Specific microarrays for breast cancer screening

• US 20030087265A1
• Filed: 05/20/2002
• Published: 05/08/2003
• Est. Priority Date: 01/21/2000
• Status: Abandoned Application

• Current Assignee: Thoams Jefferson University
• Original Assignee: Thoams Jefferson University
• Inventors: Sauter, Edward, Dubois, Garrett
• Application Number:
  US10/151,847
• Publication Number:
  US 20030087265A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: G01N 2800/52 Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
• CPC Class Codes: G01N 33/57415 of breast

Abstract

Microarrays specific for breast cancer are provided. Also provided are methods for detecting breast cancer in patients or screening therapeutics for the treatment or prevention of breast cancer by analyzing expression levels of specific genes in BECs or quantifying specific protein levels in breast ductal fluid.

Claims

1. A microarray comprising a plurality of oligonucleotide probes immobilized on a surface of a solid support, wherein

a) each different oligonucleotide probe is localized in a predetermined region of said surface;

and

b) said each oligonucleotide probe selectively hybridizes to an mRNA or a nucleic acid derived therefrom, wherein said mRNA is a transcript of a gene, wherein changes in expression levels of said gene are associated with breast cancer.

2. The microarray of claim 1, wherein said gene or a gene product thereof is involved in apoptosis.

3. The microarray of claim 1, wherein said gene encodes an insulin-like growth factor.

4. A kit comprising the microarray of claim 1 and one or more reagents for use in the assay to be performed.

5. A method for detecting breast cancer in a patient comprising:

a) obtaining a nucleic acid sample from BECs of said patient, wherein said nucleic acid sample contains a population of mRNA or nucleic acids derived therefrom;

b) providing a microarray according to claim 1;

c) hybridizing said nucleic acid sample to said microarray to form hybrid duplexes between nucleic acids on said nucleic acid sample and said oligonucleotide probes on said microarray; and

d) determining differences in hybridization compared to that from a non-cancer subject wherein said differences in hybridization indicate breast cancer in said patient.

6. The method of claim 5, wherein said BECs are obtained from breast ductal fluid.

7. The method of claim 6, wherein said BECs are obtained from NAF.

8. The method of claim 6, wherein said BECs are obtained from mammary ductal irrigation.

9. A method for determining efficacy of a therapeutic in treating or preventing breast cancer comprising:

a) administering an appropriate amount of said therapeutic to a patient having breast cancer;

b) obtaining a nucleic acid sample from BECs of said patient, wherein said nucleic acid sample contains a population of mRNA or nucleic acids derived therefrom;

c) providing a microarray according to claim 1;

d) hybridizing said nucleic acid sample to said microarray to form hybrid duplexes between nucleic acids on said nucleic acid sample and said oligonucleotide probes on said microarray; and

e) determining differences in hybridization compared to that prior to the administration of said therapeutic wherein said differences in hybridization indicate the efficacy of said therapeutic.

10. The method of claim 9, wherein said BECs are obtained from breast ductal fluid.

11. The method of claim 10, wherein said BECs are obtained from NAF.

12. The method of claim 10, wherein said BECs are obtained from mammary ductal irrigation.

13. A microarray comprising a plurality of protein-capture agents immobilized on a surface of a solid support, wherein

a) each different protein-capture agent is localized in a predetermined region of said surface;

and

b) said each protein-capture agent selectively hybridizes to a protein, wherein changes in quantities of said protein is associated with breast cancer.

14. The microarray of claim 13, wherein said protein-capture agents aptamers.

15. The microarray of claim 13, wherein said protein-capture agents are polypeptides.

16. The microarray of claim 13, wherein said protein is selected from erbB-1;

HER-2/neu;

hTERT;

erbB-2;

hst-1;

KDR;

int-2;

cyclin D1, 2, 3;

CEA;

H-ras;

K-ras;

mammoglobin;

PSA;

IGFBP-1, -2, -4, -5, -6;

hK2;

IGFBP-3;

or p53.

