Diagnosis of Melanoma and Solar Lentigo by Nucleic Acid Analysis

Abstract

The present invention provides methods for diagnosing melanoma and/or solar lentigo in a subject by analyzing nucleic acid molecules obtained from the subject. The present invention also provides methods for distinguishing melanoma from solar lentigo and/or dysplastic nevi and/or normal pigmented skin. The methods include analyzing expression or mutations in epidermal samples, of one or more skin markers. The methods can include the use of a microarray to analyze gene or protein profiles from a sample.

1 . A method for characterizing a skin lesion in a subject comprising analyzing a nucleic acid molecule from one or more genes listed in Tables 1-8, 10-12, and 15 in a sample of the skin lesion, thereby characterizing a skin lesion of the subject. 
     
     
         2 . The method of  claim 1 , wherein the nucleic acid molecule is RNA. 
     
     
         3 . The method of  claim 1 , wherein analyzing the nucleic acid molecule comprises detecting one or more mutations in the nucleic acid sequence of the nucleic acid molecule. 
     
     
         4 . The method of  claim 3 , wherein the one or more mutations are selected from the group consisting of a substitution, a deletion, and an insertion. 
     
     
         5 . The method of  claim 1 , further comprising amplifying the nucleic acid molecule obtained from the sample prior to analyzing. 
     
     
         6 . The method of  claim 1 , wherein the sample is obtained by applying an adhesive tape to a target area of skin in a manner sufficient to isolate the sample adhering to the adhesive tape. 
     
     
         7 . The method of  claim 1 , further comprising using the characterizing to determine a treatment regimen. 
     
     
         8 . The method of  claim 2 , wherein the isolated nucleic acid molecule or an amplification product thereof, is applied to a microarray. 
     
     
         9 . The method of  claim 8 , wherein an expression profile is detected using a microarray. 
     
     
         10 . The method of  claim 1 , wherein the sample is obtained from a biopsy taken at the site of the skin lesion or surrounding margin. 
     
     
         11 . The method of  claim 6 , wherein the tape comprises a rubber adhesive on a polyurethane film. 
     
     
         12 . The method of  claim 6 , wherein about one to ten adhesive tapes or one to ten applications of a tape are applied and removed from the skin. 
     
     
         13 . The method of  claim 6 , wherein about one to eight adhesive tapes or one to eight applications of a tape are applied and removed from the skin. 
     
     
         14 . The method of  claim 6 , wherein about one to five adhesive tapes or one to five applications of a tape are applied and removed from the skin. 
     
     
         15 . The method of  claim 6 , wherein the method further comprises taking a biopsy of the target area of the skin. 
     
     
         16 . The method of  claim 2 , wherein the analyzing is performed in situ. 
     
     
         17 . A method of distinguishing melanoma from dysplastic nevi or normal pigmented skin in a subject comprising analyzing a nucleic acid molecule from one or more genes listed in Table 8, in a sample from the subject, thereby distinguishing melanoma from dysplastic nevi or normal pigmented skin in a subject. 
     
     
         18 - 32 . (canceled) 
     
     
         33 . A method of distinguishing solar lentigo from melanoma or dysplastic nevi or normal pigmented skin in a subject comprising analyzing a nucleic acid molecule from one or more genes listed in Tables 10-12 and 15, in a sample from the subject, thereby distinguishing melanoma from dysplastic nevi or normal pigmented skin in a subject. 
     
     
         34 - 48 . (canceled) 
     
     
         49 . A method for diagnosing melanoma in a subject comprising detecting an altered level of a target protein in a sample from the subject, as compared to the level of the target protein in a corresponding sample from a subject that does not have melanoma, wherein the protein is an expression product of a gene listed in Tables 8, thereby diagnosing melanoma in the subject. 
     
     
         50 - 62 . (canceled) 
     
     
         63 . A method for diagnosing solar lentigo in a subject comprising detecting an altered level of a target protein in a sample from the subject, as compared to the level of the target protein in a corresponding sample from a subject that does not have melanoma, wherein the protein is an expression product of a gene listed in Tables 10-12, thereby diagnosing melanoma in the subject. 
     
