Proteomic analysis of signaling network regulation in renal cell carcinomas with differential hypoxia-inducible factor-2α expression.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:23940778", "kind": "science-record", "revision": 8, "content_hash": "sha256:f173d354cc5badd41f42657c460e87875b4f4fcc8dcd5ffddaccfd8d7d70029a", "created_at": "2026-11-01T15:40:03Z", "updated_at": "2026-11-01T22:41:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic analysis of signaling network regulation in renal cell carcinomas with differential hypoxia-inducible factor-2α expression.", "doi": "10.1371/journal.pone.0071654", "pmid": "23940778", "authors": ["Lokesh Dalasanur Nagaprashantha", "Tatjana Talamantes", "Jyotsana Singhal", "Jia Guo", "Rit Vatsyayan", "Navin Rauniyar", "Sanjay Awasthi", "Sharad S Singhal", "Laszlo Prokai"], "journal": "PloS one", "year": 2013, "abstract": "BACKGROUND: The loss of von Hippel-Lindau (VHL) protein function leads to highly vascular renal tumors characterized by an aggressive course of disease and refractoriness to chemotherapy and radiotherapy. Loss of VHL in renal tumors also differs from tumors of other organs in that the oncogenic cascade is mediated by an increase in the levels of hypoxia-inducible factor-2α (HIF2α) instead of hypoxia-inducible factor-1α (HIF1α).\nMETHODS AND PRINCIPAL FINDINGS: We used renal carcinoma cell lines that recapitulate the differences between mutant VHL and wild-type VHL genotypes. Utilizing a method relying on extracted peptide intensities as a label-free approach for quantitation by liquid chromatography-mass spectrometry, our proteomics study revealed regulation of key proteins important for cancer cell survival, proliferation and stress-resistance, and implicated differential regulation of signaling networks in VHL-mutant renal cell carcinoma. We also observed upregulation of cellular energy pathway enzymes and the stress-responsive mitochondrial 60-kDa heat shock protein. Finding reliance on glutaminolysis in VHL-mutant renal cell carcinoma was of particular significance, given the generally predominant dependence of tumors on glycolysis. The data have been deposited to the ProteomeXchange with identifier PXD000335.\nCONCLUSIONS AND SIGNIFICANCE: Pathway analyses provided corroborative evidence for differential regulation of molecular and cellular functions influencing cancer energetics, metabolism and cell proliferation in renal cell carcinoma with distinct VHL genotype. Collectively, the differentially regulated proteome characterized by this study can potentially guide translational research specifically aimed at effective clinical interventions for advanced VHL-mutant, HIF2α-over-expressing tumors.", "claims": [{"id": "claim-method", "statement": "Proteins were accepted as differentially expressed following analysis of variance (ANOVA, P<0.05), requiring at least a twofold change in expression and also passing validation by Peptide Prophet and Protein Prophet using protein identifications from Scaffold.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:23940778", "locator": "sections[9] \"Data Compilation, Relative Quantification and Analysis of Signaling Networks\" paragraph 3", "quote": "Proteins were accepted as differentially expressed following analysis of variance (ANOVA, P<0.05), requiring at least a twofold change in expression and also passing validation by Peptide Prophet and Protein Prophet using protein identifications from Scaffold."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [22] with the dataset identifier PXD000335 and DOI 10.6019/PXD000335.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:23940778", "locator": "sections[9] \"Data Compilation, Relative Quantification and Analysis of Signaling Networks\" paragraph 3", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [22] with the dataset identifier PXD000335 and DOI 10.6019/PXD000335."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study found that VHL-mutant renal cell carcinoma relies on glutaminolysis; this was assessed using label-free quantification of peptide intensities extracted from full-scan MS spectra, followed by Progenesis LC-MS analysis and acceptance criteria of at least a twofold change with ANOVA P<0.05.", "kind": "quantitative", "target": {"value": 2.0, "unit": "fold change", "tolerance": null, "source": "Specifically, we required proteins to match Scaffold protein IDs, as well as have a minimum 2-fold change and an ANOVA P-value of <0.05 as determined by Progenesis LC-MS analyses (MS)."