Set of genes for use in a method of predicting the likelihood of a breast cancer patient's survival

Abstract

The present invention relates to a set of genes for use in a method of predicting the likelihood of a breast cancer patient's survival or of predicting the likelihood of a recurrence and/or aggressiveness of a breast cancer in a breast cancer patient. The present invention also relates to a method for predicting the likelihood of a breast cancer patient's survival or the likelihood of the recurrence or aggressiveness of a breast cancer in a breast cancer patient, as well as to a kit for use in such method.

1 . A method for predicting the likelihood of a breast cancer patient's 5-year survival or the likelihood of recurrence of a breast cancer over a 5-year period in a breast cancer patient or the likelihood of a breast cancer patient's distant metastasis free survival (DMFS) over a 5-year period, said method comprising the steps:
 measuring, in a tumor sample of said breast cancer patient, mRNA expression levels of at least 5 genes of a set of genes consisting of:   BIRC5, CCNB2, CDC6, MMP13, NEK2, RRM2, TOP2A, CENPE, and MKI67   comparing the measured mRNA expression levels from said tumor sample of said breast cancer patient with mRNA expression levels of the same genes in a non-tumor sample of a healthy individual or with mRNA expression levels of the same genes in a healthy, non-tumor sample of the same breast cancer patient, and either   determining, based on such comparison, whether there is an overexpression of the respective genes in said tumor sample of said breast cancer patient,   wherein an overexpression of the mRNAs of each gene in said tumor sample of said patient in comparison to the mRNA expression levels of the same genes of said healthy individual or in said healthy, non-tumor sample of the same breast cancer patient is indicative of a likelihood of 5-year survival of <70% and/or of a likelihood of recurrence of said breast cancer over 5-year period of >30% or of a likelihood of DMFS over a 5-year period of <70%,   or   determining, based on such comparison, whether there is a low overexpression, an intermediate overexpression or a high overexpression of the respective genes in said tumor sample of said breast cancer patient,   wherein a low overexpression of the mRNAs of each gene in said tumor sample of said patient in comparison to the mRNA expression levels of the same genes of said healthy individual or in said healthy, non-tumor sample of the same breast cancer patient is indicative of a likelihood of 5-year survival of <95% and/or of a likelihood of recurrence of said breast cancer over 5-year period of >5% or of a likelihood of DMFS over a 5-year period of <95%, and   wherein an intermediate overexpression of the mRNAs of each gene in said tumor sample of said patient in comparison to the mRNA expression levels of the same genes of said healthy individual or in said healthy, non-tumor sample of the same breast cancer patient is indicative of a likelihood of 5-year survival of <85% and/or of a likelihood of recurrence of said breast cancer over 5-year period of >15% or of a likelihood of DMFS over a 5-year period of <85%, and   wherein a high overexpression of the mRNAs of each gene in said tumor sample of said patient in comparison to the mRNA expression levels of the same genes of said healthy individual or in said healthy, non-tumor sample of the same breast cancer patient is indicative of a likelihood of 5-year survival of <70% and/or of a likelihood of recurrence of said breast cancer over 5-year period of >30% or of a likelihood of DMFS over a 5-year period of <70%.   
     
     
         2 . The method according to  claim 1 , wherein said method additionally comprises:
 measuring the mRNA expression levels of ZFP36 (TTP) and ELAVL1 (HuR) in said tumor sample of said patient, wherein measuring ELAVL1 mRNA levels is a measuring of (i) all ELAVL1 variants or of (ii) a 1.5 kb and a 2.7 kb ELAVL1 variant or of (iii) a 6 kb ELAVL1 variant,   
       and wherein a) an underexpression of ZFP36 or of the 6 kb ELAVL1 variant, or b) an overexpression of the 1.5 kb and 2.7 kb ELAVL1 variants, in comparison to the respective expression in a non-tumour sample of a healthy individual or in a healthy non-tumour sample of the same patient, or c) a ratio of ZFP36 mRNA expression: ELAVL1 1.5 and 2.7 kb variant mRNA expression <1 
       is indicative of a likelihood of 5-year survival of <70% and/or of a likelihood of recurrence over a 5-year period of >30% of said breast cancer. 
     
     
         3 . The method according to  claim 1 , wherein said method additionally comprises
 measuring mRNA expression levels of ERBB2, ESR1 and PGR in said tumor sample of said breast cancer patient to classify the type of breast cancer of said breast cancer patient according to its expression or non-expression of ERBB2, ESR1 and/or PGR.   
     
     
         4 . The method according to  claim 1 , wherein said method additionally comprises
 measuring mRNA expression levels of one or more housekeeping genes selected from GAPDH, GUS, RPLPO, TUB, ACTB and 18SRNA   
       in said tumor sample of said breast cancer patient, wherein any measured mRNA expression levels of these housekeeping gene(s) serves for normalization purposes, and wherein the measured mRNA expression levels of said at least 5 genes of said set of genes, and optionally of any other gene, such as ZFP36, ELAVL1, ERBB2, ESR1 and/or PGR, are normalized against the measured mRNA expression level(s) of said housekeeping gene(s). 
     
     
         5 . The method according to  claim 1 , wherein said tumor sample of said breast cancer patient is a sample obtained from a breast cancer tumor of said breast cancer patient or is a body fluid sample containing exosomes of said breast cancer patient. 
     
     
         6 . The method according to  claim 1 , wherein said method additionally comprises:
 assigning a treatment by chemotherapy if said likelihood of 5-year survival has been determined as being <70% and/or if said likelihood of recurrence over a 5-year period has been determined as being >30%, and/or   assigning a treatment by hormones, if said likelihood of 5-year survival has been determined as being >70% and/or if said likelihood of recurrence over a 5-year period has been determined as being <30%.   
     
