METHODS AND PLATFORMS FOR DRUG DISCOVERY

• US 20090324559A1
• Filed: 06/12/2009
• Published: 12/31/2009
• Est. Priority Date: 06/15/2007
• Status: Active Grant

• Current Assignee: Kyoto University
• Original Assignee: iZumi Bio, Inc. (Bristol-Myers Squibb Company)
• Inventors: Seidenman, Kenneth J., SAKURADA, Kazuhiro
• Granted Patent: US 8,257,941 B2
• Time in Patent Office: Days
• US Class Current: 424/93.7
• CPC Class Codes: A61P 25/28 for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
• CPC Class Codes: A61P 3/10 for hyperglycaemia, e.g. antidiabetics
• CPC Class Codes: C12N 15/85 for animal cells
• CPC Class Codes: C12N 2501/602 Sox-2
• CPC Class Codes: C12N 2501/603 Oct-3/4
• CPC Class Codes: C12N 2501/604 Klf-4
• CPC Class Codes: C12N 2501/606 c-Myc
• CPC Class Codes: C12N 2510/00 Genetically modified cells
• CPC Class Codes: C12N 2799/027 where the vector is derived from a retrovirus
• CPC Class Codes: C12N 5/0696 Artificially induced pluripotent stem cells, e.g. iPS

Abstract

The present invention involves methods for identifying an agent that corrects a phenotype associated with a health condition or a predisposition for a health condition. The invention also involves methods for identifying a diagnostic cellular phenotype, determining the risk of a health condition in a subject, methods for reducing the risk of drug toxicity in a human subject, and methods for identifying a candidate gene that contributes to a human disease. The invention also discloses human induced pluripotent stem cell lines.

Claims

1. A method for identifying an agent that corrects a phenotype associated with a health condition or a predisposition for the health condition, comprising:

(i) contacting a first population of cells from a human induced pluripotent stem cell line, or cells differentiated from the human induced pluripotent stem cell line, with a candidate agent;

(ii) contacting a second population of cells from the human induced pluripotent stem cell line, or cells differentiated from the human induced pluripotent stem cell line, with a negative control agent;

(iii) assaying the phenotype in the first population and second population after the contacting steps; and

(iv) identifying the candidate agent as correcting the phenotype if the assayed phenotype of the first population after the contacting step is closer to a normal phenotype than the phenotype of the second population after the contacting step;

wherein the cells in the first and second populations of human induced pluripotent stem cells;

(a) comprise at least one endogenous allele associated with the health condition or the predisposition for the health condition;

or

(b) are generated from a subject suffering from the health condition or the predisposition for the health condition.

2. The method of claim 1, wherein the health condition is a neurodegenerative disorder, a neurological disorder, a mood disorder, a cardiovascular disease, a metabolic disorder, a respiratory disease, a drug sensitivity condition, an eye disease, an immunological disorder, or a hematological disease.

3. The method of claim 1, wherein the first and second populations of cells are cells differentiated from the human induced pluripotent stem cell line.

4. The method of claim 3, wherein the differentiated cells are neural stem cells, neurons, cardiomyocytes, hepatic stem cells, or hepatocytes.

5. The method of claim 1, wherein the phenotype is apoptosis, intracellular calcium level, calcium flux, protein kinase activity, mitochondrial oxidative stress, enzyme activity, cell morphology, receptor activation, protein trafficking, intracellular protein aggregation, organellar composition, motility, intercellular communication, protein expression, or gene expression.

6. The method of claim 1, further comprising comparing a plurality of polymorphic alleles present in the genome of the human induced pluripotent stem cell line to a plurality of polymorphic alleles present in the genome of a human other than the human from which the induced pluripotent stem cell line was generated.

7. The method of claim 1, further comprising genotyping the human induced pluripotent stem cell line for a plurality of polymorphisms.

8. The method of claim 1, further comprising comparing the genome sequence of the human induced pluripotent stem cell line, or a portion thereof, to the genome sequence, or a portion thereof, of a human other than the human from which the induced pluripotent stem cell line was generated.

9. The method of claim 1, further comprising sequencing the genome of the human induced pluripotent stem cell line.

10. A method for reducing the risk of drug toxicity in a human subject, comprising:

(i) contacting one or more cells differentiated from an induced pluripotent stem cell line generated from the subject with a dose of a pharmacological agent;

(ii) assaying the contacted one or more differentiated cells for toxicity; and

(iii) prescribing or administering the pharmacological agent to the subject if, and only if, the assay is negative for toxicity in the contacted cells.

11. A human induced pluripotent stem cell line generated from a subject diagnosed as suffering from a health condition.

12. The human induced pluripotent stem cell line of claim 11, wherein the health condition is a neurodegenerative disorder, a neurological disorder, an eye disease, a mood disorder, a respiratory disease, a cardiovascular disease, an immunological disorder, a hematological disease, a metabolic disorder, or a drug sensitivity condition.

