Methods of treating non-small cell lung carcinoma (NSCLC)

Patent metadata

Field	Value
Publication number	US-9523130-B2
Application number	US-201615225998-A
Country	US
Kind code	B2
Filing date	Aug 2, 2016
Priority date	Apr 14, 2006
Publication date	Dec 20, 2016
Grant date	Dec 20, 2016

Abstract

Novel gene deletions and translocations involving chromosome 2 resulting in fusion proteins combining part of Anaplastic Lymphoma Kinase (ALK) kinase with part of a secondary protein have been identified herein in human solid tumors, e.g. non-small cell lung carcinoma (NSCLC). Secondary proteins include Echinoderm Microtubule-Associated Protein-Like 4 (EML-4) and TRK-Fusion Gene (TFG). The EML4-ALK fusion protein, which retains ALK tyrosine kinase activity, was confirmed to drive the proliferation and survival of NSCLC characterized by this mutation. The invention therefore provides, in part, isolated polynucleotides and vectors encoding the disclosed mutant ALK kinase polypeptides, probes for detecting it, isolated mutant polypeptides, recombinant polypeptides, and reagents for detecting the fusion and truncated polypeptides. The disclosed identification of this new fusion protein enables methods for screening for compounds that inhibit the proteins, and methods for inhibiting the progression of a cancer characterized by the mutant polynucleotides or polypeptides.

First claim

What is claimed is:

1. A method for treating a human subject having a non-small cell lung carcinoma (NSCLC) that expresses a human Echinoderm Microtubule-Associated Protein-Like 4 (EML4)-Anaplastic Lymphoma Kinase (ALK) fusion polypeptide, comprising
administering to the human subject a small molecule that a) binds to the ATP-binding cleft and b) directly inhibits the kinase activity of the EML4-ALK fusion polypeptide, in an amount effective to treat the NSCLC, wherein i) the EML4-ALK fusion polypeptide comprises an amino acid sequence that is at least 95% identical to an amino acid sequence comprising EML4 amino acid residues 1-222 of SEQ ID NO: 3 and ALK amino acid residues 1116-1383 of SEQ ID NO: 5 and ii) the EML4 amino acid residues are amino-terminal to the ALK amino acid residues.

2. The method of claim 1 , wherein the amino acid sequence of the EML4-ALK fusion polypeptide comprises EML4 amino acid residues 1-222 of SEQ ID NO: 3.

3. The method of claim 1 , wherein the amino acid sequence of the EML4-ALK fusion polypeptide comprises ALK amino acid residues 1116-1383 of SEQ ID NO: 5.

4. The method of claim 1 , wherein the amino acid sequence of the EML4-ALK fusion polypeptide comprises EML4 amino acid residues 1-222 of SEQ ID NO: 3 and the ALK amino acid residues 1116-1383 of SEQ ID NO: 5.

5. The method of claim 1 , wherein the EML4-ALK fusion polypeptide comprises an amino acid sequence that is at least 97% identical to an amino acid sequence comprising EML4 amino acid residues 1-222 of SEQ ID NO: 3 and ALK amino acid residues 1116-1383 of SEQ ID NO: 5.

6. The method of claim 5 , wherein the amino acid sequence of the EML4-ALK fusion polypeptide comprises EML4 amino acid residues 1-222 of SEQ ID NO: 3.

7. The method of claim 5 , wherein the amino acid sequence of the EML4-ALK fusion polypeptide comprises ALK amino acid residues 1116-1383 of SEQ ID NO: 5.

8. The method of claim 1 , wherein the EML4-ALK fusion polypeptide comprises an amino acid sequence that is at least 98% identical to an amino acid sequence comprising EML4 amino acid residues 1-222 of SEQ ID NO: 3 and ALK amino acid residues 1116-1383 of SEQ ID NO: 5.

9. The method of claim 8 , wherein the amino acid sequence of the EML4-ALK fusion polypeptide comprises EML4 amino acid residues 1-222 of SEQ ID NO: 3.

10. The method of claim 8 , wherein the amino acid sequence of the EML4-ALK fusion polypeptide comprises ALK amino acid residues 1116-1383 of SEQ ID NO: 5.

11. The method of claim 1 , wherein the EML4-ALK fusion polypeptide comprises an amino acid sequence that is at least 99% identical to an amino acid sequence comprising EML4 amino acid residues 1-222 of SEQ ID NO: 3 and ALK amino acid residues 1116-1383 of SEQ ID NO: 5.

12. The method of claim 11 , wherein the amino acid sequence of the EML4-ALK fusion polypeptide comprises EML4 amino acid residues 1-222 of SEQ ID NO: 3.

