Methods for Identifying Progression of a Primary Melanoma

Abstract

Methods of using T cell frequency (TCFR) in melanoma, e.g., as determined by high throughput DNA sequencing of the TCRB gene, as a predictor of disease progression and survival in patients with primary melanoma, and to select and treat subjects.

What is claimed is: 
     
         1 . A method of treating a subject who has primary melanoma, the method comprising:
 obtaining a biopsy sample from the primary melanoma;   determining the T cell frequency (TCFr) of said sample; and   treating said subject with an aggressive treatment when the TCFr is greater than a reference level.   
     
     
         2 . A method of selecting a subject with primary melanoma for aggressive treatment, the method comprising:
 obtaining a biopsy sample from the primary melanoma;   determining the T cell frequency (TCFr) of said sample; and   selecting a subject who has a TCFr below a reference level for aggressive treatment.   
     
     
         3 . A method of predicting whether a subject with primary melanoma is likely to progress to metastatic melanoma, the method comprising:
 obtaining a biopsy sample from the primary melanoma;   determining the T cell frequency (TCFr) of said sample; and   identifying a subject who has a TCFr below a reference level as likely to progress to metastatic melanoma.   
     
     
         4 . The method of  claim 1 , wherein the primary melanoma is cutaneous melanoma. 
     
     
         5 . The method of  claim 4 , wherein the primary melanoma is 1-4 mm thick. 
     
     
         6 . The method of  claim 5 , wherein the primary melanoma is stage I to IIC. 
     
     
         7 . The method of  claim 1 , wherein determining the T cell frequency (TCFr) of said skin sample comprises analyzing T-cell receptor beta (TCR β) gene sequences in substantially every T cell in the sample, quantitating total nucleated cells and calculating the proportion of T cells in the sample relative to its total number of nucleated cells. 
     
     
         8 . The method of  claim 7 , wherein said analyzing is performed by high-throughput DNA sequencing. 
     
     
         9 . The method of  claim 1 , wherein the aggressive treatment is targeted treatment, immunotherapy, chemotherapy, and/or radiation, or a combination thereof. 
     
     
         10 . The method of  claim 9 , wherein the chemotherapy comprises administration of one or more nitrosoureas; alkylating agents; microtubule targeting agents; or platinum-containing agents. 
     
     
         11 . The method of  claim 9 , wherein the targeted treatment comprises a BRAF inhibitor and/or a MEK inhibitor. 
     
     
         12 . The method of  claim 9 , wherein the immunotherapy comprises administration of a checkpoint inhibitor. 
     
     
         13 . The method of  claim 9 , wherein the immunotherapy comprises administration of a vaccines targeting melanoma cells, peptide-based vaccine, viral vector-based vaccine, or dendritic cell vaccine. 
     
     
         14 . The method of  claim 1 , wherein the reference level is 20%. 
     
     
         15 . The method of  claim 1 , further comprising determining one or more of Breslow thickness; ulceration status; levels of mitoses/mm 2 ; and nodal disease in the sample, and determining prognosis or selecting therapy based on TCFr and Breslow thickness; ulceration status; levels of mitoses/mm 2 ; and/or nodal disease in the sample.