ArrayExpress Uploader04454Normal cortexnot specified64wild typefemalenot specified14wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor364wild typefemaleT1N0M014mutantwild typeINormal cortexnot specified77wild typefemalenot specified26wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor277wild typefemaleT2N0Mx26wild typemutantn/aNormal cortexnot specified45wild typemalenot specified42wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor245wild typemaleT2N0M042mutantmutantIINormal cortexnot specified48wild typefemalenot specified75wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor248wild typefemaleT2N0M075mutantmutantIINormal cortexnot specified85wild typefemalenot specified83wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor285wild typefemaleT1N0M083lossmutantINormal cortexnot specified72wild typefemalenot specified111wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor272wild typefemaleT1NxMx111wild typewild typen/aNormal cortexnot specified51wild typemalenot specified131wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor251wild typemaleT1NxMx131wild typemutantn/aNormal cortexnot specified63wild typemalenot specified209wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor263mutantmaleT1N0M0209wild typemutantINormal cortexnot specified79wild typefemalenot specified233wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor279wild typefemaleT1N0Mx233mutantmutantn/aNormal cortexnot specifiedn/awild typefemalenot specified260wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor2n/awild typefemaleT1N0Mx260wild typemutantn/aNormal cortexnot specified43wild typefemalenot specified265wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor243wild typefemaleT1N0M0265mutantmutantINormal cortexnot specified60wild typemalenot specified324wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor260wild typemaleT1NxMx324wild typemutantn/aNormal cortexnot specified80wild typefemalenot specified325wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor180wild typefemaleT1NxMx325wild typewild typen/aNormal cortexnot specified83wild typemalenot specified1393wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor183wild typemaleT1NxMx1393wild typemutantn/aNormal cortexnot specified70wild typemalenot specified1524wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor270wild typemaleT1NxMx1524mutantmutantn/aClear-cell renal cell carcinoma (ccRCC) tumor367wild typemaleT3N0M0T22wild typemutantIIIClear-cell renal cell carcinoma (ccRCC) tumor473mutantmaleT3NxM1T26wild typemutantIVNormal cortexnot specified59wild typemalenot specifiedT79wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor459wild typemaleT3NxM0T79mutantmutantn/aClear-cell renal cell carcinoma (ccRCC) tumor452wild typemaleT4N1M1T84mutantmutantIVNormal cortexnot specified35wild typemalenot specifiedT127wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor335wild typemaleT3NxM0T127wild typemutantn/aNormal cortexnot specified56wild typefemalenot specifiedT142wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor356wild typefemaleT3NxM0T142mutantmutantn/aClear-cell renal cell carcinoma (ccRCC) tumor474wild typefemaleT4NxM0T143wild typewild typeIVNormal cortexnot specified74wild typemalenot specifiedT144wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor474wild typemaleT2N1M0T144wild typemutantIIINormal cortexnot specified82wild typefemalenot specifiedT158wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor382wild typefemaleT3NxM1T158mutantmutantIVNormal cortexnot specified52wild typemalenot specifiedT163wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor452mutantmaleT1N0M0T163wild typemutantINormal cortexnot specified75wild typemalenot specifiedT164wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor475wild typemaleT4NxM0T164wild typewild typeIVClear-cell renal cell carcinoma (ccRCC) tumor340wild typemaleT3NxM0T165mutantmutantn/aNormal cortexnot specified56wild typemalenot specifiedT166wild typewild typenot specifiedClear-cell renal cell carcinoma (ccRCC) tumor456mutantmaleT3N1M0T166wild typemutantIIIClear-cell renal cell carcinoma (ccRCC) tumor256wild typemaleT1NxM1T183mutantmutantIVMouse tumorgraft, cohort 0not specified67wild typemalenot specifiedT22wild typemutantnot specifiedMouse tumorgraft, cohort 0not specified73mutantmalenot specifiedT26wild typemutantnot specifiedMouse tumorgraft, cohort 4not specified73mutantmalenot specifiedT26wild