Comprehensive proteogenomic characterization of rare kidney tumors

Comprehensive proteogenomic characterization of rare kidney tumors CPTAC Charlotte Sack… Fri, 03/20/2026 - 14:30 CPTAC Cell . Volume 5 , Issue 5, 21 May 2024 10.1016/j.xcrm.2024.101547 Non-clear cell renal cell carcinomas (non-ccRCCs) encompass diverse malignant and benign tumors. Refinement of differential diagnosis biomarkers, markers for early prognosis of aggressive disease, and therapeutic targets to complement immunotherapy are current clinical needs. Multi-omics analyses of 48 non-ccRCCs compared with 103 ccRCCs reveal proteogenomic, phosphorylation, glycosylation, and metabolic aberrations in RCC subtypes. RCCs with high genome instability display overexpression of IGF2BP3 and PYCR1. Integration of single-cell and bulk transcriptome data predicts diverse cell-of-origin and clarifies RCC subtype-specific proteogenomic signatures. Expression of biomarkers MAPRE3, ADGRF5, and GPNMB differentiates renal oncocytoma from chromophobe RCC, and PIGR and SOSTDC1 distinguish papillary RCC from MTSCC. This study expands our knowledge of proteogenomic signatures, biomarkers, and potential therapeutic targets in non-ccRCC. Instructions for Data Download Open Access Data Download the appropriate manifest file from the publication page Use the manifest file to download data using the GDC Data Transfer Tool (DTT) or the GDC API GDC DTT ( Download , User’s Guide ) GDC API ( User’s Guide ) Controlled Access Data Download the appropriate manifest file from the publication page Download a token from the GDC Data Portal GDC Data Portal ( Launch , User’s Guide ) Use the manifest file and token to download data using the GDC DTT or the GDC API GDC DTT ( Download , User’s Guide ) GDC API ( User’s Guide ) For assistance, please contact the GDC Help Desk: support@nci-gdc.datacommons.io .