Transcription biomarkers of biological responses and methods

Inventors: Shelley Force Aldred (Hayward, CA); Nathan D. Trinklein (Redwood City, CA); Michael Rose (Walnut Creek, CA); Patrick Collins (Millbrae, CA)

Assignee: SwitchGear Genomics, Inc.

C12Q1/6883 C12Q2600/136 C12Q1/6886

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Quick Facts

Patent No.: US 8,815,779
App. No.: 12/586,131
Granted: Aug 26, 2014
Kind: B2

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Abstract

This invention provides transcription regulatory control sequences, the activity of which function as biomarkers for a variety of biological responses. This invention also provides expression constructs in which a biomarker transcription regulatory sequence is operably linked with a sequence for a reporter. Cells that comprise these expression constructs can be used in assays to identify conditions that modulate activity of the biological response.

Claims (76)

1. A method for determining activation of an estrogen response in a cell comprising:

a) providing at least one cell comprising an expression construct comprising a sequence comprising an estrogen response biomarker promoter operatively linked with a heterologous sequence encoding a reporter, wherein the estrogen response biomarker promoter is selected from:

(1) SEQ ID NO. 19, SEQ ID NO. 20, SEQ ID NO. 23, SEQ ID NO. 25, SEQ ID NO. 28, SEQ ID NO. 29, SEQ ID NO. 533, SEQ ID NO. 565, SEQ ID NO. 634, SEQ ID NO. 641 or SEQ ID NO. 653;

(2) a sequence of at least 50 nucleotides having at least 95% sequence identity to a sequence of (1); and

(3) a fragment of at least 50 nucleotides of a sequence of (1);

b) contacting the cell with a sample comprising a test compound;

c) after step (b), measuring expression of the reporter; and

d) correlating the measurement of expression of the reporter with the estrogen response, wherein increased expression of the reporter compared to a control, results from activation of the estrogen response in the cell.

2. The method of claim 1 further comprising:

i) measuring the activity of the reporter in an absence of the test compound or with a control compound;

ii) measuring activity of the reporter in a presence of the test compound;

iii) measuring a difference or ratio of reporter activity between a cell exposed to the test compound and a cell not exposed to the test compound; and

iv) correlating the difference or ratio with the estrogen response

wherein an increase in activity of the reporter in the presence of the test compound compared with activity of the reporter in the absence of the test compound or with a control compound indicates that the test compound induces the estrogen response.

3. The method of claim 1 wherein the estrogen response biomarker promoter has an induction ratio of at least 2 when the cell is exposed to a medium having a concentration of β-estradiol of 10 nM.

4. The method of claim 1 wherein the test compound is a small organic molecule having a size up to about 5000 Da.

5. The method of claim 1 wherein the test compound is a nucleic acid derivative selected from a small interfering RNA, a micro RNA mimic and a micro RNA inhibitor.

6. The method of claim 1 wherein the at least one cell is a plurality of cells, each cell of the plurality comprising an expression construct comprising an estrogen response biomarker promoter of a different gene.

7. The method of claim 1 wherein the expression construct is comprised in a plasmid, a virus, a transposon vector, or an artificial chromosome vector.

8. The method of claim 1 wherein the expression construct is integrated into a chromosome in the cell.

9. The method of claim 1 wherein the reporter is a light-emitting reporter, a fluorescent reporter or a colorimetric reporter.

10. The method of claim 1 wherein the estrogen response biomarker promoter is SEQ ID NO. 19.

11. The method of claim 1 wherein the estrogen response biomarker promoter is SEQ ID NO. 20.

12. The method of claim 1 wherein the estrogen response biomarker promoter is SEQ ID NO. 23.

13. The method of claim 1 wherein the estrogen response biomarker promoter is SEQ ID NO. 25.

14. The method of claim 1 wherein the estrogen response biomarker promoter is SEQ ID NO. 28.

15. The method of claim 1 wherein the estrogen response biomarker promoter is SEQ ID NO. 29.

16. The method of claim 1 wherein the estrogen response biomarker promoter is SEQ ID NO. 533.

17. The method of claim 1 wherein the estrogen response biomarker promoter is SEQ ID NO. 634.

18. The method of claim 1 wherein the estrogen response biomarker promoter is SEQ ID NO. 641.

19. The method of claim 1 wherein the estrogen response biomarker promoter is SEQ ID NO. 653.

20. The method of claim 1 wherein the estrogen response biomarker promoter is selected from:

(I) SEQ ID NO. 19;