METHODS FOR DIAGNOSING, PROGNOSING, OR THERANOSING A CONDITION USING RARE CELLS

• US 20100233693A1
• Filed: 04/16/2008
• Published: 09/16/2010
• Est. Priority Date: 04/16/2007
• Status: Abandoned Application

• Current Assignee: On-Q-ity
• Original Assignee: On-Q-ity
• Inventors: Stoughton, Roland, Wu, Lena, Kopf-Sill, Anne R.
• Application Number:
  US12/595,949
• Publication Number:
  US 20100233693A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G01N 1/31 Apparatus therefor
• CPC Class Codes: G01N 2333/705 Assays involving receptors, cell surface antigens or cell surface determinants
• CPC Class Codes: G01N 2333/71 for growth factors; for growth regulators
• CPC Class Codes: G01N 2333/912 transferring phosphorus containing groups, e.g. kinases (2.7)
• CPC Class Codes: G01N 2333/96433 Serine endopeptidases (3.4.21)
• CPC Class Codes: G01N 33/5091 for testing the pathological state of an organism
• CPC Class Codes: G01N 33/57484 involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
• CPC Class Codes: G01N 33/57488 involving compounds identifable in body fluids
• CPC Class Codes: G01N 33/57492 involving compounds localized on the membrane of tumor or cancer cells

Abstract

The invention encompasses methods for diagnosing, theranosing, or prognosing a condition in a patient based on the results of one or more analysis methods. The methods can comprise enriching a sample obtained from the patient for one or more rare cells. The analysis methods can include performing enumeration of the one or more rare cells or cell subtypes, performing nucleic acid analysis, or detecting a serum marker.

Claims

1. A method for diagnosing, theranosing, or prognosing a condition in a patient comprising:

detecting a serum marker shed from a primary tumor in a first sample;

enumerating one or more circulating tumor cells in a second sample from said patient; and

diagnosing, prognosing, or theranosing the condition in said patient based on said detecting a serum marker and said enumerating one or more circulating tumor cells.

2. The method of claim 1, wherein the first or second sample is a blood sample.

3. The method of claim 1, wherein the first and second sample are the same sample.

4. The method of claim 1, further comprising performing one or more nucleic acid analysis on said circulating tumor cells.

5. The method of claim 1, wherein the serum marker is hTR, hTERT, TEP1, estrogen, epidermal growth factor, transforming growth factor, prostaglandin E2, estrogen-regulated proteins such as pS2, interleukins (eg., IL-10), S-100 protein, vimentin, epithelial membrane antigen, prostate specific antigen, bcl-2, CA15-3, CA 19-9, mucin core carbohydrate, Tn antigen, Tn-like antigen, alpha-lactalbumin, lipid-associated sialic acid, galactose-N-acetylgalactosamine, GCDFP-15, Le(y)-related carbohydrate antigen, CA 125, urokinase-type plasminogen activator, uPA related antigen, uPA related complex, uPA receptor, beta-glucuronidase, CD31, CD44 splice variants, blood group antigens, ABH, Lewis, MN, MK, DUPAN2, LCAP, TAG-12, TPA, TPS, carcinoembryonic antigen, squamous cell carcinoma antigen, tissue polypeptide specific antigen, sialyl TN mucin, placental alkaline phosphatase, BPC-1, or CC2.

6. The method of claim 1, wherein enumerating the number of CTCs in a sample from said patient comprises flowing said sample through a microfluidic device that selectively enriches one or more circulating tumor cells.

7. The method of claim 5, wherein the microfluidic device enriches one or more CTCs based on size, affinity, deformability, or shape.

8. The method of claim 5, wherein the microfluidic device comprises an array of obstacles and/or one or more binding moieties.

9. The method of claim 8, wherein the one or more binding moieties comprise anti-EpCAM.

10. The method of claim 1, further comprising subjecting said patient to one or more therapeutic treatments;

repeating said detecting a serum marker and said enumerating one or more circulating tumor cells; and

diagnosing, prognosing or theranosing the condition in the patient.

11. A method for diagnosing, theranosing, or prognosing a condition in a patient comprising:

performing one or more nucleic acid analysis on a first sample obtained from said patient;

enumerating one or more rare cells in a second sample from said patient; and

diagnosing, theranosing, or prognosing the condition in said patient based on said enumerating one or more rare cells and said performing one or more nucleic acid analysis.

