PDC Study ID | Study | Project | Program | Cases # | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Available files for data category | |||||||||||||||
Raw | Processed Mass Spectra | Metadata | PSM | Protein Assembly | Quality Metrics | ||||||||||
PDC000553 | CPTAC GBM Discovery Study - Lipidome | CPTAC3 Discovery and Confirmatory | Clinical Proteomic Tumor Analysis Consortium | Glioblastoma; Other | Brain | Lipidome | Label Free | 83 | 166 | 0 | 0 | N/A | N/A | N/A | |
PDC000552 | CPTAC GBM Discovery Study - Metabolome | CPTAC3 Discovery and Confirmatory | Clinical Proteomic Tumor Analysis Consortium | Glioblastoma; Other | Brain | Metabolome | Label Free | 83 | 83 | 83 | 0 | N/A | N/A | N/A | |
PDC000547 | CPTAC GBM Confirmatory Study - Lipidome | CPTAC3 Discovery and Confirmatory | Clinical Proteomic Tumor Analysis Consortium | Breast Invasive Carcinoma; Glioblastoma; Gliomas; Lung Adenocarcinoma; Meningiomas; Other | Brain; Breast; Bronchus and lung; Not Reported | Lipidome | Label Free | 82 | 170 | 0 | 0 | N/A | N/A | N/A | |
PDC000546 | CPTAC GBM Confirmatory Study - Metabolome | CPTAC3 Discovery and Confirmatory | Clinical Proteomic Tumor Analysis Consortium | Breast Invasive Carcinoma; Glioblastoma; Gliomas; Lung Adenocarcinoma; Meningiomas; Other | Brain; Breast; Bronchus and lung; Not Reported | Metabolome | Label Free | 85 | 88 | 88 | 0 | N/A | N/A | N/A | |
PDC000544 | CPTAC non-ccRCC Study - Metabolome | CPTAC3 Discovery and Confirmatory | Clinical Proteomic Tumor Analysis Consortium | Non-Clear Cell Renal Cell Carcinoma; Other | Kidney; Not Reported | Metabolome | Label Free | 32 | 106 | 0 | 2 | N/A | N/A | N/A | |
PDC000535 | CPTAC CCRCC Confirmatory Study - Validation - Metabolome | CPTAC3 Discovery and Confirmatory | Clinical Proteomic Tumor Analysis Consortium | Clear Cell Renal Cell Carcinoma | Kidney | Metabolome | Label Free | 56 | 142 | 0 | 0 | N/A | N/A | N/A | |
PDC000534 | CPTAC CCRCC Confirmatory Study - Training - Metabolome | CPTAC3 Discovery and Confirmatory | Clinical Proteomic Tumor Analysis Consortium | Clear Cell Renal Cell Carcinoma; Non-Clear Cell Renal Cell Carcinoma; Other | Kidney; Not Reported | Metabolome | Label Free | 61 | 142 | 0 | 0 | N/A | N/A | N/A | |
PDC000527 | CPTAC PDAC Proteins in Serum - Glycoproteome | CPTAC3-Other | Clinical Proteomic Tumor Analysis Consortium | Not Applicable; Other; Pancreatic Ductal Adenocarcinoma | Not Applicable; Pancreas | Glycoproteome | Label Free | 118 | 118 | 0 | 1 | 0 | 0 | 0 | |
PDC000526 | CPTAC PDAC Proteins in Serum - Proteome | CPTAC3-Other | Clinical Proteomic Tumor Analysis Consortium | Not Applicable; Other; Pancreatic Ductal Adenocarcinoma | Not Applicable; Pancreas | Proteome | Label Free | 118 | 118 | 0 | 1 | 0 | 0 | 0 | |
PDC000515 | KNCC Glioblastoma Evolution - Phosphoproteome | Cancer Proteogenomics Group of National Cancer Center Korea | International Cancer Proteogenome Consortium | Glioblastoma; Other | Brain; Not Applicable | Phosphoproteome | TMT11 | 91 | 264 | 264 | 0 | 528 | 6 | 2 |
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PDC Study Identifier | PDC000534 | Analytical Fraction | Metabolome |
Study ID | 7d40ea67-752b-4842-8252-0ef594c47617 | Disease Types | Clear Cell Renal Cell Carcinoma;Non-Clear Cell Renal Cell Carcinoma;Other |
Study Name | CPTAC CCRCC Confirmatory Study - Training - Metabolome | Project ID | CPTAC3 Discovery and Confirmatory |
Experiment Type | Label Free |
Clear cell renal cell carcinomas (ccRCCs) represent ~75% of RCC cases and account for most RCC-associated deaths. Inter- and intra-tumoral heterogeneity (ITH) results in varying prognosis and treatment outcomes. Prior large-scale ccRCC studies evaluated either histologic variation or molecular profiles. To obtain a more comprehensive profile of ccRCC, we carried out integrative histopathologic, proteogenomic, and metabolomic analyses from 305 ccRCC tumor segments and 166 paired normal adjacent tissues from 213 cases. Combining histologic and molecular profiles revealed ITH in 90% of ccRCCs, with 50% demonstrating immune signature heterogeneity. High tumor grade along with BAP1 mutation, genome instability, increased hypermethylation, and a specific protein glycosylation signature defined a new high-risk disease subset, where UCHL1 expression displayed prognostic value. Single nuclei RNA-seq of the adverse sarcomatoid and rhabdoid phenotypes uncovered gene signatures and potential insights into tumor evolution. This study molecularly stratifies an aggressive ccRCC subtype that may inform more effective treatment strategies.
Data Category | Files (n=142) |
---|---|
Raw Mass Spectra (Proprietary) | 142 |
External References | |
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The Cancer Imaging Archive | CPTAC-CCRCC |
Database of Genotypes and Phenotypes | phs001287 |
Imaging Data Commons | CPTAC-CCRCC |
Genomic Data Commons | CPTAC-3 |
Related PDC studies | |
---|---|
CPTAC CCRCC Discovery Study - DIA Proteome | PDC000200 |
CPTAC CCRCC Confirmatory Study - DIA Proteome | PDC000411 |
CPTAC CCRCC Confirmatory Study - DIA Phosphoproteome | PDC000412 |
CPTAC CCRCC Confirmatory Study - DIA Intact Glycoproteome | PDC000413 |
CPTAC CCRCC Confirmatory Study - Intratumor Heterogeneity - DIA Proteome | PDC000414 |
CPTAC CCRCC Confirmatory Study - Kinase Inhibition - DIA Phosphoproteome | PDC000415 |
CPTAC CCRCC Confirmatory Study - Validation - Metabolome | PDC000535 |