Reagent sets and gene signatures for renal tubule injury

• US 20060057066A1
• Filed: 07/18/2005
• Published: 03/16/2006
• Est. Priority Date: 07/19/2004
• Status: Active Grant

• Current Assignee: US Department of Health and Human Services (Government of the United States of America)
• Original Assignee: Entelos, Inc. (SilkRoad Inc.)
• Inventors: Jarnagin, Kurt, Fielden, Mark, Natsoulis, Georges, Kolaja, Kyle
• Granted Patent: US 7,588,892 B2
• Time in Patent Office: Days
• US Class Current: 424/9.100
• CPC Class Codes: G01N 2500/00 Screening for compounds of potential therapeutic value
• CPC Class Codes: G01N 2800/347 Renal failures; Glomerular diseases; Tubulointerstitial diseases, e.g. nephritic syndrome, glomerulonephritis; Renovascular diseases, e.g. renal artery occlusion, nephropathy
• CPC Class Codes: G01N 33/6893 related to diseases not provided for elsewhere

Abstract

The invention discloses reagent sets and gene signatures for predicting onset of renal tubule injury in a subject. The invention also provides a necessary set of 186 genes useful for generating signatures of varying size and performance capable of predicting onset of renal tubule injury. The invention also provides methods, apparatuses and reagents useful for predicting future renal tubule injury based on expression levels of genes in the signatures. In one particular embodiment the invention provides a method for predict whether a compound will induce renal tubule injury using gene expression data from sub-acute treatments.

Claims

1. A method for testing whether a compound will induce renal tubule injury in a test subject, the method comprising:

a) administering a dose of compound to at least one test subject;

b) after a selected time period, obtaining a biological sample from the at least one test subject;

c) measuring the expression levels in the biological sample of at least a plurality of genes selected from Table 4; and

d) determining whether the sample is in the positive class for renal tubule injury using a classifier comprising at least the plurality of genes for which the expression levels are measured.

2. The method of claim 1, wherein the test subject is a mammal selected from the group consisting of a human, cat, dog, monkey, mouse, pig, rabbit, and rat.

3. The method of claim 1, wherein the test compound is administered by route of IV, PO, or IP.

4. The method of claim 1, wherein the dose administered does not cause histological or clinical evidence of renal tubule injury at about 5 days.

5. The method of claim 1, wherein the biological sample comprises kidney tissue.

6. The method of claim 1, wherein the selected period of time is about 5 days or fewer.

7. The method of claim 1, wherein said selected period of time is at least about 28 days.

8. The method of claim 1, wherein the expression levels are measured as log₁₀ ratios of a compound-treated biological sample to a compound-untreated biological sample.

9. The method of claim 1, wherein the classifier is a non-linear classifier.

10. The method of claim 1, wherein the classifier is a linear classifier.

11. The method of claim 10, wherein the linear classifier comprises the genes and weights corresponding to any one of iterations 1 through 5 in Table 4.

12. The method of claim 11, wherein the linear classifier for renal tubule injury classifies the nephrotoxic versus non-nephrotoxic compounds listed in Table 2 with a training log odds ratio of greater than or equal to 4.35.

13. The method of claim 1, wherein the plurality of genes from Table 4 includes at least 4 genes selected having at least 2% of the total impact of all of the genes in Table 4.

14. The method of claim 1, wherein the plurality of genes from Table 4 includes at least 8 genes selected having at least 4% of the total impact of all of the genes in Table 4.

15. A reagent set for testing whether renal tubule injury will occur in a test subject comprising a plurality of polynucleotides or polypeptides representing a plurality of genes selected from Table 4.

16. The reagent set of claim 15, wherein the plurality of genes is the set of genes in any one of iterations 1 through 5 in Table 4.

17. The reagent set of claim 15, wherein the plurality of genes are selected from a linear classifier capable of classifying renal tubule injury with a training log odds ratio of greater than or equal to 4.35.

18. The reagent set of claim 15, wherein the plurality of genes includes at least 4 genes having at least 2% of the total impact of all of the genes in Table 4.

19. The reagent set of claim 15, wherein the plurality of genes includes at least 8 genes having at least 4% of the total impact of the genes in Table 4.

20. The reagent set of claim 15, wherein the reagents are polynucleotide probes capable of hybridizing to the plurality of genes selected from Table 4.

21. The reagent set of claim 20, wherein the polynucleotide probes are primers for amplification of the plurality of genes.

22. The reagent set of claim 20, wherein the polynucleotide probes are immobilized on one or more solid surfaces.

23. The reagent set of claim 15, wherein the reagents are polypeptides that bind to a plurality of proteins encoded by the plurality of genes selected from Table 4.

24. The reagent set of claim 23, wherein the proteins are secreted proteins.

25. An apparatus for predicting whether renal tubule injury will occur in a test subject comprising a reagent set according to claim 15.

26. The apparatus of claim 25, wherein the reagents are polynucleotides.

27. The apparatus of claim 25, wherein the reagents are polypeptides.

28. A set of genes useful for testing whether a compound will induce renal tubule injury comprising a random selection of at least 10% of the genes from Table 4, wherein the addition of said randomly selected genes to a fully depleted gene set for the renal tubule injury classification question increases the average logodds ratio of the linear classifiers generated by the depleted set to at least about 4.0.

29. The set of claim 28, wherein the randomly selected percentage of genes from the necessary set is at least 20% and the average logodds ratio is increased to at least about 4.5.

30. A reagent set for classifying renal tubule injury comprising a set of polynucleotides or polypeptides representing a plurality of genes selected from Table 4, wherein the addition of a random selection of at least 10% of said plurality of genes to the fully depleted set for the renal tubule injury classification question increases the average logodds ratio of the linear classifiers generated by the depleted set by at least 3-fold.

31. The reagent set of claim 30, wherein the random selection is of at least 20% of said plurality of genes and the average logodds ratio of the linear classifiers generated by the depleted set by at least 2-fold.

32. An apparatus comprising a set of polynucleotides capable of specifically binding to the reagent set of claim 30.