Compositions for detecting mutant anaplastic lymphoma kinase in human lung cancer

Patent metadata

Field	Value
Publication number	US-10955416-B2
Application number	US-201815898275-A
Country	US
Kind code	B2
Filing date	Feb 16, 2018
Priority date	Apr 14, 2006
Publication date	Mar 23, 2021
Grant date	Mar 23, 2021

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 now been identified 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 polypeptides, probes for detecting it, isolated mutant polypeptides, and reagents for detecting the fusion and truncated polypeptides. The invention also provides methods for determining the presence of these mutant polypeptides in a biological sample, 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 composition, comprising
a biological sample from a human having lung cancer, wherein the biological sample comprises a circulating lung cancer cell,
a DNA polymerase, and
a nucleic acid reagent, wherein the nucleic acid reagent comprises a primer pair that hybridizes to a polynucleotide encoding an Echinoderm Microtubule-Associated Protein-Like 4 (EML4)-Anaplastic Lymphoma Kinase (ALK) fusion polypeptide, wherein the EML4-ALK fusion polypeptide comprises SEQ ID NO: 1 or SEQ ID NO: 18, and wherein the primer pair amplifies at least a fragment of said polynucleotide comprising the fusion junction.

2. The composition of claim 1 , wherein said lung cancer is non-small cell lung cancer (NSCLC).

3. The composition of claim 1 , wherein the polynucleotide is mRNA.

4. The composition of claim 1 , wherein one primer of the primer pair hybridizes to exon 6 of an EML4 gene.

5. The composition of claim 1 , wherein one primer of the primer pair hybridizes to exon 13 of an EML4 gene.

6. The composition of claim 1 , wherein one primer of the primer pair hybridizes to exon 20 of an ALK gene.

7. A composition, comprising
a biological sample from a human having lung cancer, wherein the biological sample comprises a circulating lung cancer cell,
a DNA polymerase, and
a nucleic acid reagent, wherein the nucleic acid reagent comprises a primer pair that hybridizes to
(i) a region of a polynucleotide encoding a polypeptide with ALK kinase activity, wherein the region consists of a nucleotide sequence coding for amino acids 234-796 of SEQ ID NO: 1; or

(ii) nucleotides 701-2391 of the polynucleotide of SEQ ID NO: 2.

8. The composition of claim 7 , wherein said lung cancer is non-small cell lung cancer (NSCLC).

9. The composition of claim 7 , wherein the polynucleotide is mRNA.

Assignees

• Cell Signaling Technology Inc

Inventors

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

Classifications

• G01N33/5758

  involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites · CPC title

• G01N33/575 Primary

  for cancer · CPC title

• C12N9/1205 Primary

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

• C12Q2600/136

  Screening for pharmacological compounds · CPC title

• Y10T436/117497

  with a continuously flowing sample or carrier stream · CPC title