title: A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma.
abstract: We performed a pilot proteogenomic study to compare lung adenocarcinoma to lung squamous cell carcinoma using quantitative proteomics (6-plex TMT) combined with a customized Affymetrix GeneChip. 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.
authors.affiliation: Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Stewart
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria.
authors.forename: Katja
authors.initials: K
authors.lastname: Parapatics
authors.affiliation: Cancer Informatics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612.
authors.forename: Eric A
authors.initials: EA
authors.lastname: Welsh
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria.
authors.forename: André C
authors.initials: AC
authors.lastname: Müller
authors.affiliation: Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612.
authors.forename: Haoyun
authors.initials: H
authors.lastname: Cao
authors.affiliation: Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612.
authors.forename: Bin
authors.initials: B
authors.lastname: Fang
authors.affiliation: Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612.|Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612.
authors.forename: John M
authors.initials: JM
authors.lastname: Koomen
authors.affiliation: Cancer Informatics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612.|Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Eschrich
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria.
authors.forename: Keiryn L
authors.initials: KL
authors.lastname: Bennett
authors.affiliation: Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612.
authors.forename: Eric B
authors.initials: EB
authors.lastname: Haura
mesh_terms: D000230:Adenocarcinoma / Q000175:diagnosis / Q000235:genetics*; D000077192:Adenocarcinoma of Lung; D014408:Biomarkers, Tumor / Q000235:genetics*; D002294:Carcinoma, Squamous Cell / Q000175:diagnosis / Q000235:genetics; D005260:Female; D015870:Gene Expression / Q000235:genetics; D051272:Glucose Transporter Type 1 / Q000235:genetics*; D006801:Humans; D008175:Lung Neoplasms / Q000175:diagnosis / Q000235:genetics*; D008297:Male; D027501:Monocarboxylic Acid Transporters / Q000235:genetics*; D010865:Pilot Projects; D011379:Prognosis; D040901:Proteomics / Q000379:methods; D016019:Survival Analysis; D027981:Symporters / Q000235:genetics*; D000099233:Monocarboxylate Transport Protein 1
chemical_list: D014408:Biomarkers, Tumor; D051272:Glucose Transporter Type 1; D027501:Monocarboxylic Acid Transporters; D027981:Symporters; D000099233:Monocarboxylate Transport Protein 1; C495677:SLC2A1 protein, human