Six-Gene Biomarker of Survival and Response to Platinum Based Chemotherapy in Serious Ovarian Cancer Patients

Abstract

Described herein are methods of predicting the risk of developing ovarian cancer recurrence of a subject comprising the steps of detecting the expression levels of at least four of the six genes selected from the group consisting of AKT2, KRAS, RAC1, CALM3, RPS6KA2 and YWHAB or the gene products thereof, wherein the presence of increased expression levels of the genes or the gene products is predictive of the increased risk of developing ovarian cancer recurrence in the subject. Kits for practicing the methods are also disclosed.

We claim: 
     
         1 . A method of predicting the risk of developing ovarian cancer recurrence of a subject comprising the steps of:
 (a) obtaining a sample from a subject; and   (b) analyzing the expression levels of at least four genes selected from the group consisting of AKT2, KRAS, RAC1, CALM3, RPS6KA2 and YWHAB or the gene products thereof in the sample, wherein the presence of increased expression levels of the genes or the gene products is predictive of increased risk of ovarian cancer recurrence in the subject.   
     
     
         2 . The method of  claim 1  further comprising step (c) of treating the subject with alternative therapies. 
     
     
         3 . The method of  claim 1 , wherein the subject is a patient with advanced stage ovarian cancer. 
     
     
         4 . The method of  claim 2 , wherein the alternative therapy is selected from the group consisting of treatment with taxane, bevacizumab, docetaxel, doxorubicin, gemcitabine, pemetrexed, tamoxifen, topotecan and mixtures thereof. 
     
     
         5 . The method of  claim 4 , wherein the alternative therapy is used with platinum or taxane. 
     
     
         6 . The method of  claim 4 , wherein the alternative therapy is used without platinum or taxane. 
     
     
         7 . A method of determining the effectiveness of a platinum-based therapy for a subject with ovarian cancer comprising the steps of:
 (a) obtaining a sample from a subject;   (b) analyzing the expression levels of at least four genes selected from the group consisting of AKT2, KRAS, RAC1, CALM3, RPS6KA2 and YWHAB or the gene products thereof in the sample, wherein the presence of increased expression levels of the genes or the gene products is predictive of increased resistance to platinum-based therapy in the subject; and   (c) treating the subject with alternative therapies.   
     
     
         8 . The method of  claim 7 , wherein the subject is a patient with advanced stage ovarian cancer. 
     
     
         9 . The method of  claim 7 , wherein the alternative therapy is selected from the group consisting of treatment with taxane, bevacizumab, docetaxel, doxorubicin, gemcitabine, pemetrexed, tamoxifen, topotecan and mixtures thereof. 
     
     
         10 . The method of  claim 9 , wherein the alternative therapy is used with platinum or taxane. 
     
     
         11 . The method of  claim 9 , wherein the alternative therapy is used without platinum or taxane. 
     
     
         12 . A kit for predicting the risk of developing ovarian cancer recurrence of a subject comprising:
 (a) at least one reagent that is capable of detecting the expression levels of at least four genes selected from the group consisting of AKT2, KRAS, RAC1, CALM3, RPS6KA2 and YWHAB or the gene products thereof in a patient sample;   wherein the presence of increased expression of levels of the genes or the gene products is predictive of the increased risk of ovarian cancer recurrence in the subject.   
     
     
         13 . The kit of  claim 12 , wherein the reagent comprises antibodies immunologically specified for the proteins encoded by the genes. 
     
     
         14 . The kit of  claim 13 , wherein the antibodies are used in an ELISA. 
     
     
         15 . The kit of  claim 12 , wherein the reagent comprises probes complementary to the genes. 
     
     
         16 . The kit of  claim 12 , wherein the reagent comprises primers complementary to the genes. 
     
     
         17 . A kit for determining the resistance to a platinum-based therapy for a subject with ovarian cancer comprising:
 (a) at least one reagent capable of detecting the expression levels of at least four genes selected from the group consisting of AKT2, KRAS, RAC1, CALM3, RPS6KA2 and YWHAB or the gene products thereof in a sample, wherein the presence of increased expression levels of the genes or the gene products is predictive of increased resistance to the platinum-based therapy in the subject.   
     
     
         18 . The kit of  claim 17 , wherein the reagent comprises antibodies immunologically specified for the proteins encoded by the genes. 
     
     
         19 . The kit of  claim 18 , wherein the antibodies are used in an ELISA. 
     
     
         20 . The kit of  claim 17 , wherein the reagent comprises probes complementary to the genes. 
     
     
         21 . The kit of  claim 17 , wherein the reagent comprises primers complementary to the genes. 
     
     
         22 . A method of diagnosing the risk of developing ovarian cancer recurrence of a subject comprising the steps of:
 (a) obtaining a sample from a subject; and   (b) analyzing the expression levels of at least four genes selected from the group consisting of AKT2, KRAS, RAC1, CALM3, RPS6KA2 and YWHAB or the gene products thereof in the sample, wherein the presence of increased expression of level of the genes or the gene products is predictive of increased risk of ovarian cancer recurrence in the subject.   
     
     
         23 . A method of amplifying at least four of six target gene sequences comprising the steps of
 (a) providing a reaction mixture comprising a double-stranded target DNA, wherein the DNA is obtained from a subject, and (i) at least one pair of primers selected from the group designed to amplify at least four genes selected from the group consisting of target genes AKT2, KRAS, RAC1, CALM3, RPS6KA2 and YWHAB, wherein the primer pair comprises a first and a second primer that are complementary to the target DNA sequence, (ii) a polymerase and (iii) a plurality of free nucleotides comprising adenine, thymine, cytosine and guanine;   (b) heating the reaction mixture to a first predetermined temperature for a first predetermined time to separate the strands of the target DNA from each other;   (c) cooling the reaction mixture to a second predetermined temperature for a second predetermined time under conditions to allow the first and second primers to hybridize with their complementary sequences on the target DNA and to allow the polymerase to extend the primers; and   (d) repeating steps (b) and (c) at least 10 times.   
     
     
         24 . The method of  claim 23  wherein (iv) PCR reaction buffer and (v) MgCl 2  are additionally added to step (a). 
     
     
         25 . The method of  claim 23  additionally comprising the step of analyzing the products of step (e) to determine whether increased risk of ovarian cancer in the subject is indicated. 
     
     
         26 . The method of  claim 23  additionally comprising the step of analyzing the products of step (e) to determine whether the products are predictive of increased resistance to platinum-based cancer therapies. 
     
     
         27 . The method of  claim 23  additionally comprising the step of treating the subject with alternative therapies.