13. The human induced pluripotent stem cell line of claim 12, wherein the health condition is a neurodegenerative disorder, a neurological disorder, or a mood disorder.

14. The human induced pluripotent stem cell line of claim 13, wherein the neurodegenerative disorder is Spinal Muscular Atrophy, Amyotrophic Lateral Sclerosis, or Parkinson'"'"'s Disease.

15. A neural stem cell or neuron differentiated from the human induced pluripotent stem cell line of claim 13.

16. The human induced pluripotent stem cell line of claim 12, wherein the health condition is a cardiovascular disease.

17. A cardiac progenitor cell or a cardiomyocyte differentiated from the human induced pluripotent stem cell of claim 16.

18. A differentiated cell generated by differentiating the human induced pluripotent stem cell of claim 11.

19. The differentiated cell of claim 18, wherein the differentiated cell is a neural stem cell or a neuron.

20. The differentiated cell of claim 19, wherein the neuron is a dopaminergic neuron, a motor neuron, or a glutamatergic neuron.

21. The differentiated cell of claim 18, wherein the differentiated cell is a glial progenitor cell or a glial cell.

22. The differentiated cell of claim 18, wherein the differentiated cell is a cardiac progenitor cell or a cardiomyocyte.

23. The differentiated cell of claim 18, wherein the differentiated cell is a pancreatic beta cell or a pancreatic progenitor cell.

24. The differentiated cell of claim 18, wherein the differentiated cell is a hepatic stem cell or a hepatocyte.

25. A human induced pluripotent stem cell line, comprising at least one endogenous allele associated with a health condition or a predisposition for the health condition.

26. A differentiated cell generated by differentiating the human pluripotent stem cell line of claim 25.

27. An isolated population of human cells comprising neural stem cells or neurons from a subject having at least one endogenous allele associated with a neurodegenerative disorder, a neurological disorder, or a mood disorder, or from a subject diagnosed with the neurodegenerative disorder, neurological disorder, or mood disorder.

28. A method for generating the isolated population of human cells of claim 27, comprising generating an induced pluripotent stem cell line from the subject.

29. The method of claim 28, further comprising differentiating the induced pluripotent stem cell line into a population of cells comprising neurons.

30. The method of claim 27, wherein the human subject is diagnosed with the neurodegenerative disorder, neurological disorder, or mood disorder.

31. An isolated population of human cells comprising human cardiac progenitor cells or cardiomyocytes from a subject having at least one endogenous allele associated with a cardiovascular disease, or from a subject diagnosed with the cardiovascular disease.

32. A method for generating the isolated population of human cells of claim 31 comprising generating an induced pluripotent stem cell line from the human subject.

33. The method of claim 32, further comprising genotyping the human subject for the presence or absence of the at least one endogenous allele.

34. The method of claim 32, further comprising differentiating the induced pluripotent stem cell line into a population of cells comprising cardiac progenitor cells or cardiomyocytes.

35. An isolated population of human cells comprising hepatic stem cells or hepatocytes from a subject having at least one endogenous allele associated with a drug sensitivity condition, or from a subject diagnosed with the drug sensitivity condition.

36. A method for generating the isolated population of human cells of claim 35, comprising generating an induced pluripotent stem cell line from the human subject.

37. A panel of genetically diverse human induced pluripotent stem cell lines, comprising human induced pluripotent stem cell lines generated from a plurality of individuals each of which carry at least one polymorphic allele that is unique among the plurality of individuals.

38. The panel of claim 37, comprising human induced pluripotent stem cell lines generated from at least 50 individuals.

39. The panel of claim 37, wherein the plurality of individuals suffer from the same health condition.

40. The panel of claim 39, wherein the health condition is a neurodegenerative disorder, a neurological disorder, an eye disease, a mood disorder, a respiratory disease, a cardiovascular disease, an immunological disorder, a hematological disease, a metabolic disorder, or a drug sensitivity condition.

41. The panel of claim 40, wherein the neurodegenerative disorder is Spinal Muscular Atrophy, Amyotrophic Lateral Sclerosis, or Parkinson'"'"'s Disease.

42. A panel of differentiated human cells comprising cells differentiated from the panel of human induced pluripotent stem cells of claim 37.

43. The panel of differentiated human cells of claim 42, wherein the differentiated human cells are neural stem cells, neurons, glial progenitor cells, glial cells, cardiac progenitor cells, cardiomyocytes, pancreatic progenitor cells, pancreatic beta cells, hepatic stem cells, hepatocytes or lung progenitor cells.

44. The panel of differentiated human cells of claim 42, wherein the differentiated human cells are neural stem cells or neurons.

45. The panel of differentiated human cells of claim 42, wherein the differentiated human cells are cardiac progenitor cells or cardiomyocytes.

46. The panel of differentiated human cells of claim 42, wherein the differentiated human cells are hepatic stem cells or hepatocytes.