Methods and products related to drug screening using gene expression patterns

• US 20040009495A1
• Filed: 12/06/2002
• Published: 01/15/2004
• Est. Priority Date: 12/07/2001
• Status: Abandoned Application

• Current Assignee: Dana-Farber Cancer Institute, Whitehead Institute for Biomedical Research
• Original Assignee: Dana-Farber Cancer Institute, Whitehead Institute for Biomedical Research
• Inventors: Stockwell, Brent, Ross, Ken, OʼMalley, Shawn, Stegmaier, Kim, Golub, Todd
• Application Number:
  US10/313,335
• Publication Number:
  US 20040009495A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/10 Ploidy or copy number detection
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/50 Compression of genetic data

Abstract

The invention involves high throughput methods for identifying properties of cells under a variety of cellular conditions. The high throughput methods have a variety of uses, including methods for identifying cellular modulators such as pharmacological agents or environmental conditions, methods for identifying a cellular phenotype and methods for identifying novel genes.

Claims

1. A method of determining a gene expression profile for a cellular phenotype comprising:

establishing two or more sets of gene expression profiles;

defining a set of marker genes that defines the differences between the two or more sets of gene expression profiles; and

recording the set of marker genes in a database that defines the cellular phenotype.

2. A method of screening a cell population comprising:

defining a set of marker genes that represents a cellular phenotype;

amplifying the set of marker genes from the cell population;

determining the expression of the marker genes present in the cell population; and

scoring the expression of the marker genes to screen the cell population for the cellular phenotype.

3. The method of claim 2, wherein the cell population is a cultured cell line.

4. The method of claim 2, wherein the cell population is an in vivo cell population.

5. The method of claim 2, wherein the marker genes are scored relative to the expression of a control gene.

6. The method of claim 2, wherein the marker genes are scored relative to each other.

7. The method of claim 2, wherein the marker genes are scored on a binary basis.

8. The method of claim 2, wherein the control gene is GAPDH.

9. The method of claim 2, wherein the cellular phenotype is of a cancer cell.

10. The method of claim 2, wherein the cellular phenotype is of a metastatic cancer cell.

11. The method of claim 2, wherein the cellular phenotype is of a cell resistant to radiation.

12. The method of claim 2, wherein the cellular phenotype is of a cell resistant to chemotherapy.

13. The method of claim 2, wherein the cellular phenotype is of a cancer cell that releases angiogenic factors.

14. The method of claim 2, wherein the cellular phenotype is of a cell with a positive drug response.

15. The method of claim 2, wherein the set of marker genes defines a set of phenotypic markers.

16. The method of claim 2, wherein the set of marker genes defines a set of therapeutic markers.

17. The method of claim 2, wherein the set of marker genes defines a set of diagnostic markers.

18. The method of claim 2, wherein the cell population is a population of cells from human peripheral blood.

19. The method of claim 2, wherein the set of marker genes defines 1 or more novel genes.

20. The method of claim 2, wherein the set of marker genes represents a biological pathway.

21. The method of claim 2, wherein the set of marker genes defines a transcriptome.

22. The method of claim 2, wherein the cell population is screened in response to a chemical compound.

23. The method of claim 22, wherein the chemical compound is selected from the group consisting of small molecule libraries, FDA approved drugs and synthetic chemical libraries.

24. The method of claim 2, wherein 1 or more of the marker genes is selected from the group consisting of IL1RN and SPP1.

25. The method of claim 2, wherein 1 or more of the marker genes is selected from the group consisting of ORM1 and NCF1.

26. The method of claim 2, wherein the expression of the marker gene is detected using a bipartite probe.

27. The method of claim 2, wherein the expression of the marker gene is detected using direct gene dendrimer methods.

28. The method of claim 2, further comprising:

defining one or more metagenes in response to one or more drugs.

29. The method of claim 28, wherein the drug is an anti-cancer drug.

30. A method for identifying an active compound, comprising:

contacting cells with a plurality of chemical compounds,

amplifying a set of marker genes from the cells to determine the expression of marker genes present in the cells, and

scoring the expression of the marker genes to identify a cellular phenotype, the presence of a specific cellular phenotype being indicative of an active compound.

31. The method of claim 30, wherein the plurality of chemical compounds is a set of compounds selected from the group consisting of small molecule libraries, FDA approved drugs, synthetic chemical libraries, phage display libraries, dosage libraries.

