PXD009300

PXD009300 is an original dataset announced via ProteomeXchange.

Title	Proteomic Distinction of Renal Oncocytomas and Eosinophilic Chromophobe Renal Cell Carcinomas
Description	Background Renal oncocytomas (ROs) are benign epithelial tumors of the kidney that may progress into malignant chromophobe renal cell carcinoma (chRCCs), with the latter constituting 5 – 7 % of renal neoplasias. ROs and chRCCs show pronounced molecular and histological similarities, which renders their differentiation demanding. We aimed for the differential proteome profiling of ROs and chRCCs in order to better understand distinguishing protein patterns. Methods We employed formalin-fixed, paraffin-embedded samples (six RO cases, six chRCC cases) together with isotopic triplex dimethylation and a pooled reference standard to enable cohort-wide quantitative comparison. For lysosomal-associated membrane protein 1 (LAMP1) and integrin alpha-V (ITGAV) we performed corroborative immunohistochemistry (IHC) in an extended cohort of 42 RO cases and 31 chRCC cases lacking any overlap with the smaller proteomic cohort. Results: At 1 % false discovery rate, we identified > 3900 proteins, of which >2400 proteins were consistently quantified in at least four RO and four chRCC cases. The proteomic expression profiling discriminated ROs and chRCCs and highlighted established features such as accumulation of mitochondrial proteins in ROs together with emphasizing the accumulation of endo-lysosomal proteins in chRCCs. In line with the proteomic data, IHC showed enrichment of LAMP1 in chRCC and of ITGAV in RO. Conclusion We present one of the first differential proteome profiling studies on ROs and chRCCs and highlight differential abundance of LAMP1 and ITGAV in these renal tumors.
HostingRepository	PRIDE
AnnounceDate	2018-08-13
AnnouncementXML	Submission_2018-08-13_08:51:43.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Oliver Schilling
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-03-23 02:17:13	ID requested
⏵ 1	2018-08-13 08:51:45	announced

Drendel V, Heckelmann B, Schell C, Kook L, Biniossek ML, Werner M, Jilg CA, Schilling O, Proteomic distinction of renal oncocytomas and chromophobe renal cell carcinomas. Clin Proteomics, 15():25(2018) [pubmed]

curator keyword: Biomedical

submitter keyword: renal cell tumors formalin-fixation, paraffin embedment proteomics immunohistochemistry

Oliver Schilling
contact affiliation	PD Dr. Oliver Schilling Heisenberg Fellow Institute of Molecular Medicine and Cell Research University of Freiburg Stefan-Meier-Str. 17, Room 02 027 D-79104 Freiburg, Germany +49 761 203 9615 oliver.schilling@mol-med.uni-freiburg.de
contact email	oliver.schilling@mol-med.uni-freiburg.de
lab head
Oliver Schilling
contact affiliation	University of Freiburg
contact email	oliver.schilling@mol-med.uni-freiburg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD009300
     1. Label: PRIDE project
     2. Name: Proteomic Distinction of Renal Oncocytomas and Eosinophilic Chromophobe Renal Cell Carcinomas