Methods for Treating Urothelial Carcinoma Using Genotypic and Phenotypic Biomarkers

Abstract

New methods for treating patents for urothelial cancer (UC) include combining selected phenotypic variables with levels of genotypic expression into a metric, the “G+P INDEX.” The G+P INDEX combines age, sex, smoking history, presence of hematuria, and frequency of hematuria with genotypic expression of the genetic markers, MDK, CDC2, HOXA13, IGFBP5, and optionally IL8Rb, then determining of the G+P INDEX value obtained for a patient is within one of three groups, either: (1) at High Risk of UC, (2) at Risk of UC, or (3) at Low Risk of UC. For groups 1 and 2, further clinical and laboratory work up or treatment is indicated, and patients in group 3 are monitored periodically to determine the need for further clinical workup. Using the G+P INDEX can save substantial time, effort, and funds by avoiding unnecessary medical diagnostic procedures for patients having or are at risk for developing UC.

We claim: 
     
         1 . A method for treating a patient for urothelial carcinoma comprising the steps:
 a) providing a sample of urine from a patient;   b) quantifying a value, M1, comprising detecting and quantifying the levels of expression of the human genotypic markers, midkine (MDK) using a forward primer having the sequence of SEQ ID NO.3, cyclin dependent kinase 1 (CDC2), homeobox A13 (HOXA13), insulin like growth factor binding protein (IGFBP5) in said sample where MI=[IGFBP5]−[HOXA13]+[MDK]+[CDC2] in said sample, where the square brackets “[ ]” are defined as the log of concentrations in the sample of urine of each of said genotypic markers;   c) detecting the log concentration of IL8Rb in said sample;   d) assessing the phenotypic variables: detecting in the urine of 3 or more red blood cells per high power field in a 6-month period (HFREQ), subject's age greater than 50 years AgeGT50), gender, smoking history (SMK), and detecting the red blood cell count (RBC) of said patient and   e) quantifying a value of G+P INDEX according to either:
     G+P  INDEX=(1 *H FREQ+3*Gender+4* SMK )+(5* M 1+2* IL 8 Rb ), or  formula (i),
 
     G+P  INDEX=( w 1 *H FREQ+ w 2*AgeGT50+ w 3*Gender+ w 4* SMK+w 5* RBC )+( w 6* M 1+ w 7* IL 8 Rb ), or  formula (ii),
 
     G+P  INDEX=−8.46+0.79  IGF− 1.60  HOXA+ 2.10  MDK+ 0.95  CDC− 0.38  IL 8 Rb+ 0.98  SNS+ 0.56  H freq+1.11 Gender+0.64 Age; where the terms  w 1- w 7 are respectively the weights assigned to each of the variables; where  formula (iii),
 
   HFREQ means the frequency of finding 3 or more red blood cells per high power field in a 6-month period; if frequency is low, then HFREQ is set to 0, and if higher than 3 red blood cells per high power field, then HFREQ is set to 1;   AgeGT50 refers to subject's age, if greater than 50 years then AgeGT50 is set to 1, and if less than 50 years, then AgeGT50 is set to 0;   Gender is assigned a value of 1 for male, and 0 for female;   SMK means whether the subject is a current or ex-smoker; if non-smoker then SMK is set to 0 and if a smoker, then SMK is set to 1;   RBC means red blood cell count: if 25 or more then RBC is set to 1, and if less than 25, then RBS is set to 0;   if M1>4.5 then M1 is set to 1, if M1 is less than 4.5, then M1 is set to 0;   if IL8Rb>2.5 then IL8Rb is set to 1, if IL8Rb is less than 2.5, IL8Rb is set to 0;   the symbols “*” means the multiplication operator, and   weighting factors, w1-w7 are respectively the weights assigned to each of the variables listed in the G+P INDEX; and if the G+P INDEX has value of from 6-10, said patient undergoes additional clinical or laboratory tests, cytology, uretoscopy, and/or CT scan.   
     
     
         2 . The method of  claim 1 , where if the G+P INDEX has a value of from 11-15, said patient is tested for flexibile cystoscopy, abdonimal ultrasound, or is treated immediately for urothelial carcinoma. 
     
     
         3 . The method of  claim 1 , wherein if the G+P INDEX has a value from 0 to 5, said patient receives the normal standard of care and be placed on a waiting list. 
     
     
         4 . The method of  claim 1 , wherein expression of MDK is determined using a reverse primer having the sequence of SEQ ID No. 4. 
     
     
         5 . The method of  claim 1 , wherein expression of MDK is determined using a probe having the sequence of SEQ ID NO.5. 
     
     
         6 . The method of  claim 1 , wherein expression of CDC2 is determined using a forward primer having the sequence of SEQ ID NO.9. 
     
     
         7 . The method of  claim 1 , wherein expression of CDC2 is determined using a reverse primer having the sequence of SEQ ID NO.10. 
     
     
         8 . The method of  claim 1 , wherein expression of CDC2 is determined using a probe having the sequence of SEQ ID NO.11. 
     
     
         9 . The method of  claim 1 , wherein expression of CDC2 is determined using a forward primer having the sequence of SEQ ID NO.9. 
     
     
         10 . The method of  claim 1 , wherein expression of HOXA13 is determined using a forward primer having the sequence of SEQ ID NO.12. 
     
     
         11 . The method of  claim 1 , wherein expression of HOXA13 is determined using a reverse primer having the sequence of SEQ ID NO.13. 
     
     
         12 . The method of  claim 1 , wherein expression of HOXA13 is determined using a probe having the sequence of SEQ ID NO.14. 
     
     
         13 . The method of  claim 1 , wherein expression of IGFBP5 is determined using a forward primer having the sequence of SEQ ID NO.6. 
     
     
         14 . The method of  claim 1 , wherein expression of IGFBP5 is determined using a reverse primer having the sequence of SEQ ID NO.7. 
     
     
         15 . The method of  claim 1 , wherein expression of IGFBP5 is determined using a probe having the sequence of SEQ ID NO.8. 
     
     
         16 . The method of  claim 1 , wherein expression of IL8Rb is determined using a forward primer having the sequence of SEQ ID NO.15. 
     
     
         17 . The method of  claim 1 , wherein expression of IL8Rb is determined using a reverse primer having the sequence of SEQ ID NO.16. 
     
     
         18 . The method of  claim 1 , wherein expression of IL8Rb is determined using a probe having the sequence of SEQ ID NO.15. 
     
     
         19 . The method of  claim 1  for treating a patient having an inflammatory condition of the bladder, comprising the steps:
 a) providing a sample of urine from said patient; 
 b) detecting the log concentration of IL8Rb in said sample using a forward primer having the sequence of SEQ ID NO.15, wherein if the level of IL8Rb in said sample is greater than the levels of IL8Rb in a group of patients not having an inflammatory condition of the bladder, said patient is treated using an antiinflammatory agent. 
 
     
     
         20 . The method of  claim 1 , where said human genotypic markers are measured as mRNA or as cDNA.