Molecular Indicators of Breast Cancer Prognosis and Prediction of Treatment Response

Abstract

The present invention relates to quantitative molecular indicators that can guide clinical decisions in breast cancer, such as estrogen receptor (ESR1)-positive, lymph node-negative breast cancer. In particular, the invention concerns certain genes, the varied expression of which indicates the likelihood of recurrence of surgically resected breast cancer in patients who are not treated with a therapeutic agent in the adjuvant setting. In addition, the invention concerns the use of quantitative measurement of the expression of certain genes, including the ESR1 gene, that measure as a continuous variable, to determine (a) the likelihood of a beneficial response to the anti-estrogen therapeutic agent, such as tamoxifen; and (b) the potential magnitude of beneficial response to chemotherapy.

1 . A method for the prognosis of disease outcome in a breast cancer patient, comprising
 (a) quantitatively determining, in a biological sample comprising cancer cells obtained from said patient, the value of one or more of the following variables:
 (i) Proliferation Group Score; 
 (ii) Invasion Group Score; 
 (iii) Proliferation Group Threshold Score; and 
 (iv) the expression levels of the RNA transcripts of one or more of the following individual genes CCNB1, BIRC5, MYBL2, PGR, STK6, MKI67, GSTM1, GAPD, RPLPO, and MMP11, or their expression products; wherein 
   (b1) for every unit of an increase in the value of one or more of (i)-(iii) and/or of the RNA transcript(s) of one or more of the individual genes CCNB1, BIRC5, MYBL2, STK6, MKI67, GAPD, and MMP11, or the corresponding expression product(s), said patient is identified to have a proportionately increased risk of poor disease outcome; and   (b2) for every unit of increased expression level(s) of the RNA transcript(s) of one or more of the individual genes PGR, GSTM1, and RPLO, or the corresponding expression product(s), said patient is identified to have a proportionately decreased risk of poor disease outcome,   wherein
   Proliferation Group Score=( BIRC 5+ MKI 67+ MYBL 2+ CCNB 1+ STK 6)/5; 
   Invasion Group Score=( CTSL 2+ MMP 11)/2; 
   Proliferation Group Threshold Score equals 6.5, if the Proliferation Group Score is less than 6.5; and is identical with the Proliferation Group Score, if the Proliferation Group Score is 6.5 or more, wherein   the gene symbols in the equations represent the expression levels of the RNA transcripts of the respective genes, or their expression products; and   wherein every individual gene or gene present in any of said variables can be substituted by another gene that coexpresses in the applicable tumor type with said gene in said cancer with a Pearson's coefficient of ≧0.5.   
     
     
         2 . The method of  claim 1 , wherein said patient is a human patient. 
     
     
         3 . The method of  claim 2 , wherein said disease outcome is expressed as overall patient survival. 
     
     
         4 . The method of  claim 2 , wherein said disease outcome is expressed as recurrence-free survival. 
     
     
         5 . The method of  claim 2 , wherein said disease outcome is expressed as distant recurrence-free survival. 
     
     
         6 . The method of  claim 2  wherein said prognosis assumes that the patient receives no further treatment after surgical resection of said breast cancer. 
     
     
         7 . The method of  claim 2  wherein said expression levels are normalized relative to the expression levels of one or more reference genes, or their expression products. 
     
     
         8 . The method of  claim 7  wherein said reference genes are selected from the group consisting of ACTB, GAPD, GUS, RPLPO, and TFRC. 
     
     
         9 . The method of  claim 7  wherein said expression levels are normalized relative to the mean of the expression levels of ACTB, GAPD, GUS, RPLPO, and TFRC. 
     
     
         10 . The method of  claim 2  wherein the quantitative value of said disease outcome is directly proportionate with the value of the variable or variables determined over a continuum. 
     
     
         11 . The method of  claim 2  comprising the determination of the Proliferation Score. 
     
     
         12 . The method of  claim 11  further comprising the determination of the Proliferation Group Threshold Score. 
     
     
         13 . The method of  claim 12  further comprising determination of the Invasion Group Score. 
     
     
         14 .- 46 . (canceled) 
     
     
         47 . A method for quantitative determination of the likelihood of a beneficial response of an BSR1 positive breast cancer patient to treatment with an anti-estrogen drug, comprising quantitatively determining, in a biological sample comprising cancer cells obtained from said patient, one or more of the following variables:
 (i) ESR1 Group Score; and   (ii) the expression levels of the RNA transcripts of one or more of the following individual genes ESR1, SCUBE2, TFRC, and BCL2, or their expression products; wherein   for every unit of increased numerical value of the ESR1 group score, ESR1, SCUBE2, or BCL2 variables said patient is identified to have a proportionately increased likelihood of a beneficial response to treatment with an anti-estrogen drug, and for every unit of increased numerical value of the TFRC variable said patient is identified to have a proportionately decreased likelihood of a beneficial response to treatment with an anti-estrogen drug.   
     
     
         48 . The method of  claim 47  wherein the ESR1 group score, or the expression level of the ESR1 gene or its expression product is determined. 
     
     
         49 . The method of  claim 48  wherein the expression level of the ESR1 gene or its expression product is determined. 
     
     
         50 . The method of  claim 47  wherein the anti-estrogen drug is selected from the group consisting of tamixofen, toremifene, anastrozole, and megasterol acetate. 
     
     
         51 . The method of  claim 50  wherein the anti-estrogen drug is tamoxifen. 
     
     
         52 . The method of  claim 47  further comprising the step of preparing a report for said patient, including a treatment recommendation. 
     
     
         53 . The method of  claim 52  wherein treatment with anti-estrogen alone, chemotherapy alone, or chemotherapy plus anti-estrogen is recommended by consulting a table or graph along one axis of which ESR1 expression level is displayed, either as a continuous variable or in ESR1 expression ranges, and along the other axis of which likelihood of cancer recurrence is displayed, either as a continuous variable or in risk ranges. 
     
     
         54 .- 75 . (canceled)