Homo sapiens
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE10939
PROVIDER: PRJNA108781 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gene expression differences between adenocarcinoma and squamous cell carcinoma in human NSCLC (qRT-PCR)
| PRJNA108779 | ENA
Project description:Transcriptomic profiling of metastatic NSCLC cancer patients from tumor tissue and organ-matched normal tissue as reference which were taken as part of the WINTHER clinical trial. The organ-matched normal tissues were used in order to eliminate host gene expression variability while discarding most genetic variability between individuals. The goal was to trial was to navigate patients to therapy on the basis of fresh biopsy-derived DNA sequencing or RNA expression
2021-04-09 | GSE171702 | GEO
Project description:Gene expression differences between between matched tumor and normal samples were analyzed using paired t-test. Keywords: disease state analysis
2009-10-01 | GSE10937 | GEO
Project description:Introduction: Macrophage phenotype in the tumor microenvironment correlates with prognosis in non-small cell lung cancer (NSCLC). Immunosuppressive macrophages promote tumor progression, while pro-inflammatory macrophages may drive an anti-tumor immune response. How individual NSCLCs impact macrophage phenotype is a major knowledge gap. Methods: To systematically study the impact of lung cancer cells on macrophage phenotypes, we developed an in vitro co-culture model comprised of molecularly and clinically-annotated patient-derived NSCLC lines, human cancer-associated fibroblasts, and murine macrophages. Induced macrophage phenotype was studied through qRT-PCR and validated in vivo using NSCLC xenografts through quantitative immunohistochemistry and clinically with TCGA “matched” patient tumors. Results: 72 NSCLC cell lines were studied. The most frequent highly induced macrophage-related gene was Arginase-1, reflecting an immunosuppressive M2-like phenotype. This was independent of multiple clinicopathologic factors, which also did not impact M2:M1 ratios in matched TCGA samples. In vivo, tumors established from high Arginase-1-inducing lines (Arghi) had a significantly elevated density of Arg1+ macrophages. Matched TCGA clinical samples to Arghi NSCLC lines had a significantly higher ratio of M2:M1 macrophages. Conclusions: In our preclinical model, a large panel of patient-derived NSCLC lines most frequently induced high expression Arginase-1 in co-cultured mouse macrophages, independent of major clinicopathologic and oncogenotype-related factors. Arghi cluster-matched TCGA tumors contained a higher ratio of M2:M1 macrophages. Thus, this preclinical model reproducibly characterizes how individual NSCLCs modulate macrophage phenotype, correlates with macrophage polarization in clinical samples, and can serve as an accessible platform for further investigation of macrophage-specific therapeutic strategies.
2023-04-01 | GSE200627 | GEO
Project description:Lung tumors, as well as normal tumor-adjacent (NTA) tissue of non-small cell lung cancer (NSCLC) patients, were collected and subjected label-free quantitation shotgun proteomics in data-independent mode to identify differences between the tumors and adjacent tissue. By employing in-depth proteomics, we identified several pathways that are up- or downregulated in the tumors of non-small cell lung cancer patients.
