Multiplexed cell analysis system

• US 20030059764A1
• Filed: 04/10/2002
• Published: 03/27/2003
• Est. Priority Date: 10/18/2000
• Status: Active Grant

• Current Assignee: Millipore Corporation (Merck & Co., Inc.)
• Original Assignee: Millipore Corporation (Merck & Co., Inc.)
• Inventors: Beske, Oren E., Zarowitz, Michael A., Hyun, William C., Goldbard, Simon, Ravkin, Ilya
• Granted Patent: US 7,557,070 B2
• Time in Patent Office: Days
• US Class Current: 435/4
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00

Abstract

Systems including apparatus, methods, compositions, and kits for multiplexed analysis of biological systems using nonpositional and/or positional arrays of coded carriers.

Claims

1. A system for conducting a multiplexed cellular experiment comprising

a set of microcarriers including a first class of microcarriers each having a detectably distinct first code and a second class of microcarriers each having a detectably distinct second code, the first class of microcarriers carrying a first population of cells, and the second class of microcarriers carrying a second population of cells, so that the set of microcarriers can be analyzed in the same multiplexed experiment by identifying populations of cells according to the codes on their respective microcarriers.

2. The system of claim 1 further comprising

one or more additional class of microcarrier having a detectably distinct code for identifying a population of cells associated with the microcarrier.

3. The system of claim 1, wherein at least one of the populations of cells is modified for the purpose of drug discovery.

4. The system of claim 1, wherein at least one of the populations of cells is modified to express a potential drug target or set of drug targets.

5. The system of claim 1, wherein at least one of the cell populations is modified to express different nuclear hormone receptors.

6. The system of claim 1, wherein at least one of the cell populations has been exposed to one or more compounds selected as a modulator candidate for activating, inhibiting, or potentiating cellular receptor activity.

7. The system of claim 6 further comprising

a mechanism for detecting cellular receptor activity.

8. The system of claim 7, wherein the detection mechanism uses spectroscopic, hydrodynamic, or imaging methods.

9. The system of claim 1, wherein each class of microcarrier includes one or more microcarriers.

10. The system of claim 1, wherein the codes are optically detectable.

11. The system of claim 1, wherein the codes are detectable with electromagnetic radiation.

12. The system of claim 1, wherein the codes are positional.

13. The system of claim 1, wherein the microcarriers carry tissue sample.

14. The system of claim 1, wherein each class of microcarrier carries a sample of tissue from a different location in a patient sample.

15. The system of claim 14, wherein each class of microcarrier carries a sample of tissue from a different location along an axis of a core sample.

16. The system of claim 14, wherein each class of microcarrier carries a sample of tissue obtained by dividing a slice of tissue into smaller pieces.

17. The system of claim 1, wherein one or more of the cell populations is modified to detect the subcellular distribution of a cellular component.

18. The system of claim 17, wherein the cellular component is selected from the group consisting of cell cycle regulators, nuclear hormone receptors, kinases, phosphatases, ions, lipids, carbohydrates, and potential drug targets.

19. The system of claim 1, wherein one or more of the cell populations is modified to detect the quantity of a cellular component.

20. The system of claim 1, wherein one or more of the cell populations is labeled with a nuclear stain to quantify cellular DNA content.

21. The system of claim 1, wherein at least one of the cell populations has at least two different labels to detect changes in cell morphology.

22. The system of claim 1, wherein one or more of the cell populations is labeled with a cytoplasmic label and a nuclear label to detect the number of nuclei per cell as an indicator of cytokinesis modulation.

23. The system of claim 1, wherein one or more of the cell populations has labeled nuclei, and has been exposed to a toxic agent that causes formation of micronuclei.

24. The system of claim 23, wherein one or more of the cell populations has labeled nuclei, and has been exposed to a toxic agent that causes formation of micronuclei, and a modulator being tested as a potential inhibitor of micronuclei formation.

25. The system of claim 1, wherein one or more of the cell populations has labeled microtubules for detecting spindle defects.

26. The system of claim 1, wherein one or more of the cell populations has labeled microtubule organizing centers for detecting spindle defects.

27. The system of claim 1, wherein one or more of the cell populations has labeled microtubules and labeled microtubule organizing centers for detecting spindle defects.

28. The system of claim 1, wherein one or more of the cell populations is derived from a tumor biopsy or a needle aspirate.

29. The system of claim 1, wherein one or more of the cell populations is labeled with a DNA marker or markers for a particular gene or set of genes.

