US 2009/0156475 A1 · Gene defects and mutant ALK kinase in human solid tumors

Abstract

In accordance with the invention, 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 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 new methods for determining the presence of these mutant ALK kinase 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, which are also provided by the invention.

Claims43

Dependent claims

An isolated polynucleotide comprising a nucleotide sequence at least 95% identical to a sequence selected from the group consisting of:

(a) a nucleotide sequence encoding an Echinoderm Microtubule-Associated Protein-Like 4/Anaplastic Lymphoma Kinase (EML4-ALK) fusion polypeptide comprising the amino acid sequence of SEQ ID NO:
1 or SEQ ID NO:
18;
(b) a nucleotide sequence encoding an EML4-ALK fusion polypeptide, said nucleotide sequence comprising the nucleotide sequence of SEQ ID NO:
2 or SEQ ID NO:
19;
(c) a nucleotide sequence encoding an EML4-ALK fusion polypeptide comprising the N-terminal amino acid sequence of EML-4 (residues 1-233 of SEQ ID NO:
3 or residues 1-495 of SEQ ID NO:
3) and the kinase domain of ALK (residues 1116-1383 of SEQ ID NO:
5);
(d) a nucleotide sequence comprising the N-terminal nucleotide sequence of EML-4 (nucleotides 1-700 of SEQ ID NO:
4 or nucleotides 1-1486 of SEQ ID NO:
4) and the kinase domain nucleotide sequence of ALK (nucleotides 3348-4149 of SEQ ID NO:
6);
(e) a nucleotide sequence comprising at least six contiguous nucleotides encompassing the fusion junction (nucleotides 700-701 of SEQ ID NO:
2 or nucleotides 1486-1487 of SEQ ID NO:
19) of an EML4-ALK fusion polynucleotide;
(f) a nucleotide sequence encoding a polypeptide comprising at least six contiguous amino acids encompassing the fusion junction (residues 233-234 of SEQ ID NO:
1 or residues 495-496 of SEQ ID NO:
18) of an EML4-ALK fusion polypeptide;
and
(g) a nucleotide sequence complementary to any of the nucleotide sequences of (a)-(f).

19 more elements

Dependencies are inferred from the claim text.

Gene defects and mutant ALK kinase in human solid tumors

Life of this patent

Gene defects and mutant ALK kinase in human solid tumors

Life of this patent

Abstract

Claims43