13. The method of claim 11 , wherein the amino acid sequence of the EML4-ALK fusion polypeptide comprises ALK amino acid residues 1116-1383 of SEQ ID NO: 5.

14. A method for treating a human subject having a non-small cell lung carcinoma (NSCLC) that expresses a human Echinoderm Microtubule-Associated Protein-Like 4 (EML4)-Anaplastic Lymphoma Kinase (ALK) fusion polypeptide, wherein the EML4-ALK fusion polypeptide comprises an amino acid sequence that is at least 95% identical to the amino acid sequence of SEQ ID NO: 1, the method comprising
administering to the human subject a small molecule that a) binds to the ATP-binding cleft and b) directly inhibits the kinase activity of the EML4-ALK fusion polypeptide, in an amount effective to treat the NSCLC.

15. The method of claim 14 , wherein the EML4-ALK fusion polypeptide comprises an amino acid sequence that is at least 96% identical to the amino acid sequence of SEQ ID NO: 1.

16. The method of claim 14 , wherein the EML4-ALK fusion polypeptide comprises an amino acid sequence that is at least 97% identical to the amino acid sequence of SEQ ID NO: 1.

17. The method of claim 1 , wherein the EML4-ALK fusion polypeptide comprises an amino acid sequence that is at least 98% identical to the amino acid sequence of SEQ ID NO: 1.

18. The method of claim 14 , wherein the EML4-ALK fusion polypeptide comprises an amino acid sequence that is at least 99% identical to the amino acid sequence of SEQ ID NO: 1.

19. The method of claim 14 , wherein the EML4-ALK fusion polypeptide consists of an amino acid sequence that is at least 99% identical to the amino acid sequence of SEQ ID NO: 1.

20. The method of claim 14 , wherein the EML4-ALK fusion polypeptide comprises the amino acid sequence of SEQ ID NO: 1.

21. The method of claim 14 , wherein the EML4-ALK fusion polypeptide consists of the amino acid sequence of SEQ ID NO: 1.

22. A method for treating a human subject having a non-small cell lung carcinoma (NSCLC) that expresses a human Echinoderm Microtubule-Associated Protein-Like 4 (EML4)-Anaplastic Lymphoma Kinase (ALK) fusion polypeptide, wherein the EML4-ALK fusion polypeptide comprises an amino acid sequence that is at least 95% identical to the amino acid sequence of SEQ ID NO: 18, the method comprising
administering to the human subject a small molecule that a) binds to the ATP-binding cleft and b) directly inhibits the kinase activity of the EML4-ALK fusion polypeptide, in an amount effective to treat the NSCLC.

23. The method of claim 22 , wherein the EML4-ALK fusion polypeptide comprises an amino acid sequence that is at least 96% identical to the amino acid sequence of SEQ ID NO: 18.

24. The method of claim 22 , wherein the EML4-ALK fusion polypeptide comprises an amino acid sequence that is at least 97% identical to the amino acid sequence of SEQ ID NO: 18.

25. The method of claim 22 , wherein the EML4-ALK fusion polypeptide comprises an amino acid sequence that is at least 98% identical to the amino acid sequence of SEQ ID NO: 18.

26. The method of claim 22 , wherein the EML4-ALK fusion polypeptide comprises an amino acid sequence that is at least 99% identical to the amino acid sequence of SEQ ID NO: 18.

27. The method of claim 22 , wherein the EML4-ALK fusion polypeptide consists of an amino acid sequence that is at least 99% identical to the amino acid sequence of SEQ ID NO: 18.

28. The method of claim 22 , wherein the EML4-ALK fusion polypeptide comprises the amino acid sequence of SEQ ID NO: 18.

29. The method of claim 22 , wherein the EML4-ALK fusion polypeptide consists of the amino acid sequence of SEQ ID NO: 18.

Assignees

• Cell Signaling Technology Inc

Inventors

• Rikova Klarisa
• Haack Herbert
• Sullivan Laura
• Guo Ailan
• Possemato Anthony
• Macneill Joan
• Gu Ting-Lei
• Yu Jian

Classifications

• C12N9/1205

  Phosphotransferases with an alcohol group as acceptor (2.7.1), e.g. protein kinases · CPC title

• A61K38/00

  Medicinal preparations containing peptides (peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00) · CPC title

• A61K31/713

  Double-stranded nucleic acids or oligonucleotides · CPC title

• C12Q1/6886 Primary

  for cancer (immunoassay for cancer G01N33/575) · CPC title

• G01N2333/912

  transferring phosphorus containing groups, e.g. kinases (2.7) · CPC title