typemutantnot specifiedMouse tumorgraft, cohort 8not specified73mutantmalenot specifiedT26wild typemutantnot specifiedMouse tumorgraft, cohort 0not specified59wild typemalenot specifiedT79mutantmutantnot specifiedMouse tumorgraft, cohort 0not specified52wild typemalenot specifiedT84mutantmutantnot specifiedMouse tumorgraft, cohort 0not specified35wild typemalenot specifiedT127wild typemutantnot specifiedMouse tumorgraft, cohort 2not specified35wild typemalenot specifiedT127wild typemutantnot specifiedMouse tumorgraft, cohort 1not specified56wild typefemalenot specifiedT142mutantmutantnot specifiedMouse tumorgraft, cohort 2not specified56wild typefemalenot specifiedT142mutantmutantnot specifiedMouse tumorgraft, cohort 0not specified74wild typefemalenot specifiedT143wild typewild typenot specifiedMouse tumorgraft, cohort 4not specified74wild typefemalenot specifiedT143wild typewild typenot specifiedMouse tumorgraft, cohort 9not specified74wild typefemalenot specifiedT143wild typewild typenot specifiedMouse tumorgraft, cohort 0not specified74wild typemalenot specifiedT144wild typemutantnot specifiedMouse tumorgraft, cohort 3not specified74wild typemalenot specifiedT144wild typemutantnot specifiedMouse tumorgraft, cohort 7not specified74wild typemalenot specifiedT144wild typemutantnot specifiedMouse tumorgraft, cohort 1not specified82wild typefemalenot specifiedT158mutantmutantnot specifiedMouse tumorgraft, cohort 2not specified82wild typefemalenot specifiedT158mutantmutantnot specifiedMouse tumorgraft, cohort 1not specified75wild typemalenot specifiedT164wild typewild typenot specifiedMouse tumorgraft, cohort 0not specified40wild typemalenot specifiedT165mutantmutantnot specifiedMouse tumorgraft, cohort 0not specified56mutantmalenot specifiedT166wild typemutantnot specifiedMouse tumorgraft, cohort 4not specified56mutantmalenot specifiedT166wild typemutantnot specifiedMouse tumorgraft, cohort 8not specified56mutantmalenot specifiedT166wild typemutantnot specifiedMouse tumorgraft from metastasis, cohort 1not specified56wild typemalenot specifiedT183mutantmutantnot specifiedarrayexpress_sid4Renal cell carcinoma (RCC) exhibits some unusual features and genes commonly mutated in cancer are rarely mutated in clear-cell RCC...22683710E-GEOD-36895/profile/8773/arrayexpressuploader1076cancercarcinomacellchromosomegenomekidneyrenal cell carcinomaDec.12, 2014FalseE-GEOD-36895_A-AFFY-44molecular-genetic-classification-of-clear-cell-renMolecular Genetic Classification of clear-cell Renal Cell Carcinoma (ccRCC) based on the Gene Expression Profiling of Tumors and Tumorgrafts deficient for BAP1 or PBRM1Sep.19, 2014Renal cell carcinoma (RCC) exhibits some unusual features and genes commonly mutated in cancer are rarely mutated in clear-cell RCC (ccRCC), the most common type. The most prevalent genetic alteration in ccRCC is the inactivation of the tumor suppressor gene VHL. Using whole-genome and exome sequencing we discovered BAP1 as a novel tumor suppressor in ccRCC that shows little overlap with mutations in PBRM1, another recent tumor suppressor. Whereas VHL was mutated in 81% of the patients (142/176), PBRM1 was lost in 58% and BAP1 in 15% of the patients analyzed. All these tumor suppressor genes are located in chromosome 3p, which is partially or completely lost in most ccRCC patients. However, BAP1 but not PBRM1 loss was associated with higher Fuhrman grade and, therefore, poorer outcome. Xenograft tumors (tumorgrafts) implanted orthotopically in mice exhibited similar gene expression profiling to corresponding primary tumors. Gene expression profiling of tumors and tumorgrafts displayed different signatures for BAP1- and PBRM1-deficient samples. Thus, after inactivation of VHL, the acquisition of a mutation in BAP1 or PBRM1 defines a different program that might alter the fate of the patient. Our results establish the foundation for an integrated pathological and molecular genetic classification of about 70% of ccRCC patients, paving the way for subtype-specific treatments exploiting genetic vulnerabilities. The RNA of clear-cell renal cell carcinoma (ccRCC) primary tumors, tumors growing in immunodeficient mice (tumorgrafts), and normal kidney cortices were labeled and hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays.http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36895humanhttp://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36895/samples/