Gene classifiers and uses thereof in skin cancers
AssigneeDermtech, Inc.
InventorsJohn Daniel DOBAK, III, Burkhard JANSEN, Zuxu YAO
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Abstract
Disclosed herein, in certain embodiments, are methods of detecting the presence of a skin cancer based on molecular risk factors. In some instances, the skin cancer is cutaneous T cell lymphoma (CTCL). In some cases, the skin cancer is mycosis fungoides (1VIF) or Sézary syndrome (SS).
Claims25
A method of analyzing a gene expression signature associated with cutaneous T cell lymphoma (CTCL) in a skin sample, comprising:
- a) isolating nucleic acids from the skin sample obtained from a subject suspected of having CTCL by applying an adhesive patch to a skin region of the subject in a manner sufficient to adhere skin sample cells to the adhesive patch, and removing the adhesive patch from the skin region in a manner sufficient to retain the adhered skin sample cells to the adhesive patch, wherein the skin sample cells comprise cells from the stratum corneum;
- b) measuring expression level of a panel of target genes known to be upregulated or downregulated in subjects with CTCL compared to the expression level of equivalent target genes in a paired control skin sample;
- c) using a software program or module to evaluate the gene expression levels determined in step (b) to determine the gene expression signature of the skin sample;
- and;
- d) providing a sample score indicative of the presence or absence and/or the progression of CTCL based on the gene expression signature determined in step (c).
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A method of treating a subject with cutaneous T cell lymphoma (CTCL), comprising:
- a. identifying a subject suspected of having CTCL;
- b. isolating nucleic acids from a skin sample obtained from the subject by applying an adhesive patch to a skin region of the subject in a manner sufficient to adhere skin sample cells to the adhesive patch, and removing the adhesive patch from the skin region in a manner sufficient to retain the adhered skin sample cells to the adhesive patch, wherein the skin sample cells comprise cells from the stratum corneum;
- c. measuring or detecting an expression level of at least one target gene known to be upregulated or downregulated in subjects with CTCL by:
- contacting the isolated nucleic acids with a set of probes that recognize the target gene;
- and
- measuring or detecting binding between the at least one target gene and the set of probes;
- d. determining whether the subject has CTCL based on the expression level of the at least one target gene;
- and
- e. administering a CTCL treatment to the subject when the subject is determined to have CTCL based on the expression level of the at least one target gene, and not administering the CTCL treatment to the subject when the subject is not determined to have CTCL based on the expression level of the at least one target gene.
A kit for determining the presence of cutaneous T cell lymphoma (CTCL) in a skin sample, comprising:
- a. an adhesive patch comprising an adhesive matrix configured to adhere skin sample cells from the stratum corneum of a subject;
- b. a nucleic acid isolation reagent;
- and
- c. a plurality of probes that recognize at least one target gene known to be upregulated or downregulated in subjects with CTCL.
Dependencies are inferred from the claim text.