17. A kit comprising the microarray of claim 13 and one or more reagents for use in the assay to be performed.

18. A method for detecting breast cancer in a patient comprising:

a) obtaining a sample from breast ductal fluid of said patient, wherein said sample contains a population of proteins;

b) providing a microarray according to claim 13;

c) hybridizing said sample to said microarray to form hybrid duplexes between said proteins on said sample and said protein-capture agents on said microarray; and

d) determining differences in hybridization compared to that from a non-cancer subject, wherein said differences in hybridization indicate breast cancer in said patient

19. The method of claim 18, wherein said breast ductal fluid is NAF or mammary ductal irrigation.

20. A method for determining efficacy of a therapeutic in treating or preventing breast cancer comprising:

a) administering an appropriate amount of said therapeutic to a patient having breast cancer;

b) obtaining a sample from breast ductal fluid of said patient, wherein said sample contains a population of proteins;

c) providing a microarray according to claim 13;

d) hybridizing said sample to said microarray to form hybrid duplexes between said proteins on said sample and said protein-capture agents on said microarray; and

e) determining differences in hybridization compared to that prior to the administration of said therapeutic, wherein said differences in hybridization indicate the efficacy of said therapeutic.

21. The method of claim 20, wherein said breast ductal fluid is NAF or mammary ductal irrigation.

22. A method for identifying proteins associated with breast cancer comprising:

a) obtaining a sample from mammary ductal fluid of a patient having breast cancer;

b) providing a proteinchip array having a selectivity condition, wherein the selectivity condition is defined by an adsorbent and an eluant;

c) contacting said sample to said proteinchip array;

d) washing said proteinchip array with said eluant; and

e) detecting and quantifying proteins retained by said proteinchip array by a laser desorption/ionization time-of-flight mass spectrometer, wherein one or more said proteins differentially present on said proteinchip array compared to that from a non-cancer subject are identified as the proteins associated with breast cancer.

23. The method of claim 22, wherein said breast ductal fluid is NAF or mammary ductal irrigation.

24. A method for detecting breast cancer in a patient comprising:

a) obtaining a sample from mammary ductal fluid of said patient, wherein said sample comprises at least one breast cancer related protein;

b) providing a proteinchip array having a selectivity condition, wherein the selectivity condition is defined by an adsorbent and an eluant, wherein the selectivity condition allows said at least one breast cancer related protein be retained by said proteinchip array;

c) contacting said sample to said proteinchip array;

d) washing said proteinchip array with said eluant;

e) detecting and quantifying said at least one breast cancer related protein retained by said proteinchip array by a laser desorption/ionization time-of-flight mass spectrometer; and

f) determining differences in quantities of said at least one breast cancer related protein retained by said proteinchip array compared to that from a non-cancer patient, wherein any differences in quantities indicate breast cancer in said patient.

25. The method of claim 24, wherein said breast ductal fluid is NAF or mammary ductal irrigation.

26. A method for determining efficacy of a therapeutic in treating or preventing breast cancer comprising:

a) administering an appropriate amount of said therapeutic to a patient having breast cancer;

b) obtaining a sample from mammary ductal fluid of said patient, wherein said sample comprises at least one breast cancer related protein;

c) providing a proteinchip array having a selectivity condition, wherein the selectivity condition is defined by an adsorbent and an eluant, wherein the selectivity condition allows said at least one breast cancer related protein be retained by said proteinchip array;

d) contacting said sample to said proteinchip array;

e) washing said proteinchip array with said eluant;

f) detecting and quantifying said at least one breast cancer related protein retained by said proteinchip array by a laser desorption/ionization time-of-flight mass spectrometer; and

g) detecting differences in quantities of said at least one breast cancer related protein retained by said proteinchip array compared to that prior to the administration of said therapeutic, wherein any differences in quantities indicate the efficacy of said therapeutic.

27. The method of claim 26, wherein said breast ductal fluid is NAF or mammary ductal irrigation.