Method for Detection of Melanoma

Abstract

The present invention provides non-invasive methods for detecting, monitoring, staging, and diagnosing malignant melanoma in a skin sample of a subject. The methods include analyzing expression in skin sample of one or more melanoma skin markers. The melanoma skin markers include IL-1 RI, endothelin-2, ephrin-A5, IGF Binding Protein 7, HLA-A0202 heavy chain, Activin A (βA subunit), TNF RII, SPC4, and CNTF Rα. The skin sample can include nucleic acids, and can be a human skin sample from a lesion suspected of being melanoma.

1 . A non-invasive method for detecting malignant melanoma in a skin sample of a subject, the method comprising analyzing expression in the skin sample of one or more melanoma skin markers selected from Interleukin-1 RI (IL-1 RI), endothelin-2, ephrin-A5, Insulin-like Growth Factor (IGF) Binding Protein 7, Human Leukocyte Antigen (HLA)-A0202 heavy chain, Activin A (A subunit), Tumor Necrosis Factor (TNF) RII, SPC4, and Ciliary Neurotrophic Factor (CNTF) Rα, wherein expression of the melanoma skin markers is related to melanoma, thereby detecting melanoma in the skin sample. 
     
     
         2 . The method of  claim 1 , wherein the skin sample is obtained by applying at least one application of an adhesive to the skin and removing the adhesive from the skin, or scraping the skin with an instrument, to remove a sample comprising a nucleic acid from the skin. 
     
     
         3 . The method of  claim 1 , wherein expression is analyzed for at least one of IL-1 RI, endothelin-2, and ephrin-A5, and wherein a decrease in IL-1 RI expression levels, or an increase in endothelin-2 or ephrin-A5 expression levels is indicative of melanoma. 
     
     
         4 . The method of  claim 1 , wherein expression is analyzed for IL-1 RI, endothelin-2, and ephrin-A5, and wherein a decrease in IL-1 RI expression levels, and an increase in endothelin-2 or ephrin-A5 expression levels is indicative of early stage melanoma. 
     
     
         5 . The method of  claim 1 , wherein expression is analyzed for one or more of IGF Binding Protein 7, HLA-A0202 heavy chain, Activin A (βA subunit), TNF RII, SPC4, and CNTF Ra wherein an increase in expression levels of the one or more melanoma skin markers is indicative of melanoma. 
     
     
         6 . The method of  claim 1 , wherein expression is analyzed for IGF Binding Protein 7, HLA-A0202 heavy chain, Activin A (βA subunit), TNF RII, SPC4, and CNTF Ra wherein an increase in expression levels of the melanoma skin markers is indicative of melanoma. 
     
     
         7 . The method of  claim 2 , wherein the sample is obtained in a manner such that the skin nucleic acid profile after application is not affected for up to about two hours. 
     
     
         8 . The method of  claim 2 , wherein the skin sample is isolated by applying the adhesive surface to the skin between one and two times to obtain the skin sample. 
     
     
         9 . The method of  claim 2 , wherein the adhesive surface comprises an adhesive tape and the skin sample is isolated from a lesion suspected to be melanoma. 
     
     
         10 . The method of  claim 2 , wherein the skin sample is isolated by scraping an outer layer of skin with a rigid instrument and the skin sample is isolated from a lesion suspected to be melanoma. 
     
     
         11 . The method of  claim 2 , wherein the nucleic acid comprises RNA, and expression is analyzed by analyzing RNA levels of one or more of the melanoma skin markers. 
     
     
         12 . The method of  claim 11 , wherein the RNA comprises mRNA, and expression is analyzed by analyzing mRNA levels of one or more of the melanoma skin markers. 
     
     
         13 . The method of  claim 1 , wherein the skin sample comprises nucleic acids, and wherein expression of the melanoma skin markers is analyzed by detecting polynucleotides encoding melanoma skin markers. 
     
     
         14 . The method of  claim 1 , wherein the skin sample comprises nucleic acids, wherein expression of the melanoma skin markers is analyzed by measuring the amount of polynucleotides encoding the melanoma skin markers, and wherein an increase or a decrease in expression of the melanoma skin markers is indicative of malignant melanoma. 
     
     
         15 . The method of  claim 2 , wherein expression of the melanoma skin markers is analyzed by applying the nucleic acids to a bioarray. 
     
     
         16 . The method of  claim 1 , wherein the skin sample is a human skin sample isolated from a lesion suspected to be melanoma. 
     