     
         7 . The method according to  claim 1 , wherein measurement of mRNA expression levels occurs by hybridization, next-generation sequencing, in-situ hybridization, RT-PCR flow cytometry, immunohistochemistry or any combination of the foregoing. 
     
     
         8 . The method according to  claim 1 , wherein measuring mRNA expression levels of said genes is done using a set of probes that is complementary to said genes or to the respective mRNAs of said genes. 
     
     
         9 . The method according to  claim 1 , wherein expression of the mRNAs is an overexpression if said mRNA expression levels in said tumor sample are at least 1.5-fold the mRNA expression levels of the same genes in a non-tumor sample of a healthy individual or in a healthy, non-tumor sample of the same patient. 
     
     
         10 . The method according to  claim 1 , wherein the genes have sequences designated as the following SEQ ID NOs: 
       
         
           
                 
                 
               
                     
                   SEQ ID NO: 1 
                 
                     
                   BIRC5 
                 
                     
                 
                     
                   SEQ ID NO: 2 
                 
                     
                   CCNB2 
                 
                     
                 
                     
                   SEQ ID NO: 3 
                 
                     
                   CDC6 
                 
                     
                 
                     
                   SEQ ID NO: 4 
                 
                     
                   MMP13 
                 
                     
                 
                     
                   SEQ ID NO: 5 
                 
                     
                   NEK2 
                 
                     
                 
                     
                   SEQ ID NO: 6 
                 
                     
                   RRM2 
                 
                     
                 
                     
                   SEQ ID NO: 7 
                 
                     
                   TOP2A 
                 
                     
                 
                     
                   SEQ ID NO: 8 
                 
                     
                   CENPE 
                 
                     
                 
                     
                   SEQ ID NO: 9 
                 
                     
                   MKI67 
                 
                     
                 
                     
                   SEQ ID NO: 10 
                 
                     
                   ZFP36 
                 
                     
                 
                     
                   SEQ ID NO: 11 
                 
                     
                   ELAVL1 (6 kb variant) 
                 
                     
                 
                     
                   SEQ ID NO: 12 
                 
                     
                   ELAVL1 (1.5 kb variant) 
                 
                     
                 
                     
                   SEQ ID NO: 13 
                 
                     
                   ELAVL1 (2.7 kb variant) 
                 
                     
                 
                     
                   SEQ ID NO: 14 
                 
                     
                   ERBB2 
                 
                     
                 
                     
                   SEQ ID NO: 15 
                 
                     
                   ESR1 
                 
                     
                 
                     
                   SEQ ID NO: 16 
                 
                     
                   PGR 
                 
                     
                 
                     
                   SEQ ID NO: 17 
                 
                     
                   GAPDH 
                 
                     
                 
                     
                   SEQ ID NO: 18 
                 
                     
                   GUS 
                 
                     
                 
                     
                   SEQ ID NO: 19 
                 
                     
                   RPLPO 
                 
                     
                 
                     
                   SEQ ID NO: 20 
                 
                     
                   TUB 
                 
                     
                 
                     
                   SEQ ID NO: 21 
                 
                     
                   ACTB 
                 
                     
                   and 
                 
                     
                 
                     
                   SEQ ID NO: 22 
                 
                     
                   18SRNA. 
                 
             
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
     
     
         11 . The method according to  claim 1 , wherein measuring the mRNA expression levels of 5 genes of said set of genes is a measuring of the expression levels of BIRC5, CCNB2, NEK2, RRM2, and TOP2A, and wherein measuring the mRNA expression levels of 6 genes of said set of genes is a measuring of the expression levels of BIRC5, CCNB2, NEK2, RRM2, TOP2A, and CENPE,
 wherein said measuring the mRNA expression levels of said 5 or 6 genes is optionally in combination with measuring the mRNA expression levels of ZFP36 (TTP) and ELAVL1 (HuR) in said tumor sample of said patient.   
     
     
         12 . The method according to  claim 1 , wherein said patient is a breast cancer patient who is either (i) ESR1-positive or ERBB2-negative, (ii) ESR1-positive and ERBB2-negative, (iii) ESR1-positive and/or PGR-positive and/or ERBB2-positive (“Luminal B breast cancer”), or (iv) ESR1-positive and/or PGR-positive, ERBB2-negative (“Luminal A breast cancer”). 
     
     
         13 . The method according to  claim 1 , wherein said patient is a patient whose lymph nodes are not affected by said breast cancer (“lymph node-negative” patient). 
     
     
         14 . A kit for use in a method of  claim 1 , said kit comprising probes for determining the expression of mRNAs of at least 5 genes of a set of genes, and
 said set of genes consisting of   BIRC5, CCNB2, CDC6, MMP13, NEK2, RRM2, TOP2A, CENPE, and MKI67, said probes being for determining the expression of mRNAs.   
     
     
         15 . The kit according to  claim 14 , additionally comprising probes for determining expression of mRNAs of each of ZFP36 and ELAVL1. 
     
     
         16 . The kit according to  claim 14 , additionally comprising probes for determining expression of mRNAs of ERBB2, ESR1 and PGR. 
     
     
         17 . The kit according to  claim 14 , additionally comprising probes for determining expression of mRNAs of at least one housekeeping gene selected from GAPDH, GUS, RPLPO, TUB, ACTB and 18SRNA. 
     
     
         18 . The kit according to  claim 14 , additionally comprising means for detecting a hybridization event between any of said probes and an mRNA in a sample of a patient. 
     
     
         19 . The kit according to  claim 14 , wherein said probes are complementary to mRNA sequences of said genes and consist of 10-100 adjacent nucleotides which are complementary to said sequences, wherein said probes are cDNA, cRNA, PNA, or DNA oligonucleotides.