Method of classifying a thyroid carcinoma using differential gene expression

Abstract

Disclosed are methods of diagnosing and treating carcinomas, including metastatic thyroid carcinomas using differential gene expression. Also disclosed are novel nucleic acid sequences whose expression is differentially regulated in metastatic and non-metastatic thyroid carcinomas.

What is claimed is:  
     
         1 . A method of categorizing a thyroid carcinoma in a subject, the method comprising: 
 a) providing a test cell population from said subject, wherein at least one cell in said test cell population is capable of expressing one or more nucleic acid sequences selected from the group consisting of MTCs: 8-51;    b) measuring the expression of one or more said nucleic acid sequences in said test cell population;    c) comparing the expression of said nucleic acid sequences to the expression of said nucleic acid sequences in a reference cell population comprising at least one cell whose thyroid carcinoma stage is known; and    d) identifying a difference in expression levels of the MTC sequence, if present, in the test cell population and reference cell population,    thereby categorizing said thyroid carcinoma in said subject.    
     
     
         2 . The method of  claim 1 , wherein said method comprises measuring the expression of one or more nucleic acid sequences selected from the group consisting of MTCs: 8-18.  
     
     
         3 . The method of  claim 1 , wherein said method comprises measuring the expression of one or more nucleic acid sequences selected from the group consisting of MTCs: 19-47.  
     
     
         4 . The method of  claim 1 , wherein said method comprises measuring the expression of one or more nucleic acid sequences selected from the group consisting of MTCs:48-51.  
     
     
         5 . The method of  claim 1 , wherein said method further comprises measuring the expression of one or more nucleic acid sequences selected from the group consisting of MTCs: 1-7.  
     
     
         6 . The method of  claim 2 , wherein said method further comprises measuring the expression of one or more nucleic acid sequences selected from the group consisting of MTCs: 19-47.  
     
     
         7 . The method of  claim 6 , wherein said method further comprises measuring the expression of one or more nucleic acid sequences selected from the group consisting of MTCs:48-51.  
     
     
         8 . The method of  claim 3 , wherein said method further comprises measuring the expression of one or more nucleic acid sequences selected from the group consisting of MTCs:48-51.  
     
     
         9 . The method of  claim 1 , wherein said carcinoma is a metastatic papillary thyroid carcinoma.  
     
     
         10 . The method of  claim 1 , wherein an alteration of the expression of said nucleic acids in said test cell population as compared to said reference cell population indicates that the test cell population has a different thyroid carcinoma stage than the cells in said reference cell population.  
     
     
         11 . The method of  claim 1 , wherein a similar expression pattern of said nucleic acids in said test cell population as compared to said reference cell population indicates that the test cell population has the same thyroid carcinoma stage as the cells in said reference cell population.  
     
     
         12 . The method of  claim 1 , wherein said subject is a human.  
     
     
         13 . The method of  claim 1 , wherein said reference cell population comprises a plurality of cells or a database.  
     
     
         14 . A method of diagnosing a thyroid carcinoma in a subject, the method comprising: 
 a) providing a test cell population from said subject, wherein at least one cell in said test cell population is capable of expressing one or more nucleic acid sequences selected from the group consisting of MTCs 8-51;    b) measuring the expression of one or more said nucleic acid sequences in said test cell population;    c) comparing the expression of said nucleic acid sequences to the expression of said nucleic acid sequences to a reference cell population comprising at least one cell whose thyroid carcinoma stage is known, and    d) identifying a difference in expression levels of the MTC sequence, if present, in the test cell population and reference cell population,    thereby diagnosing a thyroid carcinoma, if present, in said subject.    
     
     
         15 . The method of  claim 2 , wherein said thyroid carcinoma is a metastatic thyroid carcinoma.  
     
     
         16 . A method of assessing the efficacy of a treatment of a thyroid carcinoma in a subject, the method comprising: 
 a) providing a test cell population from said subject, wherein at least one cell in said test cell population is capable of expressing one or more nucleic acid sequences selected from the group consisting of MTCs 8-51;    b) detecting the expression of one or more said nucleic acid sequences in said test cell population;    c) comparing the expression of said nucleic acid sequences to the expression of said nucleic acid sequences to a reference cell population comprising at least one cell whose thyroid carcinoma stage is known; and    d) identifying a difference in expression levels of the MTC sequence, if present, in the test cell population and reference cell population,    thereby assessing the efficacy of treatment of said thyroid carcinoma in said subject.    
     
