Claims for Patent: 9,261,506

Summary for Patent: 9,261,506

Title:	SRM/MRM assay for subtyping lung histology
Abstract:	The current disclosure provides for specific peptides, and derived ionization characteristics of the peptides, from the KRT5, KRT7, NapsinA, TTF1, TP63, and/or MUC1 proteins that are particularly advantageous for quantifying the KRT5, KRT7, NapsinA, TTF1, TP63, and/or MUC1 proteins directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring (SRM) mass spectrometry, or what can also be termed as Multiple Reaction Monitoring (MRM) mass spectrometry. Such biological samples are chemically preserved and fixed wherein said biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded. A protein sample is prepared from said biological sample using the Liquid Tissue.TM. reagents and protocol and the KRT5, KRT7, NapsinA, TTF1, TP63, and/or MUC1 proteins are quantitated in the Liquid Tissue.TM. sample by the method of SRM/MRM mass spectrometry by quantitating in the protein sample at least one or more of the peptides described. These peptides can be quantitated if they reside in a modified or an unmodified form. An example of a modified form of a KRT5, KRT7, NapsinA, TTF1, TP63, and MUC1 fragment peptide is phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.
Inventor(s):	Krizman; David B. (Gaithersburg, MD), Liao; Wei-Li (Herndon, VA), Thyparambil; Sheeno (Frederick, MD), Hembrough; Todd (Gaithersburg, MD)
Assignee:	EXPRESSION PATHOLOGY, INC. (Rockville, MD)
Application Number:	14/543,610
Patent Claims:	1. A method for measuring the level of the KRT5, KRT7, TTF1, and TP63 proteins in a human biological sample of formalin-fixed tissue for diagnosis, evaluation, and/or treatment of lung cancer, comprising detecting and quantifying the amount of a KRT5 fragment peptide, a KRT7 fragment peptide, a TTF1 fragment peptide, and a TP63 fragment peptide in a protein digest prepared from said biological sample using mass spectrometry; and calculating the level of KRT5, KRT7, TTF1, and TP63 protein in said sample; wherein the KRT5 fragment peptide is the peptide of SEQ ID NO:2, the KRT7 peptide is the peptide of SEQ ID NO:3, the TTF1 peptide is the peptide of SEQ ID NO:8 and the TP63 peptide is the peptide of SEQ ID NO: 11, and wherein said amount is a relative amount or an absolute amount. 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 KRT5, KRT7, TTF1, and TP63 fragment peptides. 3. The method of claim 1, wherein said protein digest comprises a protease digest. 4. The method of claim 1, wherein quantifying the KRT5, KRT7, TTF1, and TP63 fragment peptides comprises comparing an amount of one or more KRT5, KRT7, TTF1, and TP63 fragment peptides in one biological sample to the amount of the same KRT5, KRT7, TTF1, and TP63 fragment peptides in a different and separate biological sample. 5. The method of claim 1, wherein quantifying the KRT5, KRT7, TTF1, and TP63 fragment peptides comprises determining the amount of each of the KRT5, KRT7, TTF1, and TP63, fragment peptides in a biological sample by comparison to an added internal standard peptide of known amount, wherein each of the KRT5, KRT7, TTF1, and TP63, fragment peptides in the biological sample is compared to an internal standard peptide having the same amino acid sequence. 6. The method of claim 5, wherein the internal standard peptide is an isotopically labeled peptide. 7. The method of claim 1, wherein detecting and quantifying the amount of the KRT5, KRT7, TTF1, and TP63 protein fragment peptides in the protein digest indicates the presence of KRT5, KRT7, TTF1, and TP63, protein and an association with cancer in a patient or subject. 8. The method of claim 7, further comprising correlating the results of said detecting and quantifying the amount of the KRT5, KRT7, TTF1, and TP63 fragment peptides, or the amount of said KRT5, KRT7, TTF1, and TP63 proteins to the diagnostic stage/grade/status of the cancer. 9. The method of claim 8, wherein correlating the results of said detecting and quantifying the amount of the KRT5, KRT7, TTF1, and TP63 fragment peptides, or the amount of said KRT5, KRT7, TTF1, and TP63 proteins to the diagnostic stage/grade/status of the cancer is combined with detecting and/or quantifying the amount of other proteins or peptides from other proteins in a multiplex format to provide additional information about the diagnostic stage/grade/status of the cancer. 10. The method of claim 8, further comprising administering to a patient or subject from which said biological sample was obtained a therapeutically effective amount of a therapeutic agent, wherein the therapeutic agent and/or amount of the therapeutic agent administered is based upon the amount of the KRT5, KRT7, TTF1, and TP63 fragment peptides or the amount of KRT5, KRT7, TTF1, and TP63 proteins. 11. The method of claim 10, wherein the treatment or the therapeutic agent is directed to cancer cells expressing KRT5, KRT7, TTF1, and TP63. 12. The method of claim 11, wherein said therapeutic is selected from pemetrexed and bevacizumab. 13. The method of claim 1, wherein the tissue is paraffin-embedded tissue. 14. The method of claim 1, wherein the tissue is obtained from a tumor.

Details for Patent 9,261,506

Applicant	Tradename	Biologic Ingredient	Dosage Form	BLA	Approval Date	Patent No.	Expiredate
Genentech, Inc.	AVASTIN	bevacizumab	Injection	125085	02/26/2004		2032-05-15