title: Proteotranscriptomic Analysis Reveals Stage Specific Changes in the Molecular Landscape of Clear-Cell Renal Cell Carcinoma.
abstract: Renal cell carcinoma comprises 2 to 3% of malignancies in adults with the most prevalent subtype being clear-cell RCC (ccRCC). This type of cancer is well characterized at the genomic and transcriptomic level and is associated with a loss of VHL that results in stabilization of HIF1. The current study focused on evaluating ccRCC stage dependent changes at the proteome level to provide insight into the molecular pathogenesis of ccRCC progression. To accomplish this, label-free proteomics was used to characterize matched tumor and normal-adjacent tissues from 84 patients with stage I to IV ccRCC. Using pooled samples 1551 proteins were identified, of which 290 were differentially abundant, while 783 proteins were identified using individual samples, with 344 being differentially abundant. These 344 differentially abundant proteins were enriched in metabolic pathways and further examination revealed metabolic dysfunction consistent with the Warburg effect. Additionally, the protein data indicated activation of ESRRA and ESRRG, and HIF1A, as well as inhibition of FOXA1, MAPK1 and WISP2. A subset analysis of complementary gene expression array data on 47 pairs of these same tissues indicated similar upstream changes, such as increased HIF1A activation with stage, though ESRRA and ESRRG activation and FOXA1 inhibition were not predicted from the transcriptomic data. The activation of ESRRA and ESRRG implied that HIF2A may also be activated during later stages of ccRCC, which was confirmed in the transcriptional analysis. This combined analysis highlights the importance of HIF1A and HIF2A in developing the ccRCC molecular phenotype as well as the potential involvement of ESRRA and ESRRG in driving these changes. In addition, cofilin-1, profilin-1, nicotinamide N-methyltransferase, and fructose-bisphosphate aldolase A were identified as candidate markers of late stage ccRCC. Utilization of data collected from heterogeneous biological domains strengthened the findings from each domain, demonstrating the complementary nature of such an analysis. Together these results highlight the importance of the VHL/HIF1A/HIF2A axis and provide a foundation and therapeutic targets for future studies. (Data are available via ProteomeXchange with identifier PXD003271 and MassIVE with identifier MSV000079511.).
authors.affiliation: Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, United States of America.
authors.forename: Benjamin A
authors.identifier: 0000-0001-6120-7695
authors.initials: BA
authors.lastname: Neely
authors.affiliation: Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia, United States of America.
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Wilkins
authors.affiliation: Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, United States of America.
authors.forename: Laura A
authors.initials: LA
authors.lastname: Marlow
authors.affiliation: Department of Radiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.
authors.forename: Dariya
authors.initials: D
authors.lastname: Malyarenko
authors.affiliation: Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Yunee
authors.initials: Y
authors.lastname: Kim
authors.affiliation: Princess Margaret Cancer Center, Toronto, Ontario, Canada.
authors.forename: Alexandr
authors.initials: A
authors.lastname: Ignatchenko
authors.affiliation: INCOGEN, Inc., Williamsburg, Virginia, United States of America.
authors.forename: Heather
authors.initials: H
authors.lastname: Sasinowska
authors.affiliation: INCOGEN, Inc., Williamsburg, Virginia, United States of America.|Venebio Group, LLC, Richmond, Virginia, United States of America.
authors.forename: Maciek
authors.initials: M
authors.lastname: Sasinowski
authors.affiliation: Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia, United States of America.|Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, Virginia, United States of America.
authors.forename: Julius O
authors.initials: JO
authors.lastname: Nyalwidhe
authors.affiliation: Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.|Princess Margaret Cancer Center, Toronto, Ontario, Canada.
authors.forename: Thomas
authors.initials: T
authors.lastname: Kislinger
authors.affiliation: Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, United States of America.
authors.forename: John A
authors.initials: JA
authors.lastname: Copland
authors.affiliation: Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, United States of America.
authors.forename: Richard R
authors.initials: RR
authors.lastname: Drake
mesh_terms: D000368:Aged; D002292:Carcinoma, Renal Cell / Q000235:genetics / Q000378:metabolism / Q000473:pathology*; D018450:Disease Progression; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007668:Kidney / Q000378:metabolism / Q000473:pathology*; D007680:Kidney Neoplasms / Q000235:genetics / Q000378:metabolism / Q000473:pathology*; D008297:Male; D008875:Middle Aged; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D040901:Proteomics; D015398:Signal Transduction; D059467:Transcriptome
chemical_list: D011506:Proteins