Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1182023 | ENA |
REPOSITORIES: ENA
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Project description:Tumor microenvironment plays an important role in regulating cell growth and metastasis. Recently we developed an ex vivo lung cancer model (4D) that forms perfusable tumor nodules on a lung matrix that mimics human lung cancer histopathology and protease secretion pattern. We compared the gene expression profile (Human OneArray v5 chip) of A549 cells, a human lung cancer cell line, grown on petri dish (2D), and of the same cells grown in the matrix of our ex vivo model (4D). Furthermore, we obtained gene expression data of A549 cells grown on petri dish (2D) and matrigel (3D) from a previous study and compared the 3D expression profile with that of 4D. Expression array analysis showed 2954 genes differentially expressed between 2D and 4D. Gene Ontology (GO) analysis showed up-regulation of several genes associated with extracellular matrix, polarity, and cell fate and development. Moreover, expression array analysis of 2D versus 3D showed 269 genes that were most differentially expressed, with only 35 genes (13%) having similar expression patterns as observed between 2D and 4D. Finally, the differential gene expression signature of 4D cells (versus 2D) correlated significantly with poor survival in patients with lung cancer (n=1492), while the expression signature of 3D versus 2D correlated with better survival in lung cancer patients. Since patients with larger tumors tend to have worse survival, the ex vivo 4D model may offer additional features over the 3D model, to better mimic of natural progression of tumor growth in lung cancer patients. We compared the gene expression profile (Human OneArray v5 chip) of A549 cells, human lung cancer cell line, grown on petri dish (2D) and same cells grown in the matrix of our ex vivo model (4D).
2013-09-16 | E-GEOD-45142 | biostudies-arrayexpress
Project description:MS spectrum of lung tissue metabolic analysis in 131 patients with lung cancer or benign lung tumor. These include lung cancer tissues/benign tumor tissues, adjacent normal tissues and distal normal tissues.
2020-06-19 | PXD019969 |
Project description:Tumor microenvironment plays an important role in regulating cell growth and metastasis. Recently we developed an ex vivo lung cancer model (4D) that forms perfusable tumor nodules on a lung matrix that mimics human lung cancer histopathology and protease secretion pattern. We compared the gene expression profile (Human OneArray v5 chip) of A549 cells, a human lung cancer cell line, grown on petri dish (2D), and of the same cells grown in the matrix of our ex vivo model (4D). Furthermore, we obtained gene expression data of A549 cells grown on petri dish (2D) and matrigel (3D) from a previous study and compared the 3D expression profile with that of 4D. Expression array analysis showed 2954 genes differentially expressed between 2D and 4D. Gene Ontology (GO) analysis showed up-regulation of several genes associated with extracellular matrix, polarity, and cell fate and development. Moreover, expression array analysis of 2D versus 3D showed 269 genes that were most differentially expressed, with only 35 genes (13%) having similar expression patterns as observed between 2D and 4D. Finally, the differential gene expression signature of 4D cells (versus 2D) correlated significantly with poor survival in patients with lung cancer (n=1492), while the expression signature of 3D versus 2D correlated with better survival in lung cancer patients. Since patients with larger tumors tend to have worse survival, the ex vivo 4D model may offer additional features over the 3D model, to better mimic of natural progression of tumor growth in lung cancer patients.
2013-09-16 | GSE45142 | GEO
Project description:The target sequecing vcf data of tumor and curculating tumor DNA for non-small cell lung cancer patients.
2022-05-09 | PRJEB52694 | EVA
Project description:Hypoxia triggers aggressive cancer growth and contributes to chemotherapy resistance. Novel therapeutic strategies aim at targeting hypoxia activated signaling pathways. Tumor hypoxia not only affects neoplastic tumor cells but also the surrounding stroma cells. Therefore, a novel ex vivo model was established, which allows the study of hypoxia effects in fragments of non-small cell lung cancer (NSCLC) with preserved tumor microenvironment and 3D-structure. Microarray analysis identified 107 significantly regulated genes with at least two-fold expression change in hypoxic compared to normoxic fragments. However, only four genes were significantly regulated in both subtypes, adenocarcinoma and squamous cell carcinoma. The hypoxic regulation of these four genes was verified in an independent set using quantitative PCR. Non-small cell lung cancer (NSCLC) fragments were cultured ex vivo under hypoxia or normoxia for three days. cDNA microarray analysis was performed in hypoxic and normoxic lung cancer fragments from ten patients.
