Gene Expression Profile Algorithm for Calculating a Recurrence Score for a Patient with Kidney Cancer

Abstract

The present invention provides algorithm-based molecular assays that involve measurement of expression levels of genes from a biological sample obtained from a kidney cancer patient. The present invention also provides methods of obtaining a quantitative score for a patient with kidney cancer based on measurement of expression levels of genes from a biological sample obtained from a kidney cancer patient. The genes may be grouped into functional gene subsets for calculating the quantitative score and the gene subsets may be weighted according to their contribution to cancer recurrence.

What is claimed is: 
     
         1 . A method for obtaining a recurrence score (RS) for a patient with kidney cancer, comprising:
 measuring a level of at least one RNA transcript, or expression product thereof, selected from APOLD1, EDNRB, NOS3, PPA2B, EIF4EBP1, LMNB1, TUBB2A, CCL5, CEACAM1, CX3CL1, and IL-6 in a tumor sample obtained from the patient;   normalizing the level against a level of at least one reference RNA transcript, or expression product thereof, in the tumor sample to provide a normalized level of the RNA transcript, or expression product thereof;   assigning the normalized level to a gene subset;   weighting the gene subset according to its contribution to cancer recurrence;   calculating a recurrence score (RS) for the patient using the weighted gene subset and the normalized levels; and   creating a report comprising the RS.   
     
     
         2 . A method of predicting a likelihood of a clinical outcome for a patient with kidney cancer, comprising:
 determining a level of one or more RNA transcripts, or an expression product thereof, in a tumor sample obtained from the patient, wherein the one or more RNA transcripts, or an expression product thereof, is selected from APOLD1, EDNRB, NOS3, PPA2B, EIF4EBP1, LMNB1, TUBB2A, CCL5, CEACAM1, CX3CL1, and IL-6;   assigning the one or more RNA transcripts, or an expression product thereof, to one or more gene subsets;   calculating a quantitative score for the patient by weighting the level of one or more RNA transcripts, or an expression product thereof, by their contribution to a clinical outcome; and   predicting a likelihood of a clinical outcome for the patient based on the quantitative score.   
     
     
         3 . The method of  claim 2 , wherein an increase in the quantitative score correlates with an increased likelihood of a negative clinical outcome. 
     
     
         4 . The method of  claim 2  or  3 , wherein the clinical outcome is recurrence of kidney cancer. 
     
     
         5 . The method of any one of  claims 1 - 4 , wherein the level of at least one RNA transcript is determined by quantitative RT-PCR. 
     
     
         6 . The method of any one of  claims 1 - 5 , wherein the gene subset is selected from a vascular normalization group, a cell growth/division group, and an immune response group. 
     
     
         7 . The method of any one of  claims 1 - 6 , wherein the level of at least one RNA transcript from a vascular normalization group selected from APOLD1, EDNRB, NOS3, and PPAP2B is measured. 
     
     
         8 . The method of any one of  claims 1 - 7 , wherein the level of at least one RNA transcript from a cell growth/division group selected from EIF4EBP1, LMNB1, and TUBB2A is measured. 
     
     
         9 . The method of any one of  claims 1 - 8 , wherein the level of at least one RNA transcript from an immune response group selected from CCL5, CEACAM1, and CX3CL1 is measured. 
     
     
         10 . The method of any one of  claims 1 - 9 , wherein the level of an RNA transcript of IL-6 is measured. 
     
     
         11 . A method for obtaining a recurrence score (RS) for a patient with kidney cancer, comprising:
 extracting RNA from a tumor sample obtained from the patient;   reverse transcribing an RNA transcript of at least one prognostic gene selected from APOLD1, EDNRB, NOS3, PPA2B, EIF4EBP1, LMNB1, TUBB2A, CCL5, CEACAM1, CX3CL1, and IL-6 to produce a cDNA of the prognostic gene;   amplifying the cDNA of the prognostic gene;   producing an amplicon of the RNA transcript of the prognostic gene;   assaying a level of the amplicon of the prognostic gene;   normalizing the level against the level of an amplicon of at least one reference RNA transcript in the tumor sample to provide a normalized amplicon level of the prognostic gene;   assigning the normalized amplicon level to a gene subset;   weighting the gene subset according to its contribution to cancer recurrence;   calculating a recurrence score (RS) for the patient using the weighted gene subset and the normalized amplicon level; and   generating a report comprising the RS.   
     
     
         12 . The method of  claim 11 , wherein the gene subset is selected from a vascular normalization group, a cell growth/division group, and an immune response group. 
     
     
         13 . The method of  claim 11  or  12 , wherein the level of the amplicon from a vascular normalization group selected from APOLD1, EDNRB, NOS3, and PPAP2B is measured. 
     
     
         14 . The method of any of  claims 11 - 13 , wherein the level of the amplicon from a cell growth/division group selected from EIF4EBP1, LMNB1, and TUBB2A is measured. 
     
     
         15 . The method of any one of  claims 11 - 14 , wherein the level of the amplicon from an immune response group selected from CCL5, CEACAM1, and CX3CL1 is measured. 
     
     
         16 . The method of any one of  claims 11 - 15 , wherein the level of the amplicon of IL-6 is measured. 
     
     
         17 . The method of any one of  claims 1 - 17 , wherein the kidney cancer is renal cell carcinoma (RCC). 
     
     
         18 . The method of  claim 17 , wherein the RCC is clear cell renal cell carcinoma (ccRCC). 
     
     
         19 . The method of any one of  claims 1 - 18 , wherein the tumor sample is obtained from a biopsy. 
     
     
         20 . The method of any one of  claims 1 - 19 , wherein the tumor sample is fresh, frozen, or paraffin-embedded and fixed.