and a protein whose function has not been inferred experimentally, wherein the nucleic acid molecule is operatively associated with a promoter, wherein expression of said heterologous biomolecule from said nucleic acid molecule results in a measurable phenotype in each of said host cell populations; and

(a) contacting said mixture of host cell populations with a test substance and detecting any changes in a measurable phenotype, wherein a change in a measurable phenotype indicates that said test substance is a potential modulator of said function of said heterologous biomolecule expressed in the host cell population whose measurable phenotype changed following said contacting.

2. The method of claim 1, wherein each host cell population further comprises a nucleic acid tag that distinguishes it from host cell populations that comprise different heterologous biomolecules.

3. The method of claim 1, wherein said mixture of host cell populations is contacted with a plurality of different test substances.

4. The method of claim 3, wherein said mixture of host cell populations is divided into a plurality of aliquots, and different aliquots are contacted with different test substances.

5. The method of claim 1, wherein said phenotype comprises an interference phenotype.