A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma.

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Using MaxQuant software, we identified 51,001 unique peptides that mapped to 7,241 unique proteins and from these identified 6,373 genes with matching protein expression for further analysis. We found a minor correlation between gene expression and protein expression; both datasets were able to independently recapitulate known differences between the adenocarcinoma and squamous cell carcinoma subtypes. We found 565 proteins and 629 genes to be differentially expressed between adenocarcinoma and squamous cell carcinoma, with 113 of these consistently differentially expressed at both the gene and protein levels. We then compared our results to published adenocarcinoma versus squamous cell carcinoma proteomic data that we also processed with MaxQuant. We selected two proteins consistently overexpressed in squamous cell carcinoma in all studies, MCT1 (SLC16A1) and GLUT1 (SLC2A1), for further investigation. We found differential expression of these same proteins at the gene level in our study as well as in other public gene expression datasets. These findings combined with survival analysis of public datasets suggest that MCT1 and GLUT1 may be potential prognostic markers in adenocarcinoma and druggable targets in squamous cell carcinoma. Data are available via ProteomeXchange with identifier PXD002622.", "claims": [{"id": "claim-method", "statement": "We used KM Plotter (http://www.kmplot.com) to perform survival analysis of MCT1 and GLUT1 in ADC and SCC [39].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26539827", "locator": "sections[7] \"Statistical Analyses\" paragraph 3", "quote": "We used KM Plotter (http://www.kmplot.com) to perform survival analysis of MCT1 and GLUT1 in ADC and SCC [39]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw mass spectrometry data are available via ProteomeXchange (http://www.proteomexchange.org/) with identifier PXD002622.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26539827", "locator": "sections[18] \"Data Availability\" paragraph 2", "quote": "The raw mass spectrometry data are available via ProteomeXchange (http://www.proteomexchange.org/) with identifier PXD002622."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used MaxQuant software for quantitative proteomic analysis and made its raw source data available through ProteomeXchange under identifier PXD002622. Headline result: 565 proteins and 629 genes were differentially expressed between adenocarcinoma and squamous cell carcinoma, with 113 consistently differentially expressed at both levels.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26539827", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Using MaxQuant software, we identified 51,001 unique peptides that mapped to 7,241 unique proteins and from these identified 6,373 genes with matching protein expression for further analysis."}, {"asset": "source:pmid:26539827", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We found 565 proteins and 629 genes to be differentially expressed between adenocarcinoma and squamous cell carcinoma, with 113 of these consistently differentially expressed at both the gene and protein levels."}, {"asset": "source:pmid:26539827", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD002622."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used MaxQuant software for quantitative proteomic analysis and made its raw source data available through ProteomeXchange under identifier PXD002622. 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