Browse
Submit Data
Databases
API
Help

Dataset Information

30 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tumor-microenvironment interactions studied by zonal transcriptional profiling of squamous cell lung carcinoma

ABSTRACT: To better understand the interaction between tumor cells and their microenvironment with regard to mechanisms of invasion, total RNA was isolated from the inner-tumor, tumor invasion front, adjacent lung and distant normal lung tissue from 18 patients with squamous cell lung carcinoma using punch-aided laser capture microdissection. Comprehensive mRNA expression profiles were obtained from microarray expreiments and statistical analyses revealed extensive changes in gene expression when comparing the inner tumor and tumor front with the normal lung and lung front. However, only a few genes were differentially expressed between the tumor front and the inner tumor. The identified genes indicate prostaglandin mediated inflammatory processes at the invasion front Sample for microarray experiments were taken from the inner-tumor, tumor invasion front, adjacent lung and distant normal lung tissue from 18 patients with squamous cell lung carcinoma using punch-aided laser capture microdissection. Sample RNA and Universal Reference RNA (Stratagene, La Jolla, USA) were amplified and separately labeled with both Cy3 and Cy5. All samples were subjected to two-color hybridizations (sample against reference) with color-switch experiments yielding two technical replicates, respectively.

ORGANISM(S): Homo sapiens

SUBMITTER: Haag Daniel

PROVIDER: S-ECPF-GEOD-31446 | biostudies-other |

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Tumor-microenvironment interactions studied by zonal transcriptional profiling of squamous cell lung carcinoma

Project description:To better understand the interaction between tumor cells and their microenvironment with regard to mechanisms of invasion, total RNA was isolated from the inner-tumor, tumor invasion front, adjacent lung and distant normal lung tissue from 18 patients with squamous cell lung carcinoma using punch-aided laser capture microdissection. Comprehensive mRNA expression profiles were obtained from microarray expreiments and statistical analyses revealed extensive changes in gene expression when comparing the inner tumor and tumor front with the normal lung and lung front. However, only a few genes were differentially expressed between the tumor front and the inner tumor. The identified genes indicate prostaglandin mediated inflammatory processes at the invasion front Sample for microarray experiments were taken from the inner-tumor, tumor invasion front, adjacent lung and distant normal lung tissue from 18 patients with squamous cell lung carcinoma using punch-aided laser capture microdissection. Sample RNA and Universal Reference RNA (Stratagene, La Jolla, USA) were amplified and separately labeled with both Cy3 and Cy5. All samples were subjected to two-color hybridizations (sample against reference) with color-switch experiments yielding two technical replicates, respectively.

2011-12-01 | E-GEOD-31446 | biostudies-arrayexpress

Tumor-microenvironment interactions studied by zonal transcriptional profiling of squamous cell lung carcinoma

2011-12-01 | GSE31446 | GEO

Changes in the tumor microenvironment during lymphatic metastasis of lung squamous cell carcinoma.

Project description:Metastasis and growth in neoplastic lesions requires the multistep regulation of microenvironmental factors. We aimed to elucidate the microenvironmental changes in the process of lymphatic metastasis of lung squamous cell carcinoma. We examined the morphological characteristics of 102 cases of primary tumor (PT), 50 of intralymphatic tumor (ILT), 51 of lymph node (LN) micrometastasis (LN-Mic; ?2 mm in size), and 82 of LN macrometastasis (LN-Mac; ?10 mm in size). Afterwards we evaluated the expression of nine molecules (epidermal growth factor receptor, fibroblast growth factor receptor 2, CD44, aldehyde dehydrogenase 1, Podoplanin, E-cadherin, S100A4, geminin, and ezrin) in matched PT, ILT, LN-Mic, and LN-Mac from 23 of these cases. The number of smooth muscle actin ?-positive fibroblasts, CD34-positive microvessels and CD204-positive macrophages were also examined. As a result, the mitotic index of tumor cells was significantly lower in ILT and LN-Mic than PT and LN-Mac (P < 0.001). Moreover, stromal reaction in ILT and LN-Mic was less prominent than in PT and LN-Mac (P < 0.001). Immunohistochemical study revealed that epidermal growth factor receptor expression level and frequency of geminin-positive cells in ILT and LN-Mic were significantly lower than in PT and LN-Mac (P < 0.05). The number of stromal cells indicated by staining of CD34, CD204, and smooth muscle actin ? in ILT and LN-Mic was also significantly lower than in PT and LN-Mac (P < 0.05). In lung squamous cell carcinoma, drastic microenvironmental changes (e.g., growth factor receptor expression and proliferative capacity of tumor cells and structural changes in stromal cells) occur during both the process of lymphatic permeation and the progression into macrometastases.

| S-EPMC5276828 | biostudies-other

Human lung squamous cell carcinoma expression profiling

Project description:Lung squamous cell carcinoma gene expression (LSCC) is highly variable. This study discovered and validated LSCC gene expression subtypes. RNA from tumors and a common reference were hybridized to Agilent two color microarrays

| S-ECPF-GEOD-17710 | biostudies-other

Characterization of the Tumor Immune Microenvironment in Lung Squamous Cell Carcinoma Using Imaging Mass Cytometry.