     
         17 . A method for identifying a therapeutic agent individualized for treating a thyroid carcinoma in a subject, the method comprising: 
 a) providing a test cell population from said subject, wherein at least one cell in said test cell population is capable of expressing one or more nucleic acid sequences selected from the group consisting of MTCs: 8-51;    b) contacting said test cell population with a therapeutic agent;    c) measuring the expression of said nucleic acid sequence in said test cell population;    d) comparing the expression of said nucleic acid sequences to the expression of said nucleic acid sequences in a reference cell population comprising at least one cell whose thyroid carcinoma stage is known; and    e) identifying a difference in expression levels of the MTC sequence, if present, in the test cell population and reference cell population,    thereby identifying a therapeutic agent individualized for said subject.    
     
     
         18 . The method of  claim 17 , wherein said thyroid carcinoma is a metastatic thyroid carcinoma.  
     
     
         19 . A method of identifying a candidate therapeutic agent for treating a thyroid carcinoma, the method comprising: 
 a) providing a test cell population, wherein at least one cell in said test cell population is capable of expressing one or more nucleic acid sequences selected from the group consisting of MTCs:8-51;    b) contacting said test cell population with said candidate therapeutic agent;    c) measuring the expression of said nucleic acid sequences in the test cell population;    d) comparing the expression of said nucleic acid sequences to the expression of said nucleic acid sequences in a reference cell population comprising at least one cell whose thyroid carcinoma stage is known; and    e) identifying a difference in expression levels of the MTC sequence, if present, in the test cell population and reference cell population,    thereby identifying a therapeutic agent for treating a thyroid carcinoma.    
     
     
         20 . A method of assessing the prognosis of a subject with a thyroid carcinoma, the method comprising: 
 a) providing a test cell population from said subject, wherein at least one cell in said test cell population is capable of expressing one or more of said nucleic acid sequences selected from the group consisting of MTCs: 8-51;    b) measuring the expression or one or more said nucleic acid sequences in said cell; and    c) comparing the expression of said nucleic acid sequences to the expression of said nucleic acid sequences in a reference cell population comprising at least one cell whose thyroid carcinoma stage is known; and    d) identifying a difference in expression levels of the MTC sequence, if present, in the test cell population and reference cell population,    thereby assessing the prognosis of said subject.    
     
     
         21 . A method of treating metastatic carcinoma, the method comprising administering to a patient suffering from or at risk for developing metastatic carcinoma, an agent that increases the expression or activity of one or more nucleic acid sequences selected from the group consisting of MTCs: 17, 24, 28, 32, 36, 38, 40, 43, and 46.  
     
     
         22 . The method of  claim 21 , wherein said carcinoma is thyroid carcinoma.  
     
     
         23 . A method of treating metastatic carcinoma, the method comprising administering to a patient suffering from or at risk for developing metastatic carcinoma, an agent that decreases the expression or activity of one or more nucleic acid sequences selected from the group consisting of MTCs: 8-16, 18-23, 25-27, 29-31, 33-35, 37, 39, 41-42, 44-45, 48, and 50.  
     
     
         24 . The method of  claim 23 , wherein said carcinoma is thyroid carcinoma.  
     
     
         25 . The method of  claim 23 , wherein said agent is an antibody to a polypeptide encoded by said MTC nucleic acid sequence.  
     
     
         26 . An isolated polynucleotide selected from the group consisting of: 
 a) a nucleotide sequence comprising one or more polymorphic sequences of Table 2;    b) a fragment of said nucleotide sequence, provided that the fragment includes a polymorphic site in said polymorphic sequence;    c) a complementary nucleotide sequence comprising a sequence complementary to one or more of said polymorphic sequences; and    d) a fragment of said complementary nucleotide sequence, provided that the fragment includes a polymorphic site in said polymorphic sequence.    
     