30. The system of claim 29, wherein the DNA marker is HER-2.

31. The system of claim 1, wherein the first class of microcarrier carries a cell population characterized by a first target or set of targets, and the second class of microcarrier carries a cell population characterized by a second target or set of targets, so that effects of a potential modulator on the first and second targets can be detected in a single multiplexed assay.

32. The system of claim 31, wherein the desired effect of the potential modulator on the first target or set of targets is different from the desired effect of the potential modulator on the second target or set of targets.

33. The system of claim 31, wherein interaction between the potential modulator and the first target or set of targets indicates possibly beneficial therapeutic efficacy.

34. The system of claim 33, wherein interaction between the potential modulator and the second target or set of targets indicates possibly adverse drug side- effects.

35. The system of claim 31, wherein the set of microcarriers includes a third class of microcarriers each having a detectably distinct third code, the third class of microcarrier carrying a cell type characterized by a toxicology panel.

36. The system of claim 35 further comprising

a positional array of wells, one or more of the wells containing a mixture of first, second, and third microcarrier classes, so that effects of a potential modulator on desired targets, undesired targets, and a toxicology panel can be -determined in a single multiplexed assay.

37. The system of claim 1 further comprising

a surface, a multi-class portion of the set of microcarriers being arbitrarily distributed at an examination site on the surface.

38. The system of claim 37 further comprising

an imaging device configured to acquire at least one image of the microcarriers at the examination site.

39. The system of claim 38 further comprising

an image analysis system that uses code information from the image to interpret experiments on the cells.

40. The system of claim 1, wherein the codes are defined by multi-color combinations.

41. The system of claim 1, wherein each code includes at least two distinct colored optically identifiable marks.

42. The system of claim 37, wherein the surface is glass.

43. The system of claim 38, wherein the imaging device acquires a digital image of the microcarriers at the examination site.

44. The system of claim 43, wherein the imaging device includes a CCD camera.

45. The system of claim 38, wherein the imaging device includes a microscope.

46. The system of claim 38, wherein the imaging device includes a confocal optics structure.

47. The system of claim 1, wherein each microcarrier has a cell association area and a code area.

48. The system of claim 47, wherein the cell association area and the code area substantially coincide.

49. The system of claim 47, wherein the cell association area and the code area at least partially overlap with each other.

50. The system of claim 47, wherein the cell association area and the code area are substantially separate from each other.

51. The system of claim 1, wherein the microcarriers have a substantially flat geometry.

52. The system of claim 1, wherein the microcarriers are card-shaped.

53. The system of claim 1, wherein the microcarriers are cylindrically shaped.

54. The system of claim 1, wherein each microcarmer has a dimension of between about 10 microns to about 4 millimeters in length or diameter.

55. The system of claim 1 further comprising

a microplate having a density of about 1, 4, or 16 wells per 81 millimeters squared, and at least one microcarrier from each of the first and second classes in at least one of the wells of the microplate.

56. The system of claim 1 further comprising

a microcarrier detection device including a flow channel and a detection station along the channel configured to detect codes on microcarriers as they flow through the channel.

57. A system for conducting a multiplexed cellular experiment comprising

a set of substantially planar microcarriers including a first class of microcarriers each having a detectably distinct first multi-colored positional code and a second class of microcarriers each having a detectably distinct second multi-colored positional code, the first class of microcarriers carrying a first population of cells, and the second class of microcarriers carrying a second population of cells, so that the first and second populations of cells can be analyzed in the same multiplexed experiment by identifying populations of cells according to the codes on respective microcarriers.

58. The system of claim 57, wherein the code for each class of microcarriers is formed by a combination of multi-colored fibers.

59. The system of claim 58, wherein the multi-colored fibers are fused together.

60. A system for conducting a multiplexed cellular experiment comprising

a microplate having a plurality of wells, each well containing a mixture of microcarriers including a first class of microcarriers each having a detectably distinct first code and a second class of microcarriers each having a detectably distinct second code, the first class of microcarriers carrying a first population of cells, and the second class of microcarriers carrying a second population of cells, so that the first and second populations of cells can be analyzed in the same multiplexed experiment by identifying populations of cells according to the codes on respective microcarriers.

61. The system of claim 60, wherein the microcarriers are substantially planar.

62. The system of claim 60, wherein the code on each microcarrier is formed by a combination of multi-colored fused glass fibers.