Journal: Oncotarget

Article Title: A molecular signature of lung cancer: potential biomarkers for adenocarcinoma and squamous cell carcinoma

doi: 10.18632/oncotarget.22298

Figure Lengend Snippet: (A) Representative immunoblots of tissue lysates of tumor (T) and healthy (H) lung tissues derived from lung cancer patients probed with antibodies directed against VDAC1, SMAC, HK-I, MAVS, AIF and Bcl-2. (B) Quantitative analysis of VDAC1 (37 patients, FC=6.2, p-value=5×10 −5 ); SMAC (37 patients, FC=5, p-value=3.4×10 −5 ); HK-I, (33 patients, FC=5.3, p-value=5.3×10 −3 ); MAVS (22 patients, FC=2.6, p-value=1.5×10 −4 ); AIF (35 patients, FC=3.5, p-value=1.7×10 −2 ), and Bcl-2 (22 patients, FC=1.5, p-value=1.4×10 −1 ) are presented as the mean ± SD. (C) LC-HR MS/MS data for VDAC1, HK1 and SMAC. A difference between healthy and tumor tissues was considered statistically significant when P < 0.001 ( *** ), P < 0.01 ( ** ), P< 0.05 ( * ), as determined by the Mann-Whitney test for the immunoblots and a two-way t-test for the LC-HR MS/MS data. (D) Heat map showing gene expression based on RNAseq UCSC XENA data of VDAC1, HK-I, SMAC and AIF. The gene expression profiles obtained from healthy (n=110) and tumor lung samples (n=1,017) of lung cancer patients are publicly available (TCGA lung cancer dataset, detailed in ). (E) Quantitative analysis of the RNAseq data. (F) Over-expression of VDAC1, SMAC, AIF, MAVS and Bcl-2 in lung cancer patients. Representative IHC staining for VDAC1, SMAC AIF, MAVS and Bcl-2 of healthy (n=10) and lung cancer (n=70) tissue samples from tissue microarray slides (US Biomax). The number on each image represents the percentage of patient samples that stained at the relative intensity presented by a gradient line on the left.

Article Snippet: Data for the gene expression profile and for the heat map for healthy and tumor lung samples of lung cancer patients were obtained from XENA, TCGA [RNAseq using ployA+ Illumina HiSeq] (version 2016-08-16, TCGA hub) ( http://xena.ucsc.edu ), with the unit being pan-cancer-normalized (n=1,129).

Techniques: Western Blot, Derivative Assay, Tandem Mass Spectroscopy, MANN-WHITNEY, Gene Expression, Over Expression, Immunohistochemistry, Microarray, Staining

Journal: Oncotarget

Article Title: A molecular signature of lung cancer: potential biomarkers for adenocarcinoma and squamous cell carcinoma

doi: 10.18632/oncotarget.22298

Figure Lengend Snippet: Expression patterns of twelve selected genes , previously proposed or identified in the current study, proposed to distinguish between AC and SCC. (A) Gene expression, heat map. Sample type (lung cancer, n=1017, or healthy tissue, n=110) and histological type (SCC, n=527, or AC, n=364), with relative gene expression levels, are presented, with red indicating high, black indicating medium and green indicating low expression levels. (B) RNAseq data imported from TCGA was subjected to quantitative analysis using a t-test. The ratio of the expression of the proteins in (A) SCC/AC is presented, and is considered statistically significant when P < 0.001 ( *** ). The proteins were grouped according to function as: Apop, apoptosis; Metab, metabolism; HAR, histone activity regulation; Ubiq, ubiquitination; Inflam, Inflammatory response; SP, Surfactant production; PT, protein transport. (C) Expression pattern of 24 selected genes , showing differential expression between AC and SCC based on proteomics data, were analyzed in the RNASeq dataset as presented in (A) and are presented as a gene expression map. Functional groups are indicated: TS, tumor suppressor; Metab, galactose metabolism; LM, lipid metabolism; AAM, amino acid metabolism; StP, structural proteins; PI, proteinase inhibitor; SiP, signaling pathway; NA, nuclear activity; MT, mitochondrial translocase and IR, immune response. (D) Quantitative analysis of RNAseq data from (C) carried out as in (B).

Article Snippet: Data for the gene expression profile and for the heat map for healthy and tumor lung samples of lung cancer patients were obtained from XENA, TCGA [RNAseq using ployA+ Illumina HiSeq] (version 2016-08-16, TCGA hub) ( http://xena.ucsc.edu ), with the unit being pan-cancer-normalized (n=1,129).

Techniques: Expressing, Gene Expression, Activity Assay, Ubiquitin Proteomics, Quantitative Proteomics, Functional Assay