Methods of treating breast cancer with taxane therapy

Abstract

The application describes methods for screening subjects with breast cancer to determine if the breast cancer will be responsive to a breast cancer therapy including a taxane or a taxane derivative. The application also describes methods for treating subjects with breast cancer by screening them for the likelihood of the effectiveness of treating the cancer with a therapy including a taxane or a taxane derivative and administering the therapy in subjects when it is found that a taxane or a taxane derivative is likely to be effective.

What is claimed is: 
     
         1 . A method comprising:
 (a) determining the nucleic acid expression levels of at least five genes selected from the group consisting of ANLN, BIRC5, CCNB1, CCNE1, CDC20, CDC6, CDCA1, CENPF, CEP55, EXO1, KIF2C, KNTC2, MELK, MKI67, MYBL2, ORC6L, PTTG1, RRM2, TYMS, UBE2C, and UBE2T from a biological sample obtained from a subject in need of breast cancer treatment, said determining comprising forming at least five complexes wherein each complex comprises at least one nanoreporter probe hybridized to at least one nucleic acid from one of the at least five genes, wherein each nanoreporter probe comprises an ordered series of colored fluorescent spots which create a unique barcode for each nucleic acid;   (b) assigning a proliferation signature to the biological sample based on the expression levels of each of the at least five genes; and   (c) providing a breast cancer treatment recommendation for a breast cancer treatment comprising a taxane or taxane derivative when the biological sample is assigned a low proliferation signature.   
     
     
         2 . The method of  claim 1 , wherein the at least five genes comprises at least one gene selected from ANLN, BIRC5, CCNB1, CCNE1, CDC20, CDC6, CDCA1, CENPF, CEP55, EXO1, KIF2C, KNTC2, MELK, MKI67, MYBL2, ORC6L, PTTG1, RRM2, TYMS, UBE2C and UBE2T. 
     
     
         3 . The method of  claim 1 , wherein the at least five genes include each of CDC20, CEP55, MKI67, RRM2, and UBE2C. 
     
     
         4 . The method of  claim 1 , wherein the at least five genes comprises each of the genes selected from ANLN, BIRC5, CCNB1, CCNE1, CDC20, CDC6, CDCA1, CENPF, CEP55, EXO1, KIF2C, KNTC2, MELK, MKI67, MYBL2, ORC6L, PTTG1, RRM2, TYMS, UBE2C and UBE2T. 
     
     
         5 . The method of  claim 1 , wherein the at least five genes comprises at least one gene selected from ANLN, CCNE1, CDC20, CDC6, CDCA1, CENPF, CEP55, EXO1, KIF2C, KNTC2, MELK, MKI67, ORC6L, PTTG1, RRM2, TYMS, UBE2C and UBE2T. 
     
     
         6 . The method of  claim 1 , wherein the at least five genes comprises each of the genes selected from ANLN, CCNE1, CDC20, CDC6, CDCA1, CENPF, CEP55, EXO1, KIF2C, KNTC2, MELK, MKI67, ORC6L, PTTG1, RRM2, TYMS, UBE2C and UBE2T. 
     
     
         7 . The method of  claim 1 , wherein the at least five genes comprises at least one gene selected from BIRC5, CCNB1, CDC20, CDCA1/NUF2, CEP55, KNTC2/NDC80, MKI67, PTTG1, RRM2, TYMS and UBE2C. 
     
     
         8 . The method of  claim 1 , wherein the at least five genes comprises each of the genes selected from BIRC5, CCNB1, CDC20, CDCA1/NUF2, CEP55, KNTC2/NDC80, MKI67, PTTG1, RRM2, TYMS and UBE2C. 
     
     
         9 . The method of  claim 1 , wherein the at least five genes comprises at least one gene selected from ANLN, CCNB1, CDC20, CENPF, CEP55, KIF2C, MKI67, MYBL2, RRM2 and UBE2C. 
     
     
         10 . The method of  claim 1 , wherein the at least five genes comprises each of the genes selected from ANLN, CCNB1, CDC20, CENPF, CEP55, KIF2C, MKI67, MYBL2, RRM2 and UBE2C. 
     
     
         11 . The method of  claim 1 , wherein the taxane or taxane derivative is paclitaxel. 
     
     
         12 . The method of  claim 1 , wherein the breast cancer treatment comprising a taxane or taxane derivative further comprises one or more members of the group consisting of anthracycline, cyclophosphamide, and 5-fluorouracil. 
     
     
         13 . The method of  claim 12 , wherein the anthracycline is selected from the group consisting of doxorubicin and epirubicin. 
     
     
         14 . The method of  claim 12 , wherein taxane or taxane derivative is administered before, after, or simultaneously with the administration of the anthracycline, cyclophosphamide, or 5-fluorouracil. 
     
     
         15 . The method of  claim 1 , wherein the breast cancer treatment comprising a taxane or taxane derivative further comprises each member of the group consisting of anthracycline, cyclophosphamide, and 5-fluorouracil. 
     
     
         16 . The method of  claim 15 , wherein the anthracycline is selected from the group consisting of doxorubicin and epirubicin. 
     
     
         17 . The method of  claim 15 , wherein taxane or taxane derivative is administered before, after, or simultaneously with the administration of the anthracycline, cyclophosphamide, and 5-fluorouracil. 
     
     
         18 . The method of  claim 1 , further comprising determining at least one of tumor size, tumor grade, nodal status, intrinsic subtype, estrogen receptor expression, progesterone receptor expression, or HER2/ERBB2 expression. 
     
     
         19 . The method of  claim 1 , further comprising determining each of tumor size, tumor grade, nodal status, intrinsic subtype, estrogen receptor expression, progesterone receptor expression, and HER2/ERBB2 expression. 
     
     
         20 . The method of  claim 1 , wherein the biological sample comprises a cell or a tissue. 
     
     
         21 . The method of  claim 20 , wherein the tissue is obtained from a biopsy. 
     
     
         22 . The method of  claim 1 , wherein the biological sample comprises a bodily fluid. 
     
     
         23 . The method of  22 , wherein the bodily fluid is selected from the group consisting of blood, lymph, urine, saliva, and nipple aspirate. 
     
     
         24 . The method of  claim 1 , wherein the expression levels in the isolated nucleic acid of the at least five genes is determined using a nanoreporter code system.