32. The method of claim 30, wherein the set of marker genes is a metagene.

33. The method of claim 30, wherein the active compound is an anti-cancer drug.

34. The method of claim 33, wherein the cellular phenotype is a tumorigenic status of the cell.

35. The method of claim 33, wherein the cellular phenotype is a metastatic status of the cell.

36. The method of claim 30, wherein the set of marker genes is a cancer versus non-cancer marker gene set.

37. The method of claim 30, wherein the set of marker genes is a metastatic versus non-metastatic marker gene set.

38. The method of claim 30, wherein the set of marker genes is a radiation resistant versus radiation sensitive marker gene set.

39. The method of claim 30, wherein the set of marker genes is a chemotherapy resistant versus chemotherapy sensitive marker gene set.

40. The method of claim 30, wherein the active compound is a cellular differentiation factor.

41. The method of claim 40, wherein the cellular phenotype is a cellular differentiation status.

42. The method of claim 30, wherein the expression of the marker genes is determined by custom reverse microarray analysis.

43. The method of claim 30, wherein the expression of the marker genes is determined by mass spectrometry.

44. A method for identifying a cellular phenotype, comprising:

identifying the expression of metagenes in a cell to identify a cellular phenotype of the cell.

45. The method of claim 44, wherein the expression of metagenes is identified by amplifying signature genes characteristic of the metagenes from the cells.

46. The method of claim 45, wherein the cellular phenotype is identified by scoring the expression of the metagenes on a binary basis.

47. The method of claim 45, wherein the cellular phenotype is a cellular differentiation status.

48. The method of claim 45, wherein the cellular phenotype is a tumorigenic status of the cell.

49. A method for identifying a function of a gene, comprising:

contacting cells with a diverse array of chemical compounds,

amplifying a set of marker genes characteristic of a transcriptome from the cells to determine the expression of the marker genes present in the cells,

identifying a gene with an unknown function based on the expression of the marker genes, and

correlating an activity of one or more chemical compounds from the diverse array to the gene with unknown function to identify a function for the gene.

50. A method for identifying an active compound, comprising:

contacting cells with a plurality of chemical compounds,

screening proteins isolated from the cells to determine expression of a set of marker proteins, and

scoring the expression of the marker proteins to identify a cellular phenotype, the presence of a specific cellular phenotype being indicative of an active compound.

51. A method for identifying changes in cellular proliferation, comprising:

contacting cells with a plurality of chemical compounds,

amplifying at least one control gene from the cells,

scoring the level of expression of the control gene to determine a relative amount of cellular proliferation with respect to a level of expression of the control gene in a similar cell.

52. A database representing a library of phenotypic states of cells, the database tangibly embodied on a computer-readable medium and comprising:

one or more phenotype data structures, each phenotype data structure representing a phenotypic state and including at least one marker data unit representing a marker and specifying a difference in an expression level of the marker for a cell having the phenotypic state and an expression level of the marker for a biological cell not having the phenotypic state.

53. A data structure representing a phenotypic state of a cell, the data structure tangibly embodied on a computer-readable medium and comprising:

at least one marker data unit representing a marker and specifying a difference in an expression level of the marker for a cell having the phenotypic state and an expression level of the marker for a biological cell not having the phenotypic state,

wherein the marker data unit was generated using reverse gene expression analysis.

54. A method of determining whether a chemical compound applied to undifferentiated cells produces differentiated cells exhibiting a phenotype, the method comprising acts of:

(A) receiving expression levels of nucleic acids of a sample from an array of samples, the sample produced from introducing at least one of the undifferentiated cells to a chemical well containing the chemical compound;

(B) determining whether the chemical well from which the sample resulted is a dead chemical well by determining whether the resulting expression level of a housekeeping nucleic acid of the spot sample reaches a threshold expression level value;

(C) if the expression level of the housekeeping gene reaches the threshold value, normalizing an expression level of at least a first nucleic acid that is a marker for the phenotype;

(D) determining whether the normalized expression level reaches a threshold level indicative of the chemical compound producing differentiated cells from the undifferentiated cells.

55. The method of claim H1, wherein act (A) comprises:

for each receiving a first signal representing the expression level of a housekeeping gene.

56. The method of claim H1, wherein at least part of the method is implemented using a computer.