12. The method of claim 11, wherein the first sample is a biopsy sample, the second sample is a blood sample, or the first and second sample are the same sample.

13. The method of claim 11, wherein performing one or more nucleic acid analysis comprises SNP analysis, mRNA analysis, or sequencing.

14. The method of claim 11, wherein the one or more rare cells comprise circulating tumor cells.

15. The method of claim 11, wherein the one or more rare cells are enriched using a microfluidic device.

16. The method of claim 15, wherein the microfluidic device comprises one or more binding moieties and/or an array of obstacles.

17. The method of claim 16, wherein the one or more binding moieties comprise anti-EpCAM.

18. The method of claim 11, further comprising subjecting said patient to one or more therapeutic treatments;

repeating said performing one or more nucleic acid analysis and said enumerating one or more rare cells; and

diagnosing, prognosing or theranosing the condition in the patient.

19. A method for diagnosing, theranosing, or prognosing a condition in a subject, comprising:

a) enriching one or more rare cells from a sample obtained from said subject using a microfluidic device;

b) performing a first analysis of one or more cell subtypes of said one or more rare cells; and

c) evaluating the result of said first analysis to make said diagnosis, theranosis, or prognosis.

20. The method of claim 19, further comprising labeling one or more rare cells using a first label and labeling one or more cell subtypes using a second label.

21. The method of claim 20, wherein the first label is distinct from the second label.

22. The method of claim 20, wherein the first label and the second label have a light absorption wavelength or a fluorescence emission wavelength that is separated by more than 5, 10, 25, 30, 40, or 50 nm.

23. The method of claim 19, wherein the first analysis comprises enumerating the one or more cell subtypes.

24. The method of claim 19, wherein the cell subtypes comprise circulating tumor cells, circulating tumor stem cells, circulating stem cells, or stem cells.

25. The method of claim 19, wherein the microfluidic device comprises an array of obstacles and/or one or more binding moieties.

26. The method of claim 25, wherein the one or more binding moieties comprise anti-EpCAM.

27. The method of claim 19, further comprising subjecting said enriched one or more rare cells to one or more therapeutic treatments after step b), performing a second analysis of one or more cell subtypes, and evaluating the results of said first and second analysis to make said diagnosis, theranosis, or prognosis.

28. The method of claim 19, wherein steps a)-c) are performed at a first time and a second time, and the results obtained from at the first time and the results obtained at the second time are evaluated to make said diagnosis, theranosis, or prognosis.

29. The method of claim 28, further comprising subjecting said patient to one or more therapeutic treatments between said first time and said second time.

30. A method for diagnosing, theranosing, or prognosing a condition in a patient comprising:

enriching one or more CTCs in a sample obtained from said patient;

subjecting said one or more CTCs to one or more therapeutic treatments or culturing said one or more circulating tumor cells; and

diagnosing, theranosing, or prognosing the condition in the patient.

31. The method of claim 30, wherein the one or more CTCs are enriched using a microfluidic device comprising an array of obstacles and/or one or more binding moieties.

32. The method of claim 30, wherein the one or more therapeutic treatments comprise a chemotherapy agent.

33. The method of claim 31, wherein the one or more CTCs are released or are not released from the microfluidic device prior to culturing said one or more circulating tumor cells.

34. The method of claim 30, further comprising subjecting said one or more CTCs to one or more therapeutic treatments after said culturing said one or more circulating tumor cells;

and/or

identifying one or more therapeutic treatments based on the whether said CTCs respond to said one or more therapeutic treatments.

35. The method of claim 33, further comprising analyzing said one or more CTCs before and after said subjecting said one or more CTCs to one or more therapeutic treatments.

36. A business method comprising:

enriching one or more rare cells in a first sample obtained from a patient using a microfluidic device, wherein the microfluidic comprises an array of obstacles and/or one or more binding moieties;

enumerating said one or more rare cells;

analyzing a second sample from the patient by performing nucleic acid analysis or detecting a serum marker;

diagnosing, theranosing, or prognosing a condition in the patient; and

providing a report on said condition in exchange for a fee.

37. A kit for diagnosing, theranosing, or prognosing a condition in a patient comprising:

a microfluidic device comprising an array of obstacles and/or one or more binding moieties; and

one or more reagents for performing nucleic acid analysis, detecting a serum marker, and/or culturing cells.