Project description:BackgroundLung squamous cell carcinoma (LUSC) is a major subtype of non-small cell lung cancer. The tumor immune microenvironment (TIME) affects the anti-tumor immune response and the patient's prognosis, although the TIME in LUSC patients is incompletely understood.MethodsWe retrospectively collected surgical specimens from patients with previously untreated primary LUSC. Histopathological examination was used to identify tumor regions and adjacent regions, and imaging mass cytometry was used to characterize the immune cells in those regions. The results were compared between regions and between patients.ResultsWe identified heterogeneity in the TIME on comparing different patients with LUSC, although the tumor region and adjacent region both exhibited an immune response to the tumor. The TIME typically included a large number of infiltrating and activated T-cells, especially CD8+ T-cells, which closely interacted with the tumor cells in the tumor region. There was limited infiltration of B-cells, NK cells, and NKT cells, while the major immune suppressor cells were CD33+ myeloid-derived cells. We also identified a novel population of CD3-CD4+ cells with high expression of Foxp3 and TNFα, which might modulate the tumor microenvironment and play a proinflammatory role in the TIME.ConclusionsThe TIME of LUSC appears to be immunogenic and heterogenous, with predominant infiltration of activated CD8+ T-cells. The interactions between the tumor cells and T-cells facilitate the anti-tumor activity. A novel subpopulation of CD3-CD4+ cells with high TNFα and Foxp3 expression may modulate the tumor microenvironment and play a proinflammatory role.

| S-EPMC8047498 | biostudies-literature

Immunogenomic classification of lung squamous cell carcinoma characterizes tumor immune microenvironment and predicts cancer therapy.

Project description: Not available

| S-EPMC10404949 | biostudies-literature

Prognostic value of immune-related genes in the tumor microenvironment of lung adenocarcinoma and lung squamous cell carcinoma.

Project description:Non-small cell lung cancer (NSCLC), which consists mainly of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), are the leading cause of cancer deaths worldwide. In this study, we performed a comprehensive analysis of the tumor microenvironmental and genetic factors to identify prognostic biomarkers for NSCLC. We evaluated the immune and stromal scores of patients with LUAD and LUSC using data from The Cancer Genome Atlas database with the ESTIMATE algorithm. Based on these scores, the differentially expressed genes were obtained and immune-related prognostic genes were identified. Functional analysis and protein-protein interaction network further revealed the immune-related biological processes in which these genes participated. Additionally, 22 subsets of tumor-infiltrating immune cells (TIICs) in the tumor microenvironment were analyzed with the CIBERSORT algorithm. Finally, we validated these valuable genes using an independent cohort from the Gene Expression Omnibus database. The associations of the immune and stromal scores with patients' clinical characteristics and prognosis were positive in LUAD but negative in LUSC and the correlations of TIICs with clinical characteristics were clarified. Several differentially expressed genes were identified to be potential immune-related prognostic genes. This study comprehensively analyzed the tumor microenvironment and presented immune-related prognostic biomarkers for NSCLC.

| S-EPMC7138544 | biostudies-literature

Tumor-derived KLK8 predicts inferior survival and promotes an immune-suppressive tumor microenvironment in lung squamous cell carcinoma.

Project description:Lung squamous cell carcinoma (LUSC) is the second most common lung cancer worldwide, leading to millions of deaths annually. Although immunotherapy has expanded the therapeutic choices for LUSC and achieved considerable efficacy in a subset of patients, many patients could not benefit, and resistance was pervasive. Therefore, it is significant to investigate the mechanisms leading to patients' poor response to immunotherapies and explore novel therapeutic targets. Using multiple public LUSC datasets, we found that Kallikrein-8 (KLK8) expression was higher in tumor samples and was correlated with inferior survival. Using a LUSC cohort (n = 190) from our center, we validated the bioinformatic findings about KLK8 and identified high KLK8 expression as an independent risk factor for LUSC. Function enrichment showed that several immune signaling pathways were upregulated in the KLK8 low-expression group and downregulated in the KLK8 high-expression group. For patients with low KLK8 expression, they were with a more active TME, which was both observed in the TCGA database and immune marker immunohistochemistry, and they had extensive positive relations with immune cells with tumor-eliminating functions. This study identified KLK8 as a risk factor in LUSC and illustrated the associations between KLK8 and cancer immunity, suggesting the potentiality of KLK8 as a novel immune target in LUSC.

| S-EPMC10809653 | biostudies-literature

Highly Multiplexed Digital Spatial Profiling of the Tumor Microenvironment of Head and Neck Squamous Cell Carcinoma Patients.

Project description:BackgroundImmune checkpoint inhibitors (ICI) have shown durable and long-term benefits in a subset of head and neck squamous cell carcinoma (HNSCC) patients. To identify patient-responders from non-responders, biomarkers are needed which are predictive of outcome to ICI therapy. Cues in the tumor microenvironment (TME) have been informative in understanding the tumor-immune contexture.MethodsIn this preliminary study, the NanoString GeoMx™ Digital Spatial Profiling (DSP) technology was used to determine the immune marker and compartment specific measurements in a cohort of HNSCC tumors from patients receiving ICI therapy.ResultsOur data revealed that markers involved with immune cell infiltration (CD8 T-cells) were not predictive of outcome to ICI therapy. Rather, a number of immune cell types and protein markers (CD4, CD68, CD45, CD44, CD66b) were found to correlate with progressive disease. Cross platform comparison with the Opal Vectra (Perkin Elmer) for a number of markers across similar regions of interest demonstrated concordance for pan-cytokeratin, CD8, and PD-L1.ConclusionThis study, to our knowledge, represents the first digital spatial analysis of HNSCC tumors. A larger cohort of HNSCC will be required to orthogonally validate the findings.

| S-EPMC7851078 | biostudies-literature