     
         27 . The polynucleotide of  claim 26 , wherein said polynucleotide sequence is DNA.  
     
     
         28 . The polynucleotide of  claim 26 , wherein said polynucleotide sequence is RNA.  
     
     
         29 . The polynucleotide of  claim 26 , wherein said polynucleotide sequence is between about 10 and about 100 nucleotides in length.  
     
     
         30 . The polynucleotide of  claim 26 , wherein said polynucleotide sequence is between about 10 and about 90 nucleotides in length.  
     
     
         31 . The polynucleotide of  claim 26 , wherein said polynucleotide sequence is between about 10 and about 75 nucleotides in length.  
     
     
         32 . The polynucleotide of  claim 26 , wherein said polynucleotide is between about 10 and about 50 bas es in length.  
     
     
         33 . The polynucleotide of  claim 26 , wherein said polynucleotide is between about 10 and about 40 bases in length.  
     
     
         34 . An isolated allele-specific oligonucleotide that hybridizes to a first polynucleotide at a polymorphic site encompassed therein, wherein the first polynucleotide is chosen from the group consisting of: 
 a) a nucleotide sequence comprising one or more polymorphic sequences provided that the polymorphic sequence includes a nucleotide other than the nucleotide recited in Table 2 for said polymorphic sequence;    b) a nucleotide sequence that is a fragment of said polymorphic sequence, provided that the fragment includes a polymorphic site in said polymorphic sequence;    c) a complementary nucleotide sequence comprising a sequence complementary to one or more polymorphic sequences recited in Table 2, provided that the complementary nucleotide sequence includes a nucleotide other than the complement of the nucleotide recited in non polymorphic sequence Table 2; and    d) a nucleotide sequence that is a fragment of said complementary sequence, provided that the fragment includes a polymorphic site in said polymorphic sequence.    
     
     
         35 . The nucleic acid molecule of  claim 34 , wherein said nucleic acid molecule is selected from the group consisting of SEQ ID NOS:15-63.  
     
     
         36 . A method of identifying a base occupying a polymorphic site in a nucleic acid molecule, the method comprising: 
 (a) obtaining a nucleic acid molecule from a subject;    (b) contacting said nucleic acid molecule with one or more sequences selected from the group consisting of SEQ ID NOS:15-63;    (c) detecting hybridization; and    (d) identifying the sequences that hybridize with said nucleic acid molecules    wherein the nucleic sequence of the hybridizing sequences indicates a polymorphic site in the nucleic acid molecule.    
     
     
         37 . The method of  claim 36 , wherein the subject suffers from or is at risk for metastatic thyroid carcinoma.  
     
     
         38 . The method of  claim 36 , wherein the presence of the polymorphic site is correlated with the presence of a metastatic thyroid carcinoma.  
     
     
         39 . The method of  claim 36 , wherein the nucleic acid molecule is genomic DNA.  
     
     
         40 . The method of  claim 36 , wherein the nucleic acid molecule is cDNA.  
     
     
         41 . A nucleic acid sequence 20-100 nucleotides in length comprising the polymorphic site 10 identified in the method of  claim 36 .  
     
     
         42 . The method of  claim 36 , wherein the nucleic acid molecule is obtained from a plurality of subjects, and a base occupying one of the polymorphic sites is determined in each of the subjects.  
     
     
         41 . The method of  claim 36 , wherein the subject is a human or a rodent.  
     
     
         42 . A kit comprising one or more reagents for detecting two or more nucleic acid sequences selected from the group consisting of MTCs: 8-51.  
     
     
         43 . An array of probe nucleic acids, wherein said probe nucleic acids detect two or more nucleic acid sequences selected from the group consisting of MTCs: 8-51.  
     
     
         44 . An isolated nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of MTCs: 48-51, or fragments thereof.  
     
     
         45 . A vector comprising the nucleic acid of  claim 44 .  
     
     
         46 . A cell comprising the vector of  claim 45 .  
     
     
         47 . A pharmaceutical composition comprising the nucleic acid of  claim 44 .  
     
     
         48 . A polypeptide encoded by the nucleic acid of  claim 44 .  
     
     
         49 . An antibody which specifically binds to the polypeptide of  claim 48.