Methods and materials for identifying metastatic malignant skin lesions and treating skin cancer

Abstract

This document provides methods and materials for identifying metastatic malignant skin lesions (e.g., malignant pigmented skin lesions). For example, methods and materials for using quantitative PCR results and correction protocols to reduce the impact of basal keratinocyte contamination on the analysis of test sample results to identify metastatic malignant skin lesions are provided. This document also provides methods and materials for treating skin cancer. For example, methods and materials for identifying a mammal (e.g., a human) having a pre-metastatic skin lesion (e.g., pre-metastatic melanoma) and treating that mammal with pentamidine (4,4′-[pentane-1,5-diylbis(oxy)]dibenzenecarboximidamide) are provided.

1 . A method for identifying a metastatic malignant skin lesion, wherein said method comprises:
 (a) determining, within a test sample, the expression level of a marker gene selected from the group consisting of PLAT, ITGB3, LAMB1, and TP53 to obtain a measured expression level of said marker gene for said test sample,   (b) determining, within said test sample, the expression level of a keratinocyte marker gene to obtain a measured expression level of said keratinocyte marker gene for said test sample,   (c) removing, from said measured expression level of said marker gene for said test sample, a level of expression attributable to keratinocytes present in said test sample using said measured expression level of said keratinocyte marker gene for said test sample and a keratinocyte correction factor to obtain a corrected value of marker gene expression for said test sample, and   (d) identifying said test sample as containing a metastatic malignant skin lesion based, at least in part, on said corrected value of marker gene expression for said test sample.   
     
     
         2 . The method of  claim 1 , wherein said keratinocyte marker gene is K14. 
     
     
         3 . The method of  claim 1 , wherein said marker gene is PLAT or ITGB3. 
     
     
         4 . The method of  claim 1 , wherein step (c) comprises (i) multiplying said measured expression level of said keratinocyte marker gene for said test sample by said keratinocyte correction factor to obtain a correction value and (ii) subtracting said correction value from said measured expression level of said marker gene for said test sample to obtain said corrected value of marker gene expression for said test sample. 
     
     
         5 . The method of  claim 1 , wherein said method comprises determining, within said test sample, the expression level of at least two marker genes selected from the group consisting of PLAT, ITGB3, LAMB1, and TP53 to obtain measured expression levels of said at least two marker genes for said test sample. 
     
     
         6 . The method of  claim 1 , wherein said method comprises determining, within said test sample, the expression level of at least three marker genes selected from the group consisting of PLAT, ITGB3, LAMB1, and TP53 to obtain measured expression levels of said at least three marker genes for said test sample. 
     
     
         7 . The method of  claim 1 , wherein said method comprises determining, within said test sample, the expression level of PLAT, ITGB3, LAMB1, and TP53 to obtain measured expression levels of said PLAT, ITGB3, LAMB1, and TP53 for said test sample. 
     
     
         8 . A kit for identifying a metastatic malignant skin lesion, wherein said kit comprises:
 (a) a primer pair for determining, within a test sample, the expression level of a marker gene selected from the group consisting of LAMB1 and TP53 to obtain a measured expression level of said marker gene for said test sample, and   (b) a primer pair for determining, within said test sample, the expression level of a keratinocyte marker gene to obtain a measured expression level of said keratinocyte marker gene for said test sample.   
     
     
         9 . The kit of  claim 8 , wherein said keratinocyte marker gene is K14. 
     
     
         10 . The kit of  claim 8 , wherein said marker gene is LAMB1. 
     
     
         11 . The kit of  claim 8 , wherein said marker gene is TP53. 
     
     
         12 . The kit of  claim 8 , wherein said kit comprises primer pairs for determining, within said test sample, the expression level of LAMB1 and TP53 to obtain measured expression levels of said LAMB1 and TP53 for said test sample. 
     
     
         13 . The kit of  claim 8 , wherein said kit comprises primer pairs for determining, within said test sample, the expression level of PLAT to obtain measured expression levels of said PLAT for said test sample. 
     
     
         14 . The kit of  claim 8 , wherein said kit comprises primer pairs for determining, within said test sample, the expression level of ITGB3 to obtain measured expression levels of said ITGB3 for said test sample. 
     
     
         15 . The kit of  claim 8 , wherein said kit comprises primer pairs for determining, within said test sample, the expression level of PLAT and ITGB3 to obtain measured expression levels of said ITGB3 and PLAT for said test sample. 
     
     
         16 . A method for identifying a metastatic malignant skin lesion, wherein said method comprises:
 (a) determining, within a test sample, the expression level of a marker gene selected from the group consisting of PLAT, ITGB3, LAMB1, and TP53 to obtain a measured expression level of said marker gene for said test sample,   (b) determining, within said test sample, the expression level of a keratinocyte marker gene to obtain a measured expression level of said keratinocyte marker gene for said test sample,   (c) removing, from said measured expression level of said marker gene for said test sample, a level of expression attributable to keratinocytes present in said test sample using said measured expression level of said keratinocyte marker gene for said test sample and a keratinocyte correction factor to obtain a corrected value of marker gene expression for said test sample, and   (d) identifying said test sample as containing a metastatic malignant skin lesion based, at least in part, on said corrected value of marker gene expression for said test sample.   
     
     
         17 . The method of  claim 16 , wherein said keratinocyte marker gene is K14. 
     
     
         18 . The method of  claim 16 , wherein said marker gene is LAMB1 or TP53. 
     
     
         19 . The method of  claim 16 , wherein step (c) comprises (i) multiplying said measured expression level of said keratinocyte marker gene for said test sample by said keratinocyte correction factor to obtain a correction value and (ii) subtracting said correction value from said measured expression level of said marker gene for said test sample to obtain said corrected value of marker gene expression for said test sample. 
     
     
         20 - 29 . (canceled)