     
         64 - 76 . (canceled) 
     
     
         77 . A method for diagnosing melanoma in a subject, comprising:
 a) providing a gene expression profile of a target area suspected of being melanoma on the skin of the subject, wherein the target area of the skin simultaneously expresses a plurality of genes at the protein level that are markers for melanoma; and   b) comparing the subject's gene expression profile to a reference gene expression profile obtained from a corresponding normal skin sample, wherein the reference gene expression profile comprises an expression value of a target gene selected from the group consisting of endothelin receptor type B, Hypothetical protein MGC40222, tetratricopeptide repeat domain 3, staufen RNA binding protein (Drosophila), actinin alpha 4, KIAA1212, glycoprotein M6B, v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog, c-Maf-inducing protein, adaptor-related protein complex 2 mu 1 subunit, syntaxin 5A, chemokine-like factor superfamily 4, UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase polypeptide 5, fibrosin 1, likely ortholog of mouse neighbor of Punc E11, myosin heavy polypeptide 14, preferentially expressed antigen in melanoma, jurnonji domain containing 3, BCL2-related protein A1, formin binding protein 1, or any combination thereof.   
     
     
         78 - 81 . (canceled) 
     
     
         82 . A method for diagnosing solar lentigo in a subject, comprising:
 a) providing a gene expression profile of a target area suspected of being melanoma on the skin of the subject, wherein the target area of the skin simultaneously expresses a plurality of genes at the protein level that are markers for melanoma; and   b) comparing the subject's gene expression profile to a reference gene expression profile obtained from a corresponding normal skin sample, wherein the reference gene expression profile comprises an expression value of a target gene selected from the group consisting of interferon regulatory factor 6, claudin 23, melan-A, osteopetrosis associated transmembrane protein 1, RAS-like family 11 member B, actinin alpha 4, transmembrane protein 68, Glycine-rich protein (GRP3S), Transcription factor 4, hypothetical protein FLJ20489, cytochrome c somatic, transcription factor 4, Forkhead box P1, transducer of ERBB2-2, glutaminyl-peptide cyclotransferase (glutaminyl cyclase), hypothetical protein FLJ10770, selenophosphate synthetase 2, embryonal Fyn-associated substrate, Kruppel-like factor 8, Discs large homolog 5 (Drosophila), regulator of G-protein signalling 10, ADP-ribosylation factor related protein 2, TIMP metallopeptidase inhibitor 2,5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase, similar to RIKEN cDNA 5730421E18 gene, Regulator of G-protein signalling 10, Nuclear RNA-binding protein putative, tyrosinase-related protein 1, TIMP metallopeptidase inhibitor 2, Claudin 1, transcription factor 4, solute carrier family 16 (monocarboxylic acid transporters) member 6 (similar to solute carrier family 16 member 6; monocarboxylate transporter 6), selenophosphate synthetase 2, annexin A5, melan-A, pleckstrin homology-like domain, family A, member 1, breakpoint cluster region; similar to breakpoint cluster region isoform 1, Lipoma HMGIC fusion partner-like 3, A kinase (PRKA) anchor protein 13, Rho-related BTB domain containing 3, Ras association (RalGDS/AF-6) domain family 8, ADP-ribosylation factor-like 6 interacting protein 2, E74-like factor 5 (ets domain transcription factor), hypothetical protein FLJ21924, zinc finger, DM-IC-type containing 11, membrane component, chromosome 11, surface marker 1, FLJ20259 protein, Chromosome 9 open reading frame 3, serum/glucocorticoid regulated kinase, ectonucleotide pyrophosphatase/phosphodiesterase 2 (autotaxin), RNA binding protein with multiple splicing, apolipoprotein L, 2, insulin receptor substrate 2, chromosome 14 open reading frame 65, hypothetical protein MGC10911, related RAS viral (r-ras) oncogene homolog 2, T-cell immunomodulatory protein/T-cell immunomodulatory protein, KIAA0754 protein, chromosome 14 open reading frame 1, tripartite motif-containing 63, or any combination thereof.   
     
     
         83 - 86 . (canceled) 
     
     
         87 . A kit for characterizing a skin lesion in a subject comprising a skin sample collection device and one or more probes or primers that selectively bind to one or more nucleic acid molecules in Tables 10-12 and 15, or to a nucleic acid or protein expression product of a nucleic acid molecule in Tables 10-12 and 15. 
     
     
         88 - 94 . (canceled) 
     
     
         95 . A kit for characterizing a skin lesion in a subject comprising an applicator and one or more probes or primers that selectively bind to one or more of nucleic acid molecules in Tables 10-12, and 15, or to a nucleic acid or protein expression product of a nucleic acid molecule in any of Table 10-12, and 15. 
     
     
         96 - 99 . (canceled)