Compositions and methods for the identification, assessment, prevention and therapy of cancer

Abstract

The subject matter relates to newly discovered nucleic acid molecules and proteins associated with thymic lymphoma and hamartomatous tumors. Compositions and methods for detecting, characterizing, preventing, and treating human thymic lymphoma and hamartomatous tumors are provided.

1 - 99 . (canceled) 
     
     
         100 . A method of assessing
 a) whether a subject is afflicted with thymic lymphoma or a hamartomatous tumor, the method comprising comparing: i) the level of expression of at least one or more markers in a subject sample, wherein said one or more markers is selected from any one of Tables 1-4; and ii) the normal level of expression of said one or more markers in a control non-cancer sample, wherein a significant modulation in the level of expression of said one or more markers in the subject sample and the normal level is an indication that the subject is afflicted with thymic lymphoma or the hamartomatous tumor;   b) the progression of thymic lymphoma or a hamartomatous tumor in a subject, the method comprising: i) detecting in a subject sample at a first point in time the expression of one or more markers; ii) repeating step i) at a subsequent point in time; and iii) comparing the level of expression of said one or more markers detected in steps i) and ii), and therefrom monitoring the progression of thymic lymphoma or the hamartomatous tumor; wherein at least one or more of said markers is selected from the group consisting of the markers listed in Tables 1-4;   c) the efficacy of a test compound for inhibiting thymic lymphoma or a hamartomatous tumor in a subject, the method comprising comparing: i) expression of one or more thymic lymphoma or hamartomatous tumor markers in a first sample obtained from the subject and exposed to the test compound; and ii) expression of said one or more markers in a second sample obtained from the subject, wherein the second sample is not exposed to the test compound, wherein at least one or more of said markers is selected from the group consisting of the markers listed in Tables 1-4, and a significantly modulated level of expression of one or more of said markers in the first sample, relative to the second sample, is an indication that the test compound is efficacious for inhibiting thymic lymphoma or the hamartomatous tumor in the subject;   d) the efficacy of a therapy for inhibiting thymic lymphoma or a hamartomatous tumor in a subject, the method comprising comparing: i) expression of one or more thymic lymphoma or hamartomatous tumor markers in a first sample obtained from the subject prior to providing at least a portion of therapy to the subject, and ii) expression of said one or more markers in a second sample obtained from the subject following provision of the portion of the therapy, wherein at least one or more of said markers is selected from the group consisting of the markers listed in Tables 1-4, and a significantly modulated level of expression of at least one or more of said markers in the second sample, relative to the first sample, is an indication that the therapy is efficacious for inhibiting thymic lymphoma or the hamartomatous tumor in the subject;   e) a composition for inhibiting thymic lymphoma or a hamartomatous tumor in a subject, the method comprising: i) obtaining a sample comprising cancer cells from the subject; ii) separately exposing aliquots of the sample in the presence of a plurality of test compositions; iii) comparing expression of one or more thymic lymphoma or hamartomatous tumor markers in each of the aliquots; and iv) selecting one of the test compositions which alters the level of expression of one or more of the markers in the aliquot containing the test composition, relative to other test compositions; wherein at least one or more of said markers is selected from the group consisting of the markers listed in Tables 1-4;   f) the potential of a test compound to give rise to thymic lymphoma or a hamartomatous tumor, the method comprising: i) maintaining separate aliquots of cells derived from any tissue in the presence and absence of the test compound; and ii) comparing expression of one or more thymic lymphoma or hamartomatous tumor markers in each of the aliquots, wherein at least one or more of said markers is selected from the group consisting of the markers listed in Tables 1-4, and a significantly modulated level of expression of said one or more markers in the aliquot maintained in the presence of the test compound, relative to the aliquot maintained in the absence of the test compound, is an indication that the test compound possesses potential to give rise to thymic lymphoma or the hamartomatous tumor;   g) whether thymic lymphoma or a hamartomatous tumor has metastasized in a subject, the method comprising comparing: i) the level of expression of one or more thymic lymphoma or hamartomatous tumor markers in a subject sample, and ii) the normal level or non-metastatic level of expression of said one or more markers in a control sample wherein at least one or more of said markers is selected from the group consisting of the markers listed in Tables 1-4, and a significant difference between the level of expression of said one or more markers in the subject sample and the normal level or non-metastatic level is an indication that the thymic lymphoma or the hamartomatous tumor has mestastasized;   h) the aggressiveness or indolence of thymic lymphoma or a hamartomatous tumor comprising comparing: i) the level of expression of one or more thymic lymphoma or hamartomatous tumor markers in a sample, and ii) the normal level of expression of said one or more markers in a control sample, wherein at least one or more of said markers is selected from the group consisting of the markers listed in Tables 1-4, and a significant difference between the level of expression of said one or more markers in the sample and the normal level is an indication that the thymic lymphoma or the hamartomatous tumor is aggressive or indolent;   i) a composition capable of modulating thymic lymphoma or a hamartomatous tumor, the method comprising i) obtaining a sample comprising cancer cells; ii) contacting said cells with a test compound; and iii) determining the ability of the test compound to modulate the amount and/or activity of one or more markers, wherein the one or more markers is selected from the group consisting of the markers listed in Tables 1-4, thereby identifying a modulator of thymic lymphoma or the hamartomatous tumor; or   j) a composition capable of modulating thymic lymphoma or a hamartomatous tumor, the method comprising i) contacting one or more markers selected from the group consisting of the markers listed in Tables 1-4 with a test compound; and ii) determining the ability of the test compound to modulate the amount and/or activity of a marker selected from the group consisting of the markers listed in Tables 1-4, thereby identifying a composition capable of modulating thymic lymphoma or the hamartomatous tumor.   
     