2023-11-27 | PXD046998 | Pride
Project description:The tumor microenvironment strongly influences cancer development, progression and metastasis. The role of carcinoma-associated fibroblasts (CAFs) in these processes and their clinical impact has not been studied systematically in non-small cell lung carcinoma (NSCLC). We established primary cultures of CAFs and matched normal fibroblasts (NFs) from 15 resected NSCLC. We demonstrate that CAFs have greater ability than NFs to enhance the tumorigenicity of lung cancer cell lines. Microarray gene expression analysis of the 15 matched CAF and NF cell lines identified 46 differentially expressed genes, encoding for proteins that are significantly enriched for extracellular proteins regulated by the TGF-beta signaling pathway. We have identified a subset of 11 genes that formed a prognostic gene expression signature, which was validated in multiple independent NSCLC microarray datasets. Functional annotation using protein-protein interaction analyses of these and published cancer stroma-associated gene expression changes revealed prominent involvement of the focal adhesion and MAPK signalling pathways. Fourteen (30%) of the 46 genes also were differentially expressed in laser-capture micro-dissected corresponding primary tumor stroma compared to the matched normal lung. Six of these 14 genes could be induced by TGF-beta1 in NF. The results establish the prognostic impact of CAF-associated gene expression changes in NSCLC patients. 30 samples: 15 primary NSCLC fibroblast cell lines, 15 normal lung fibroblast cell lines
2011-04-08 | E-GEOD-22862 | biostudies-arrayexpress
Project description:The tumor microenvironment strongly influences cancer development, progression and metastasis. The role of carcinoma-associated fibroblasts (CAFs) in these processes and their clinical impact has not been studied systematically in non-small cell lung carcinoma (NSCLC). We established primary cultures of CAFs and matched normal fibroblasts (NFs) from 15 resected NSCLC. We demonstrate that CAFs have greater ability than NFs to enhance the tumorigenicity of lung cancer cell lines. Microarray gene expression analysis of the 15 matched CAF and NF cell lines identified 46 differentially expressed genes, encoding for proteins that are significantly enriched for extracellular proteins regulated by the TGF-beta signaling pathway. We have identified a subset of 11 genes that formed a prognostic gene expression signature, which was validated in multiple independent NSCLC microarray datasets. Functional annotation using protein-protein interaction analyses of these and published cancer stroma-associated gene expression changes revealed prominent involvement of the focal adhesion and MAPK signalling pathways. Fourteen (30%) of the 46 genes also were differentially expressed in laser-capture micro-dissected corresponding primary tumor stroma compared to the matched normal lung. Six of these 14 genes could be induced by TGF-beta1 in NF. The results establish the prognostic impact of CAF-associated gene expression changes in NSCLC patients. 30 samples: 15 primary lung tumor stroma, 15 normal lung parenchyma
2011-04-08 | E-GEOD-22863 | biostudies-arrayexpress
Project description:Plasma samples from 100 early stage (I to IIIA) non–small-cell lung cancer (NSCLC) patients and 100 non-cancer controls were screened for 754 circulating microRNAs via qRT-PCR, using TaqMan MicroRNA Arrays. Our objective was to identify a panel of circulating microRNAs in plasma that will contribute to early detection of lung cancer.
2015-12-31 | GSE64591 | GEO
Project description:Lung tumors, as well as normal tumor-adjacent (NTA) tissue of non-small cell lung cancer (NSCLC) patients, were collected and subjected to labeling with a serine hydrolase-directed activity-based probe (ABP) immediately after excision. Labeling with the serine hydrolase-directed ABP allows for the detection of active lipid hydrolases, which are the focus of our investigation. The labeled proteins (corresponding to active enzymes at time of labeling) were enriched using a biotin-containing linker that was covalently attached using strain-promoted alkyne-azide cycloaddition (click chemistry). Shotgun proteomics of the on-bead digested enriched proteins of ABP-treated and control samples enabled identification of enriched proteins as well as comparison of activity profiles between NTA and tumor samples of NSCLC patients.
2023-11-27 | PXD046934 | Pride
Project description:To identify lncRNA expression in placentas from patients with late-onset preeclampsia (LOPE), we have employed whole genome microarray expression profiling as a discovery platform to identify differential expression of lncRNAs in placental samples from LOPE patients and normal controls. For microarray analysis, 8 randomly and blindly selected placental samples from LOPE patients and matched controls (4 samples per group) were used to extract total RNA. The expression profiles of the placental lncRNAs were detected using the Agilent Human lncRNA Microarray V4.0(OE Biotech, Shanghai, China). The threshold for a dysregulated lncRNA was set as a fold-change (FC) value of 2.0 or greater. A totle of 163 differentially expressed lncRNAs were identified. Expression of nine lncRNAs (NONHSAT145880, ENST00000587240, NONHSAT116812, NONHSAT104536, FR339600, NONHSAG018907, TCONS_l2_00014782, NONHSAT134432 and NONHSAG024318) from this microarray was quantified n placental tissues from the LOPE patients (n = 40) and controls (n = 35) delivered by caesarean section by real-time PCR, confirming low variability between the qRT-PCR results and the microarray data.
2017-04-18 | GSE97898 | GEO