Measurement of gene expression profiles in toxicity determination

• US 6,228,589 B1
• Filed: 02/28/2000
• Issued: 05/08/2001
• Est. Priority Date: 10/11/1996
• Status: Expired due to Term

• Current Assignee: Solexa Incorporated (Illumina Incorporated)
• Original Assignee: Lynx Therapeutics, Inc. (Illumina Incorporated)
• Inventors: Brenner, Sydney
• Primary Examiner(s): LeGuyader, John L.
• Assistant Examiner(s): SHIBUYA, MARK LANCE
• Application Number:
  US09/269,911
• Time in Patent Office: 435 Days
• Field of Search: 435/6, 435/440, 435/471, 536/23.1, 536/24.2, 536/24.3, 536/25.4, 536/25.32, 536/25.6
• US Class Current: 506/3
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12N 15/1065 Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
• CPC Class Codes: C12N 15/1072 Differential gene expression library synthesis, e.g. subtracted libraries, differential screening
• CPC Class Codes: C40B 40/00 Libraries per se, e.g. arrays, mixtures

Abstract

A method is provided for assessing the toxicity of a compound in a test organism by measuring gene expression profiles of selected tissues. Gene expression profiles are measured by massively parallel signature sequencing of cDNA libraries constructed from mRNA extracted from the selected tissues. Gene expression profiles provide extensive information on the effects of administering a compound to a test organism in both acute toxicity tests and in prolonged and chronic toxicity tests.

Claims

1. A method of determining the toxicity of a compound, the method comprising the steps of:

administering the compound to a test organism;

extracting a population of mRNA molecules from each of one or more tissues of the test organism;

forming a separate population of cDNA molecule from each population of mRNA molecules from the one or more tissues such that each cDNA molecule of the separate populations has an oligonucleotide tag attached, the oligonucleotide tags being selected from the same minimally cross-hybridizing set;

separately sampling each separate population of cDNA molecules such that substantially all different cDNA molecules within a sample have different oligonucleotide tags attached;

sorting the cDNA molecules of each sample by specifically hybridizing the oligonucleotide tags with their respective complements, the respective complements being attached as uniform populations of substantially identical complements in spatially discrete regions on one or more solid phase supports;

determining the nucleotide sequence of a portion of each of the sorted cDNA molecules of each separate population to form a frequency distribution of expressed genes for each of the one or more tissues; and

determining the toxicity of the compound from the frequency distribution of expressed genes in each of the one or more tissues.

2. The method of claim 1 wherein said oligonucleotide tag and said complement of said oligonucleotide tag are single stranded.

3. The method of claim 2 wherein said oligonucleotide tag consists of a plurality of subunits, each subunit consisting of an oligonucleotide of 3 to 9 nucleotides in length and each subunit being selected from the same minimally cross-hybridizing set.

4. The method of claim 3 wherein said one or more solid phase supports are microparticles and wherein said step of sorting said cDNA molecules onto the microparticles produces a subpopulation of loaded microparticles and a subpopulation of unloaded microparticles.

5. The method of claim 4 further including a step of separating said loaded microparticles from said unloaded microparticles.

6. The method of claim 5 further including a step of repeating said steps of sampling, sorting, and separating until the number of said loaded microparticles that is accumulated is at least 10,000.

7. The method of claim 6 wherein said number of loaded microparticles is at least 100,000.

8. The method of claim 7 wherein said number of loaded microparticles is at least 500,000.

9. The method of claim 5 further including a step of repeating said steps of sampling, sorting, and separating until the number of said loaded microparticles that is accumulated is sufficient to estimate the relative abundance of a cDNA molecule present in said population at a frequency within the range of from 0.1% to 5% with a 95% confidence limit no larger than 0.1% of said population.

10. The method of claim 4 wherein said test organism is a mammalian tissue culture.

11. The method of claim 10 wherein said mammalian tissue culture comprises hepatocytes.

12. The method of claim 4 wherein said test organism is an animal selected from the group consisting of rats, mice, hamsters, guinea pigs, rabbits, cats, dogs, pigs, and monkeys.

13. The method of claim 12 wherein said one or more tissues are selected from the group consisting of liver, kidney, brain, cardiovascular, thyroid, spleen, adrenal, large intestine, small intestine, pancreas, urinary bladder, stomach, ovary, testes, and mesenteric lymph nodes.

14. A method of identifying genes which are differentially expressed in a selected tissue of a test animal after treatment with a compound, the method comprising the steps of:

administering the compound to a test animal;

extracting a population of mRNA molecules from the selected tissue of the test animal;

forming a population of cDNA molecules from the population of mRNA molecules such that each cDNA molecule has an oligonucleotide tag attached, the oligonucleotide tags being selected from the same minimally cross-hybridizing set;

sampling the population of cDNA molecules such that substantially all different cDNA molecules have different oligonucleotide tags attached;

sorting the cDNA molecules by specifically hybridizing the oligonucleotide tags with their respective complements, the respective complements being attached as uniform populations of substantially identical complements in spatially discrete regions on one or more solid phase supports;

determining the nucleotide sequence of a portion of each of the sorted cDNA molecules to form a frequency distribution of expressed genes; and

identifying genes expressed in response to administering the compound by comparing the frequencing distribution of expressed genes of the selected tissue of the test animal with a frequency distribution of expressed genes of the selected tissue of a control animal.

15. The method of claim 14 wherein said oligonucleotide tag and said complement of said oligonucleotide tag are single stranded.

16. The method of claim 15 wherein said oligonucleotide tag consists of a plurality of subunits, each subunit consisting of an oligonucleotide of 3 to 9 nucleotides in length and each subunit being selected from the same minimally cross-hybridizing set.

17. The method of claim 16 wherein said one or more solid phase supports are microparticles and wherein said step of sorting said cDNA molecules onto the microparticles produces a subpopulation of loaded microparticles and a subpopulation of unloaded microparticles.

18. The method of claim 17 further including a step of separating said loaded microparticles from said unloaded microparticles.

19. The method of claim 18 further including a step of repeating said steps of sampling, sorting, and separating until the number of said loaded microparticles that is accumulated is at least 10,000.

20. The method of claim 19 wherein said number of loaded microparticles is at least 100,000.