SRM/MRM Assays For Notch Pathway Proteins

• US 20200132696A1
• Filed: 10/29/2019
• Published: 04/30/2020
• Est. Priority Date: 10/30/2018
• Status: Abandoned Application

• Current Assignee: Expression Pathology, Inc. (NantWorks, LLC)
• Original Assignee: Expression Pathology, Inc. (NantWorks, LLC)
• Inventors: HEMBROUGH, Todd, CECCHI, Fabiola, SCHWARTZ, Sarit, SCOTT, Kerry
• Application Number:
  US16/666,956
• Publication Number:
  US 20200132696A1
• Time in Patent Office: Days
• CPC Class Codes: G01N 2560/00 Chemical aspects of mass spectrometric analysis of biological material
• 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 2800/56 Staging of a disease; Further complications associated with the disease
• CPC Class Codes: G01N 33/6848 Methods of protein analysis involving mass spectrometry
• CPC Class Codes: G01N 33/6851 Methods of protein analysis involving laser desorption ionisation mass spectrometry

Abstract

Methods are provided for detecting and quantifying the DLL1, DLL3, JAG1, JAG2, Notch1, Notch 2, Notch 3, Notch 4, and/or DLL4 proteins in biological samples, such as a formalin fixed paraffin embedded tissue samples, using mass spectrometry. Additionally, methods are provided for treating cancer based upon the level of the DLL1, DLL3, JAG1, JAG2, Notch1, Notch 2, Notch 3, Notch 4, and/or DLL4 proteins in the biological samples.

Claims

1. A method for measuring the level of protein in a biological sample of formalin fixed tissue, the method comprising

detecting and/or quantifying by mass spectrometry an amount of one or more modified or unmodified fragment peptides derived from the protein in a protein digest prepared from said biological sample;

and calculating the level of said protein in said sample;

wherein said protein is selected from the group consisting of DLL1, DLL3, JAG1, JAG2, Notch1, Notch 2, Notch 3, Notch 4, and DLL4 protein.

2. The method of claim 1, further comprising the step of fractionating said protein digest prior to detecting and/or quantifying the amount of said one or more modified or unmodified fragment peptides.

3. The method of claim 2, wherein said fractionating step is selected from the group consisting of liquid chromatography, nanoreversed phase liquid chromatography, high performance liquid chromatography and reverse phase high performance liquid chromatography.

4. The method of claim 1, wherein said protein digest comprises a protease digest.

5. The method of claim 4, wherein said protein digest comprises a trypsin digest.

6. The method of claim 1, wherein said mass spectrometry comprises tandem mass spectrometry, ion trap mass spectrometry, triple quadrupole mass spectrometry, ion trap/quadrupole hybrid mass spectrometry, MALDI-TOF mass spectrometry, MALDI mass spectrometry, and/or time of flight mass spectrometry.

7. The method of claim 6, wherein a mode of mass spectrometry used is Selected Reaction Monitoring (SRM), Multiple Reaction Monitoring (MRM), multiple Selected Reaction Monitoring (mSRM), and/or intelligent Selected Reaction Monitoring (iSRM).

8. The method of claim 1, wherein said protein is DLL1 and said one or more fragment peptides are the peptides of SEQ ID NO:

1 and/or SEQ ID NO;

2.

9. The method of claim 1, wherein said protein is DLL3 and said one or more fragment peptides are the peptides of SEQ ID NO:

3 and/or SEQ ID NO;

4.

10. The method of claim 1, wherein said protein is JAG1 and said one or more fragment peptides are the peptides of SEQ ID NO:

5 and/or SEQ ID NO;

6.

11. The method of claim 1, wherein said protein is JAG2 and said one or more fragment peptides are the peptides of SEQ ID NO:

7 and/or SEQ ID NO;

8.

12. The method of claim 1, wherein said protein is Notch1 and said one or more fragment peptides are the peptides of SEQ ID NO:

9 and/or SEQ ID NO;

10.

13. The method of claim 1, wherein said protein is Notch2 and said one or more fragment peptides are the peptides of SEQ ID NO:

11 and/or SEQ ID NO;

12.

14. The method of claim 1, wherein said protein is Notch3 and said one or more fragment peptides are the peptides of SEQ ID NO:

13 and/or SEQ ID NO;

14.

15. The method of claim 1, wherein said protein is Notch4 and said one or more fragment peptides are the peptides of SEQ ID NO:

15 and/or SEQ ID NO;

16.

16. The method of claim 1, wherein said protein is DLL4 and said one or more fragment peptides are the peptides of SEQ ID NO:

17 and/or SEQ ID NO;

18.

17. The method of claim 1, wherein the tissue is paraffin embedded tissue.

18. The method of claim 1, wherein the tissue is obtained from a tumor.

19. The method of claim 18, wherein the tumor is a primary tumor.

20. The method of claim 18, wherein the tumor is a secondary tumor.

21. The method of claim 1, wherein quantifying said one or more fragment peptides comprises comparing the amount of said one or more fragment peptides in one biological sample to an amount of the same one or more fragment peptides in a different and separate biological sample.

22. The method of claim 1, wherein quantifying said one or more fragment peptides comprises determining the amount of said one or more fragment peptides in a biological sample by comparison to an added internal standard peptide of known amount having the same amino acid sequence.

23. The method of claim 22, wherein the internal standard peptide is an isotopically labeled peptide selected from ¹⁸O, ¹⁷O, ³⁴S, ¹⁵N, ¹³C, ²H and a combination thereof.

24. The method of claim 1, wherein detecting and/or quantifying the amount of the one or more fragment peptides in the protein digest indicates the presence of the corresponding protein and an association with a diagnostic stage/grade/status of cancer in a subject.

25. The method of claim 24, further comprising correlating results of said detecting and/or quantifying the amount of said one or more fragment peptides, or the level of the corresponding protein, to a cancer treatment therapy for the subject.

26. The method of claim 25, further comprising detecting and/or quantifying the amount of other proteins or peptides from other proteins in a multiplex format to provide additional information about a cancer treatment therapy for the subject.