Translocation and mutant ros kinase in human non-small cell lung carcinoma

Abstract

In accordance with the invention, a novel gene translocation, (4p15, 6q22), in human non-small cell lung carcinoma (NSCLC) that results in a fusion proteins combining part of Sodium-dependent Phosphate Transporter Isoform NaPi-3b protein (SLC34A2) with Proto-oncogene Tyrosine Protein Kinase ROS Precursor (ROS) kinase has now been identified. The SLC34A2-ROS fusion protein is anticipated to drive the proliferation and survival of a subgroup of NSCLC tumors. The invention therefore provides, in part, isolated polynucleotides and vectors encoding the disclosed mutant ROS kinase polypeptides, probes for detecting it, isolated mutant polypeptides, recombinant polypeptides, and reagents for detecting the fusion and truncated polypeptides. The disclosed identification of the new fusion protein enables new methods for determining the presence of these mutant ROS 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.

What is claimed is: 
     
         1 . A method comprising
 (a) obtaining a biological sample from a human lung cancer; and   (b) determining the presence of a ROS fusion polynucleotide or polypeptide in the sample.   
     
     
         2 . The method of  claim 1 , wherein the presence of a ROS fusion polypeptide is detected. 
     
     
         3 . The method of  claim 2 , wherein the lung cancer is a non-small cell lung cancer (NSCLC). 
     
     
         4 . The method of  claim 2 , wherein the ROS fusion polypeptide comprises an amino acid sequence at least 95% identical to residues 1945-2222 of SEQ ID NO: 7. 
     
     
         5 . The method of  claim 4 , wherein the ROS fusion polypeptide comprises amino acid residues 1945-2222 of SEQ ID NO: 7. 
     
     
         6 . The method of  claim 2 , wherein the ROS fusion polypeptide comprises an amino acid sequence at least 95% identical to residues 1750-2347 or 1853-2347 of SEQ ID NO: 7. 
     
     
         7 . The method of  claim 6 , wherein the ROS fusion polypeptide comprises amino acid residues 1750-2347 or 1853-2347 of SEQ ID NO: 7. 
     
     
         8 . The method of  claim 2 , wherein said detecting comprises the use of an antibody. 
     
     
         9 . The method of  claim 2 , wherein said method is implemented in an immunohistochemistry (IHC), immunofluorescence (IF), or flow cytometry (FC) format. 
     
     
         10 . The method of  claim 1 , wherein the presence of a ROS polynucleotide is detected. 
     
     
         11 . The method of  claim 10 , wherein the lung cancer is a non-small cell lung cancer (NSCLC). 
     
     
         12 . The method of  claim 10 , wherein said ROS polynucleotide encodes a polypeptide which comprises an amino acid sequence at least 95% identical to residues 1945-2222 of SEQ ID NO: 7. 
     
     
         13 . The method of  claim 12 , wherein said ROS polynucleotide encodes a polypeptide comprising residues 1945-2222 of SEQ ID NO: 7. 
     
     
         14 . The method of  claim 10 , wherein said ROS polynucleotide encodes a polypeptide which comprises an amino acid sequence at least 95% identical to residues 1750-2347 or 1853-2347 of SEQ ID NO: 7. 
     
     
         15 . The method of  claim 14 , wherein said ROS polynucleotide encodes a polypeptide comprising residues 1750-2347 or 1853-2347 of SEQ ID NO: 7. 
     
     
         16 . The method of  claim 10 , wherein the presence of the ROS polynucleotide is determined in a polymerase chain reaction (PCR) assay. 
     
     
         17 . The method of  claim 10 , wherein the presence of the ROS polynucleotide is determined in an in situ hybridization (ISH) assay. 
     
     
         18 . The method of  claim 17 , wherein the ISH assay is performed using break-apart gene probes. 
     
     
         19 . The method of  claim 10 , wherein the presence of the ROS polynucleotide is determined in an assay based on nucleic acid hybridization. 
     
     
         20 . A method of detecting a ROS gene rearrangement in a human lung cancer, comprising
 (a) obtaining a biological sample from said human lung cancer; and   (b) detecting a ROS gene rearrangement in the sample in an in situ hybridization assay using break-apart probes that hybridize to a wild-type chromosome at opposite sides of a breakpoint of the ROS gene.   
     
     
         21 . The method of  claim 20 , wherein the lung cancer is a non-small cell lung cancer (NSCLC). 
     
     
         22 . A method of detecting a ROS gene rearrangement in a human lung cancer, comprising
 (a) obtaining a biological sample from said human lung cancer; and   (b) detecting a ROS gene rearrangement in the sample in a FISH assay using break-apart probes, wherein said ROS gene rearrangement results in a polynucleotide sequence encoding a ROS fusion polypeptide, wherein the ROS portion in the ROS fusion polypeptide begins C-terminus to amino acid residue 1750 of SEQ ID NO: 7.   
     
     
         23 . The method of  claim 22 , wherein the lung cancer is a non-small cell lung cancer (NSCLC).