2011-07-27 | E-GEOD-30979 | biostudies-arrayexpress
Project description:Quantitative proteome profiling of 72 samples of tumor and normal tissues from pancreatic cancer (PC) patients, tissues from patients with pancreatitis samples and PDX-derived cell lines.
2022-05-20 | PXD025120 | JPOST Repository
Project description:<p>Small cell lung cancer (SCLC) accounts for nearly 15% of all patients with lung cancer. Though the response to initial therapy is favorable in many patients, a majority of patients go on to develop recurrent disease which is very difficult to treat. The response rates to chemotherapy are very low and most patients succumb to relapsed SCLC within a few months. Virtually no progress has been made in the treatment of SCLC in the last three decades. In order to better understand the molecular alterations in relapsed SCLC, we have generated exome and RNA sequence from normal, primary tumor and relapse tissues of SCLC patients.</p>
| phs001049 | dbGaP
Project description:Dr. Kate Olson's Lab is interested to expand these analysis to comparisons between human normal lung tissue and human lung tumor tissue. In hopes that this will help in finding a diagnostic marker for lung cancer. Since there will be more variability between these samples, we would like to get preliminary data on ten normal lung tissue and ten lung tumor tissues from the same patient. We have already analyzed 4 cell lines and we saw gene expression variability related to how metastatic the cell lines were. This has been written and submitted for publication. We would like to expand these analysis to comparisons between human normal lung tissue and human lung tumor tissue. We hope that this will help in finding a diagnostic marker for lung cancer. Since there will be more variability between these samples, we would like to get preliminary data on ten normal lung tissue and ten lung tumor tissues from the same patient. The samples were dissected by a pathologist prior to extraction to maximize the amount of normal tissue included in the tumor samples. RNA samples from non tumor and tumor lung cancer patients were received by Core E. The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays.
2011-06-14 | E-GEOD-29927 | biostudies-arrayexpress
Project description:Background: Lung is the largest mucosal area of the human body and directly connected to the external environment, facing microbial exposure and environmental stimuli. Therefore, studying the internal microorganisms of the lung is crucial for a deeper understanding of the relationship between microorganisms and the occurrence and progression of lung cancer. Methods: Tumor and adjacent nontumor tissues were collected from 38 lung adenocarcinoma patients and used nanopore sequencing technology to sequence the 16s full-length sequence of bacteria, and combining bioinformatics methods to identify and quantitatively analyze microorganisms in tissues, as well as to enrich the metabolic pathways of microorganisms. Results: the microbial composition in lung adenocarcinoma tissues is highly similar to that in adjacent tissues, but the alpha diversity is significantly lower than that in adjacent tissues. The difference analysis results show that the bacterial communities of Streptococcaceae, Lactobacillaceae, and Neisseriales were significantly enriched in cancer tissues. The results of metabolic pathway analysis indicate that pathways related to cellular communication, transcription, and protein synthesis were significantly enriched in cancer tissue. In addition, clinical staging analysis of nicotine exposure and lung cancer found that Haemophilus, paralinfluenzae, Streptococcus gordonii were significantly enriched in the nicotine exposure group, while the microbiota of Cardiobactereae and Cardiobacterales were significantly enriched in stage II tumors. The microbiota significantly enriched in IA-II stages were Neisseriaeae, Enterobacteriales, and Cardiobacterales, respectively. Conclusion Nanopore sequencing technology was performed on the full length 16s sequence, which preliminarily depicted the microbial changes and enrichment of microbial metabolic pathways in tumor and adjacent nontumor tissues. The relationship between nicotine exposure, tumor progression, and microorganisms was explored, providing a theoretical basis for the treatment of lung cancer through microbial targets.
2024-03-25 | GSE262090 | GEO
Project description:Fibrinogen deposition promotes metastasis in lung because fibrinogen binds circulating tumor cells and the fibrinogen-tumor cell complex is allowed to invade in the lung tissue. We used microarrays to compare gene expression profiles of the tissues near and apart from fibrinogen deposition in non-cancer patients and cancer patients.
2023-05-26 | GSE211528 | GEO