     
         17 . The method of  claim 1 , wherein expression of IL-1 RI, endothelin-2, ephrin-A5, IGF Binding Protein 7, HLA-A0202 heavy chain, Activin A (βA subunit), TNF RII, SPC4, and CNTF Rα is analyzed in the nucleic acid sample, wherein a decrease in expression levels of IL-1 RI is related to early stage melanoma, an increase in expression levels of endothelin-2 and ephrin-A5 are related to early stage melanoma, and an increase in expression levels of IGF Binding Protein 7, HLA-A0202 heavy chain, Activin A (βA subunit), TNF RII, SPC4, and CNTF Rα is related to late stage melanoma. 
     
     
         18 . The method of  claim 1 , wherein expression is analyzed for at least one of endothelin-2 and ephrin-A5. 
     
     
         19 . A non-invasive method for staging malignant melanoma in a skin sample from a human subject, the method comprising analyzing expression in the skin sample of one or more melanoma skin markers selected from Interleukin-1 RI (IL-1 RI), endothelin-2, ephrin-A5, Insulin-like Growth Factor (IGF) Binding Protein 7, Human Leukocyte Antigen (HLA)-A0202 heavy chain, Activin A (βA subunit), Tumor Necrosis Factor (TNF) RII, SPC4, and Ciliary Neurotrophic Factor (CNTF) Rα, wherein expression of the melanoma skin markers is related to a stage of melanoma, thereby staging melanoma in the skin sample. 
     
     
         20 . The method of  claim 19 , wherein the nucleic acid sample is obtained by applying at least one application of an adhesive to the skin and removing the adhesive from the skin, or scraping the skin with an instrument to remove a sample comprising a nucleic acid from the skin. 
     
     
         21 . The method of  claim 19 , wherein expression is analyzed for at least one of IL-1 RI, endothelin-2, and ephrin-A5, and wherein a decrease in expression levels of IL-1 RI is indicative of early stage melanoma, and an increase in expression levels of endothelin-2 and ephrin-A5 is indicative of early stage melanoma. 
     
     
         22 . The method of  claim 19 , wherein expression is analyzed for IL-1 RI, endothelin-2, and ephrin-A5, and wherein a decrease in expression levels of IL-1 RI and an increase in expression levels of endothelin-2 and ephrin-A5 is indicative of early stage melanoma. 
     
     
         23 . The method of  claim 19 , wherein expression is analyzed for one or more of IGF Binding Protein 7, HLA-A0202 heavy chain, Activin A (βA subunit), TNF RII, SPC4, and CNTF Ra and wherein increased expression of the one or more melanoma skin marker is indicative of late-stage melanoma. 
     
     
         24 . The method of  claim 19 , wherein expression is detected for IGF Binding Protein 7, HLA-A0202 heavy chain, Activin A (βA subunit), TNF RII, SPC4, and CNTF Rα, and wherein increased expression of the melanoma skin markers is indicative of late-stage melanoma. 
     
     
         25 . The method of  claim 19 , wherein expression is analyzed IL-1 RI, endothelin-2, ephrin-A5, IGF Binding Protein 7, HLA-A0202 heavy chain, Activin A (βA subunit), TNF RII, SPC4, and CNTF Rα in the nucleic acid sample, wherein a decrease in expression levels of IL-1 RI and an increase in expression levels of endothelin-2 and ephrin-A5 is indicative of early stage melanoma and an increase in expression of IGF Binding Protein 7, HLA-A0202 heavy chain, Activin A (βA subunit), TNF RII, SPC4, and CNTF Rα is indicative of late stage melanoma. 
     
     
         26 . A non-invasive method for staging malignant melanoma in a skin sample of a human subject, the method comprising
 a) obtaining a skin sample by applying an adhesive surface to the skin and removing the adhesive surface from the skin such that a skin sample comprising nucleic acid in an amount sufficient for subsequent detection adheres to the adhesive surface after its removal; and   b) analyzing expression in the nucleic acid of melanoma skin markers selected from Interleukin-1 RI (IL-1 RI), endothelin-2, ephrin-A5, Insulin-like Growth Factor (IGF) Binding Protein 7, Human Leukocyte Antigen (HLA)-A0202 heavy chain, Activin A (βA subunit), Tumor Necrosis Factor (TNF) RII, SPC4, and Ciliary Neurotrophic Factor (CNTF) Rα in the nucleic acid sample, wherein a decrease in expression levels of IL-1 RI and an increase in expression levels of endothelin-2 and ephrin-A5 is indicative of early stage melanoma and an increase in expression of IGF Binding Protein 7, HLA-A0202 heavy chain, Activin A (βA subunit), TNF RII, SPC4, and CNTF Rα is indicative of late stage melanoma.   
     
     
         27 . The method of  claim 26 , wherein the sample is obtained in a manner such that the skin nucleic acid profile after application is not affected for up to about two hours, thereby obtaining a skin sample for use in isolating or detecting a nucleic acid in a skin sample.