Project description:Genome wide DNA methylation profiling of normal lung tissue samples. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in nor mal lung tissue samples. Samples included 244 normal lung tissue samples from lung cancer patients. Environment and Genetics in Lung Cancer Etiology EAGLE; Population-based case-control study Bisulphite converted DNA from 244 fresh-frozen primary human lung samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2. This file has 60 samples.
Project description:Chronic obstructive pulmonary disease (COPD) is a known risk factor for developing lung cancer suggesting that the COPD stroma contains factors supporting tumorigenesis. Since cancer initiation is complex we used a multi-omic approach to identify gene expression patterns that distinguish COPD stroma in patients with or without lung cancer. Our overall objective is the identification of gene expression pathways and levels of regulation in lung stroma of patients with COPD that harbor lung cancer. We obtained lung tissue from patients with COPD and lung cancer (tumor and adjacent non-malignant tissue) and those with COPD without lung cancer for proteomic and mRNA (cytoplasmic and polyribosomal) profiling. We used the joint and individual variation explained (JIVE) method to integrate and analysis across the three datasets. JIVE identified eight latent patterns that robustly distinguished and separated the three groups of tissue samples. Predictive variables that associated with the tumor, compared to adjacent stroma, were mainly represented in the transcriptomic data, whereas, predictive variables associated with adjacent tissue compared to controls was represented at the translatomic level. Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis revealed extracellular matrix (ECM) and PI3K-Akt signaling pathways as important signals in the pre-malignant stroma. COPD stroma adjacent to lung cancer is unique and differs from non-malignant COPD tissue and is distinguished by the extracellular matrix and PI3K-Akt signaling pathways.
Project description:To evaluate the molecular changes of lung malignancy in HIV infection, we analyzed the differential gene expression profiles and screened the early detection biomarkers of HIV-associated lung cancer using Affymetrix arrays. RNA was for transcriptomic profiles analysis in the HIV lung cancer tumor tissue samples from 3 patients with AC and 1 patient with squamous cell carcinoma (SCC) including 3 pairs of tumor/adjacent normal tissue paraffin specimens and 1 pair of tumor/adjacent normal fresh tissue samples.
Project description:Selective markers are needed for earlier diagnosis, optimal staging and treatment of oesophageal adenocarcinoma. This quantitative shotgun proteomic study used patient-matched fresh frozen tissue samples of OAC, normal oesophagus and normal stomach.
Project description:In a comparative study the genome wide methylation levels using Illumina Infinium 450k chips were assigned. The specific methylation pattern of lung cancer patients (n=17), patients suffering from idiopathic lung fibrosis (n=37) as well as 32 patients suffering from chronic obstructive pulmonary disease and 43 DNA samples derived from healthy-lungs were determined. Lung biopsy samples were obtained by bronchoscopy. Thus obtained tissue was snap frozen in liquid nitrogen. Classification of lung fibrosis patients base on CT scans of the affected lung.
Project description:Genome wide DNA methylation profiling of normal and tumoral tissues of the breast. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450 thousand CpGs in fresh frozen tissue samples (40 primary breast tumours and 17 normal breast tissues). Samples included morphologically normal samples of each tissue and tumor samples.
Project description:Transcriptomic profiling of normal mouse lung, liver, kidney, and spleen tissue following 211At irradiation. Total RNA was isolated from fresh-frozen tissue samples.
