Gene defects and mutant alk kinase in human solid tumors

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.

What is claimed is: 
     
         1 . A method of characterizing a mammalian lung cancer, comprising
 (a) obtaining a biological sample from said mammalian lung cancer; and   (b) detecting the presence of an Anaplastic Lymphoma Kinase (ALK) fusion polynucleotide or polypeptide in said sample, thereby characterizing said lung cancer based on the presence or absence of the ALK fusion polynucleotide or polypeptide.   
     
     
         2 . The method of  claim 1 , wherein said lung cancer is non-small cell lung cancer (NSCLC). 
     
     
         3 . The method according to  claim 1 , wherein the presence of an ALK fusion polypeptide is being detected. 
     
     
         4 . The method of  claim 3 , wherein said ALK fusion polypeptide is detected by using an antibody. 
     
     
         5 . The method of  claim 3 , wherein the polypeptide is detected in a flow-cytometry (FC), immuno-histochemistry (IHC), or immunofluorescence (IF) assay format. 
     
     
         6 . The method according to  claim 1 , wherein the presence of an ALK fusion polynucleotide is being detected. 
     
     
         7 . The method of  claim 6 , wherein the presence of said ALK fusion polynucleotide is detected in a fluorescence in situ hybridization (FISH) assay. 
     
     
         8 . The method of  claim 7 , wherein the FISH assay is performed using break-apart gene probes. 
     
     
         9 . The method of  claim 6 , wherein the presence of said ALK fusion polynucleotide is detected in a polymerase chain reaction (PCR) assay. 
     
     
         10 . A method according to  claim 9 , wherein the ALK fusion polynucleotide being detected is an ALK fusion mRNA. 
     
     
         11 . A method of detecting an ALK gene rearrangement in a mammalian lung cancer, comprising
 (a) obtaining a biological sample from said mammalian lung cancer;   (b) detecting an ALK gene rearrangement in the sample in an in situ hybridization assay using break-apart probes.   
     
     
         12 . A method for inhibiting the progression of a mammalian lung cancer characterized by the presence of an ALK fusion polynucleotide or polypeptide, comprising administering to the patient an effective amount of an ALK inhibitor. 
     
     
         13 . The method of  claim 12 , wherein the lung cancer is a non-small cell lung carcinoma. 
     
     
         14 . The method of  claim 12 , wherein the inhibitor is a compound which inhibits the kinase activity of ALK. 
     
     
         15 . A method for inhibiting the progression of a mammalian cancer characterized by the presence of an EML4-ALK fusion polynucleotide or polypeptide, comprising administering to the patient an effective amount of an ALK inhibitor. 
     
     
         16 . The method of  claim 15 , wherein the cancer is a lung cancer. 
     
     
         17 . The method of  claim 16 , wherein the lung cancer is a non-small cell lung carcinoma. 
     
     
         18 . The method according to  claim 15 , wherein the inhibitor is a compound which inhibits the kinase activity of ALK. 
     
     
         19 . A method for treating a human lung cancer patient, the method comprising:
 obtaining a sample from said patient;   detecting in the sample the presence of a human ALK fusion polynucleotide or polypeptide; and   administering to the patient an effective amount of a compound that inhibits the kinase activity of ALK.   
     
     
         20 . The method of  claim 19 , wherein the detecting is implemented in a fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR), nucleotide sequencing, flow cytometry (FC), immunofluorescence (IF), or immunohistochemistry (IHC) assay format.