     
         101 . A method of inhibiting
 a) thymic lymphoma or a hamartomatous tumor in a subject, the method comprising: i) obtaining a sample comprising cancer cells from the subject; ii) separately maintaining aliquots of the sample in the presence of a plurality of test compositions; iii) comparing expression of one or more thymic lymphoma or hamartomatous tumor markers in each of the aliquots; and iv) administering to the subject at least one of the test compositions which alters the level of expression of said one or more markers in the aliquot containing that test composition, relative to other test compositions, wherein at least one or more of said markers is selected from the group consisting of the markers listed in Tables 1-4;   b) thymic lymphoma or a hamartomatous tumor in a subject at risk for developing thymic lymphoma or a hamartomatous tumor, the method comprising enhancing or inhibiting expression of one or markers selected from the group consisting of the markers listed in Tables 1-4; or   c) thymic lymphoma or with a hamartomatous tumor in a subject, the method comprising providing to cells of the subject an antisense oligonucleotide complementary to a polynucleotide encoded by one or markers selected from the group consisting of the markers listed in Tables 1-4, or a segment of said polynucleotide.   
     
     
         102 . A kit for assessing
 a) whether a subject is afflicted with thymic lymphoma or a hamartomatous tumor, the kit comprising reagents for assessing expression of one or more thymic lymphoma or hamartomatous tumors markers, wherein at least one or more of said markers is selected from the group consisting of the markers listed in Tables 1-4;   b) the presence of thymic lymphoma or hamartomatous tumor cells, the kit comprising a nucleic acid probe which specifically binds with a transcribed polynucleotide encoded by one or markers selected from the group consisting of the markers listed in Tables 1-4;   c) the suitability of each of a plurality of compounds for inhibiting thymic lymphoma or a hamartomatous tumor in a subject, the kit comprising: i) the plurality of compounds; and ii) a reagent for assessing expression of one or more thymic lymphoma or hamartomatous tumor markers, wherein at least one or more of said markers is selected from the group consisting of the markers listed in Tables 1-4;   d) the presence of human thymic lymphoma or hamartomatous tumor cells, the kit comprising an antibody, wherein the antibody specifically binds with a protein encoded by one or more markers selected from the group consisting of the markers listed in Tables 1-4, or a fragment of said protein; or   e) the potential of a test compound to give rise to thymic lymphoma or a hamartomatous tumor, the kit comprising cells derived from any tissue and a reagent for assessing expression of one or more markers selected from the group consisting of the markers listed in Tables 1-4.