Predicting hepatotoxicity using cell based assays

• US 20060234332A1
• Filed: 03/13/2006
• Published: 10/19/2006
• Est. Priority Date: 07/18/2003
• Status: Active Grant

• Current Assignee: Cytokinetics, Inc.
• Original Assignee: Cytokinetics, Inc.
• Inventors: Fan, Jinhong, Vaisberg, Eugeni, Trautman, Jay, Rao, Aibing, Mattheakis, Larry, Adams, Cynthia, Solar, Gregg
• Granted Patent: US 7,817,840 B2
• Time in Patent Office: Days
• US Class Current: 435/40.500
• CPC Class Codes: G01N 1/30 Staining; Impregnating ; Fixation; Dehydration; Multistep processes for preparing samples of tissue, cell or nucleic acid material and the like for analysis
• CPC Class Codes: G01N 33/5067 Liver cells
• CPC Class Codes: G06T 2207/10056 Microscopic image
• CPC Class Codes: G06T 2207/10064 Fluorescence image
• CPC Class Codes: G06T 2207/20152 Watershed segmentation
• CPC Class Codes: G06T 2207/30024 Cell structures in vitro; Tissue sections in vitro
• CPC Class Codes: G06T 7/0012 Biomedical image inspection
• CPC Class Codes: G06T 7/12 Edge-based segmentation
• CPC Class Codes: G06T 7/41 based on statistical description of texture
• CPC Class Codes: G06V 20/698 Matching; Classification

Abstract

Cell based assays are used to assess the hepatotoxicity of a stimulus. Imaging technologies are used to analyze the effects of a stimulus on hepatocytes. Image analysis may characterize the stimulus on the basis of whether it is hepatotoxic, and if so what type of pathology is exhibited; e.g., apoptosis, necrosis, cholestasis, and/or steatosis.

Claims

1. A method of characterizing the effect of a stimulus on hepatocytes, the method comprising:

(a) exposing a first sample of hepatocytes to a stimulus under a first set of conditions;

(b) exposing a second sample of hepatocytes to the stimulus under a second set of conditions;

(c) imaging the first and second samples;

(d) extracting first features from one or more images of the first sample and second features from one or more images of the second sample; and

(e) analyzing features extracted from images of both the first sample and the second sample to assess the effect of the stimulus on hepatocytes.

2. The method of claim 1, further comprising combining features from images of the first and second samples prior to assessing the effect of the stimulus.

3. The method of claim 1, wherein the first set of conditions comprises contacting the first sample with a first marker set, and wherein the second set of conditions comprises contacting the second sample with a second marker set.

4. The method of claim 3, wherein at least one of the marker sets comprises a marker for DNA.

5. The method of claim 3, wherein at least one of the marker sets comprises a marker for tubulin.

6. The method of claim 3, wherein at least one of the marker sets comprises a marker for Golgi.

7. The method of claim 1, wherein extracting features comprises segmenting the images.

8. The method of claim 1, wherein the effect of the stimulus assessed in (e) is apoptosis.

9. The method of claim 1, wherein the effect of the stimulus assessed in (e) is necrosis.

10. The method of claim 1, wherein the stimulus is exposure to a compound.

11. A computer program product comprising a machine readable medium on which are provide program instructions for characterizing the effect of a stimulus on hepatocytes, the program instructions comprising:

(a) code for receiving images of a first sample of hepatocytes exposed to a stimulus under a first set of conditions, and receiving images of a second sample of hepatocytes exposed to the stimulus under a second set of conditions;

(b) code for extracting first features from one or more images of the first sample and second features from one or more images of the second sample; and

(c) code for analyzing features extracted from images of both the first sample and the second sample to assess the effect of the stimulus on hepatocytes.

12. The computer program product of claim 11, further comprising code for combining features from images of the first and second samples prior to assessing the effect of the stimulus.

13. The computer program product of claim 11, wherein the images of the first sample comprise signals from a first marker set, and wherein the images of the second sample comprise signals from a second marker set.

14. The computer program product of claim 13, wherein at least one of the marker sets comprises a marker for DNA.

15. The computer program product of claim 13, wherein at least one of the marker sets comprises a marker for tubulin.

16. The computer program product of claim 13, wherein at least one of the marker sets comprises a marker for Golgi.

17. The computer program product of claim 11, wherein the code for extracting features comprises code for segmenting the images.

18. The computer program product of claim 11, wherein the effect of the stimulus assessed in (c) is apoptosis.

19. The computer program product of claim 11, wherein the effect of the stimulus assessed in (c) is necrosis.

20. The computer program product of claim 11, wherein the stimulus is exposure to a compound.

21. A method of generating a model for characterizing the effect of a stimulus on hepatocytes, the method comprising:

(a) receiving a training set for generating a hepatotoxicity or pathology model, wherein the training set comprises phenotypic information for various stimuli some of which are known to induce hepatotoxic responses or pathology responses and others which are known to not induce hepatotoxic or pathology responses, wherein the phenotypic information for each stimulus comprises a plurality of features derived from images of first samples of hepatocytes exposed to a stimulus under a first set of conditions and from images of second samples of hepatocytes exposed to the stimulus under a second set of conditions;

(b) from the training set, generating the hepatotoxicity model or pathology model for classifying stimuli as to hepatotoxicity or pathology based on at least some of the plurality of features obtained from hepatocytes treated with a stimulus to be classified by the hepatotoxicity model or pathology model.

22. The method of claim 21, further comprising combining features from images of the first and second samples.

23. The method of claim 21, wherein the first set of conditions comprises contacting the first sample with a first marker set, and wherein the second set of conditions comprises contacting the second sample with a second marker set.