Fusion proteins and methods thereof

Abstract

The invention discloses oncogenic fusion proteins. The invention provides methods for treating gene-fusion based cancers.

1 .- 60 . (canceled) 
     
     
         61 . A diagnostic composition for determining whether a sample from a subject exhibits a presence of a mRNA encoding a FGFR fusion protein and the presence or absence of a gene amplification of EGFR, CDK4 or MDM2, wherein the FGFR fusion protein comprises the tyrosine kinase domain of a FGFR protein fused to the TACC domain of a TACC protein, the composition comprising:
 cDNA generated from a sample from a subject;   at first oligonucleotide primer complementary to a portion of the cDNA encoding a FGFR portion of the FGFR fusion protein; and   a second oligonucleotide primer complementary to a portion of the cDNA encoding a TACC portion of the FGFR fusion protein; and   a third oligonucleotide primer complementary to a portion of a cDNA encoding EGFR, CDK4, or MDM2;   
       wherein the first and second oligonucleotide primers are complementary to opposite strands of the cDNA encoding the FGFR fusion protein; and 
       wherein the first and second oligonucleotide primers prime a polymerase reaction only when a cDNA encoding a FGFR fusion is present. 
     
     
         62 . The composition of  claim 61 , wherein the cDNA is contacted with the first and second oligonucleotide primers. 
     
     
         63 . The composition of  claim 61 , wherein the first oligonucleotide primer comprises SEQ ID NO:
 162, 166, 168, 170, 497, 499, 500, or 507.   
     
     
         64 . The composition of  claim 61 , wherein the second oligonucleotide primer comprises SEQ ID NO: 165, 167, 169, 171, 498, 501, 502, 503, 504, 505, 506, or 510. 
     
     
         65 . The composition of  claim 61 , further comprises a fourth oligonucleotide primer complementary to a portion of the cDNA encoding EGFR, CDK4, or MDM2 wherein the third and fourth oligonucleotide primers are complementary to opposite strands of the cDNA encoding the EGFR, CDK4, or MDM2. 
     
     
         66 . The composition of  claim 65 , wherein the third and fourth oligonucleotide primers are for use in quantitative PCR (qPCR). 
     
     
         67 . The composition of  claim 61 , wherein the FGFR protein is FGFR1, FGFR2, FGFR3, or FGFR4. 
     
     
         68 . The composition of  claim 61 , wherein the FGFR fusion protein comprises the tyrosine kinase domain of FGFR1 fused to the TACC domain of TACC1. 
     
     
         69 . The composition of  claim 61 , wherein the FGFR fusion protein comprises the tyrosine kinase domain of FGFR3 fused to the TACC domain of TACC3. 
     
     
         70 . The composition of  claim 68 , wherein the first oligonucleotide primer comprises SEQ ID NO: 168, 497 and the second oligonucleotide primer comprises SEQ ID NO: 169, 498. 
     
     
         71 . The composition of  claim 69 , wherein the first oligonucleotide primer comprises SEQ ID NO: 162, 166, 170, 499, 500, or 507 and the second oligonucleotide primer comprises SEQ ID NO: 165, 167, 171, 501, 502, 503, 504, 505, 506, or 510. 
     
     
         72 . The composition of  claim 69 , wherein the first oligonucleotide primer comprises SEQ ID NO: 166 and the second oligonucleotide primer comprises SEQ ID NO: 167. 
     
     
         73 . The composition of  claim 65 , wherein the third oligonucleotide primer comprises SEQ ID NO: 515 and the fourth oligonucleotide primer comprises SEQ ID NO: 516 
     
     
         74 . A method for detecting the presence of a FGFR fusion protein and the presence or absence of a gene amplification of EGFR, CDK4 or MDM2 in a human subject, wherein the FGFR fusion protein comprises the tyrosine kinase domain of a FGFR protein fused to the TACC domain of a TACC protein, the method comprising:
 (a) obtaining a biological sample from the human subject;   (b) detecting whether or not there is a FGFR fusion present in the subject; and   (c) detecting whether or not there is gene amplification of EGFR, CDK4, or MDM2.   
     
     
         75 . The method of  claim 74 , wherein the detecting of step (b) comprises detecting whether or not there is a nucleic acid sequence encoding a FGFR fusion protein in the subject 
     
     
         76 . The method of  claim 74 , wherein the detecting of step (b) comprises using amplification, wherein the amplification uses one or more primers comprising SEQ ID NO: 162, 163, 164, 165, 166, 167, 168, 169, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, or 514. 
     
     
         77 . The method of  claim 74 , further comprising (d) detecting whether or not there is a mutation in IDH1 and/or, IDH2. 
     
     
         78 . The method of  claim 74 , further comprising (d) diagnosing the human subject with a FGFR fusion associated cancer if a FGFR fusion is detected in the biological sample and the EGFR gene is not amplified, and/or the CDK4 gene is amplified, and/or the MDM2 gene is amplified in the biological sample; and (e) administering a treatment for a FGFR fusion associated cancer to the human subject if the human subject is diagnosed with a FGFR fusion associated cancer. 
     
     
         79 . A diagnostic kit for determining whether a sample from a subject exhibits a presence of a FGFR fusion protein and the presence or absence of a gene amplification of EGFR, CDK4 or MDM2, the kit comprising an antibody that specifically binds to a FGFR fusion protein, wherein the antibody will recognize the protein only when a FGFR fusion protein is present, and wherein the FGFR fusion protein comprises a tyrosine kinase domain of an FGFR protein fused to the TACC domain of a transforming acidic coiled-coil-containing (TACC) protein; the kit further comprising at least one oligonucleotide that specifically hybridizes to a nucleic acid encoding EGFR, CDK4, or MDM2. 
     
     
         80 . The kit of  claim 79 , wherein the antibody is directed to an FGFR fusion protein comprising SEQ ID NO: 79, 85, 86, 87, 88, 89, 150, 158, 159, 160, 161, 542, 543, 544, 545, 546, or 547. 
     
     
         81 . An antibody or antigen-binding fragment thereof, that specifically binds to a purified FGFR3-TACC3 fusion protein comprising the amino acid sequence of SEQ ID NO: 542, 543, 544, 545, 546, or 547. 
     
     
         82 . A composition for decreasing in a subject the expression level or activity of a FGFR3-TACC3 fusion protein comprising the amino acid sequence of SEQ ID NO: 542, 543, 544, 545, 546, or 547, the composition in an admixture of a pharmaceutically acceptable carrier comprising an inhibitor of the fusion protein. 
     
     
         83 . A method of decreasing growth of a solid tumor in a subject in need thereof, the method comprising administering to the subject an effective amount of a FGFR3-TACC3 fusion protein molecule inhibitor, wherein the inhibitor decreases the size of the solid tumor, and wherein the FGFR3-TACC3 fusion protein comprises the amino acid sequence of SEQ ID NO: 542, 543, 544, 545, 546, or 547. 
     
     
         84 . A purified FGFR3-TACC3 fusion protein comprising the amino acid sequence of SEQ ID NO: 542, 543, 544, 545, 546, or 547. 
     
     
         85 . A cDNA encoding a FGFR3-TACC3 fusion protein comprising the nucleotide sequence of SEQ ID NO: 533, 534, 535, 536, 537, or 538.