Project description:Lung cancer is the leading cause of preventable death globally and is broadly classified into adenocarcinoma and squamous cell carcinoma depending upon cell type. In this study, we carried out mass spectrometry based quantitative proteomic analysis of lung adenocarcinoma and squamous cell carcinoma primary tissue by employing the isobaric tags for relative and absolute quantitation (iTRAQ) approach. Proteomic data was analyzed using SEQUEST search algorithm which resulted in identification of 25,998 peptides corresponding to 4,342 proteins of which 610 proteins were differentially expressed (≥ 2-fold) between adenocarcinoma and squamous cell carcinoma samples. These differentially expressed proteins were further classified by gene ontology for their localizations and biological processes. Pathway analysis of differentially expressed proteins revealed distinct alterations in networks and pathways in both adenocarcinoma and squamous cell carcinoma samples. In this study, we identified a subset of proteins that shows converse expression between lung adenocarcinoma and squamous cell carcinoma samples. Such proteins may serve as signature markers to distinguish between the two subtypes.
Project description:To identify gene expression biomarkers associate with asbestos-related lung squamous cell carcinoma, we analyzed gene expression profiles for a total of 56 lung squamous cell carcinomas using 44K Illumina Gene Expression microarrays. Twenty-six cases had lung asbestos body counts above levels associated with urban dwelling (ARLC-SCC: asbestos-related lung cancer-squamous cell carcinoma) and 30 cases had no lung asbestos bodies (NARLC-SCC: non-asbestos related lung cancer- squamous cell carcinoma). Genes differentially expressed between ARLC-SCC and NARLC-SCC were identified on fold change and P-value, and then prioritised using gene ontology. Total RNA was obtained from fresh frozen lung tumour tissue and stratified by asbestos phenotype. Gene expression profiling was performed to identify differences in the gene profiles of asbestos-related and non-asbestos related lung squamous cell carcinomas.
Project description:To identify gene expression biomarkers associate with asbestos-related lung squamous cell carcinoma, we analyzed gene expression profiles for a total of 56 lung squamous cell carcinomas using 44K Illumina Gene Expression microarrays. Twenty-six cases had lung asbestos body counts above levels associated with urban dwelling (ARLC-SCC: asbestos-related lung cancer-squamous cell carcinoma) and 30 cases had no lung asbestos bodies (NARLC-SCC: non-asbestos related lung cancer- squamous cell carcinoma). Genes differentially expressed between ARLC-SCC and NARLC-SCC were identified on fold change and P-value, and then prioritised using gene ontology.
Project description:Lung squamous cell carcinoma gene expression (LSCC) is highly variable. This study discovered and validated LSCC gene expression subtypes.
Project description:Using H3K27ac ChIP-seq profile to map active enhancers in lung cancer and endometrial carcinoma cells ChIP-seq of H3K27ac was done in lung adenocarcinoma cell lines (NCI-H358 and NCI-H2009), squamous cell lung carcinoma cell lines (HCC95) and endometrial carcinoma cell lines (Ishikawa)
Project description:Our group previously reported the gene expression profiles of four stages of human lung development, and the expression of one group of genes (PTN1 genes) steadily decreased during lung development, the data included four stages of human lung development and 69 lung adenocarcinoma (ADC) samples, and their gene expression profile data are available in the GEO (GSE43767). Our group has already performed another study with 69 lung squamous cell carcinoma (SCC) tissues, the gene expression profile data are available in the Gene Expression Omnibus (GSE67061). In the present study, we performed the whole genome gene expression mircroarray of 60 paracancerous tissues of human lung squamous cell carcinoma, we aim to show expression characteristics of PTN1 genes during the four lung developmental stages and in lung ADC, lung SCC and paracancerous samples. We examined the prognostic value of the PTN1 genes in five independent lung adenocarcinoma (ADC) and five squamous cell carcinoma (SCC) microarray datasets and revealed that the expression of PTN1 genes was associated with survival in lung ADC patients but had no prognostic value for lung SCC.
Project description:Integration of LC-MS/MS data links biological processes to fragmentation of tumor epithelia, and morphological marker that associates with decreased patient survival in lung squamous cell carcinoma
Project description:Discovery of novel diagnostic and/or prognostic biomarkers of lung squamous cell carcinoma based on a whole transcriptome analysis using RNA sequencing (RNA-seq). Transcriptomic profiles of 12 available samples, out of 87 recruited patients with lung squamous cell carcinoma (SCC) were generated using Ion Proton system.
Project description:Using H3K27ac ChIP-seq profile to map active enhancers in lung cancer, endometrial carcinoma and head and neck squamous cell carcinoma cells