}, "evidence": [{"asset": "source:pmid:23940778", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Finding reliance on glutaminolysis in VHL-mutant renal cell carcinoma was of particular significance, given the generally predominant dependence of tumors on glycolysis."}, {"asset": "source:pmid:23940778", "locator": "sections[1] \"Introduction\" paragraph 4", "quote": "In this proteomics study, we performed proteomic analysis of VHL-wt and VHL-mut RCC cells using peptide intensities extracted from full-scan MS spectra to enable label-free quantification that overcomes limitations of the spectral counting method [19]."}, {"asset": "source:pmid:23940778", "locator": "sections[12] \"Results and Discussion\" paragraph 3", "quote": "Specifically, we required proteins to match Scaffold protein IDs, as well as have a minimum 2-fold change and an ANOVA P-value of <0.05 as determined by Progenesis LC-MS analyses (MS)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study found that VHL-mutant renal cell carcinoma relies on glutaminolysis; this was assessed using label-free quantification of peptide intensities extracted from full-scan MS spectra, followed by Progenesis LC-MS analysis and acceptance criteria of at least a twofold change with ANOVA P<0.05.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:23940778"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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 Proteomic analysis of signaling network regulation in renal cell carcinomas with differential hypoxia-inducible factor-2α expression", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:23940778:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:73524d40983d3c3b587905a48d5a999b88ec6b18d56de92880a75a56608e59c6", "bytes": 387, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#pone-0071654-t001", "version": null, "note": "Representative differentially expressed proteins of VHL-wt (Caki-2) and VHL-mut (786-O) RCCs identified by database search (Mascot) and quantified by extracted peptide intensity (MS) features generated with Progenesis LC-MS.", "structure": {"pmcid": "PMC3733962", "section_index": 12, "section_title": "Results and Discussion", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Representative differentially expressed proteins of VHL-wt (Caki-2) and VHL-mut (786-O) RCCs identified by database search (Mascot) and quantified by extracted peptide intensity (MS) features generated with Progenesis LC-MS.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[12]/table-wrap[1]#pone-0071654-t001"}}, {"id": "asset:table:pmid:23940778:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bfa339735b70a9a499591e3300b36f12f23506af03294e7bc5647e6c28e80c93", "bytes": 260, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#pone-0071654-t002", "version": null, "note": "IPA Analysis: Cellular Pathways Significantly Represented by HIF2α Regulation in RCC Cell Lines.", "structure": {"pmcid": "PMC3733962", "section_index": 13, "section_title": "Differential Regulation of Cellular Energy Pathways in VHL-mut and VHL-wt RCC Cells", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "IPA Analysis: Cellular Pathways Significantly Represented by HIF2α Regulation in RCC Cell Lines.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[13]/table-wrap[1]#pone-0071654-t002"}}, {"id": "asset:table:pmid:23940778:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:27e7e3448238c9a160f7b5684d2f70b3170d5fae5f41a4d8a6a6f00f0050edd7", "bytes": 263, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#pone-0071654-t003", "version": null, "note": "IPA Analysis: Toxicological Cellular Pathways Significantly Represented by HIF2α Regulation in RCC.", "structure": {"pmcid": "PMC3733962", "section_index": 14, "section_title": "Regulation of Complex Cellular Energetics, Proliferative and Metastatic Signaling Networks in VHL-mut RCC", "row_count": 0, "column_count": 0}, "table": {"label": "Table 3", "caption": "IPA Analysis: Toxicological Cellular Pathways Significantly Represented by HIF2α Regulation in RCC.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[14]/table-wrap[1]#pone-0071654-t003"}}], "gaps": ["asset:data:geo:PXD000335 not downloaded", "asset:data:geo:PXD000335 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Proteins were accepted as differentially expressed following analysis of variance (ANOVA, P<0.05), requiring at least a twofold change in expression and also passing validation by Peptide Prophet and Protein Prophet using protein identifications from Scaffold."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "bootstrap_mean_difference", "expected_value": 2.0, "unit": "fold change", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. 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