RNA-seq data from Non Small Cell Lung Cancer (NSCLC) samples
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ABSTRACT:
PROVIDER: EGAS00001004032 | EGA |
REPOSITORIES: EGA
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Project description:T lymphocytes can efficiently counteract the growth of tumors within the tumor microenvironment. Specialized immune-interacting fibroblasts, termed fibroblastic reticular cells (FRC) are responsible for the formation of specialized niches promoting immune cell activation in secondary lymphoid organs and originate from embryonic progenitors. FRCs have also been identified in tertiary lymphoid structures (TLS) in tumor tissues. However, the identity and differentiation of TLS-associated FRC subsets that promote intra-tumoral T cell activity have remained unexplored. Here, we employed single cell RNA-sequencing of fibroblasts and immune cells, sampled from subpleural margin, central margin and unaffected lung tissue in non small cell lung cancer (NSCLC), demonstrating the formation of specific tumor T cell environments (TTEs) underpinned by CCL19-expressing FRCs. We detected tumor-specific FRC subsets namely CCL19-expressing TRCs and perivascular reticular cells (PRCs) interacting with intratumoral T cells, and thus regulating FRC differentiation and T cell activation. Our results highlight a remarkable functionality of FRCs to efficiently determine protective antitumoral T cell responses in NSCLC.
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Project description:Lung cancers are a heterogeneous group of diseases with respect to biology and clinical behavior. Currently, diagnosis and classification are based on histological morphology and immunohistological methods for discrimination between two main histologic groups: small cell lung cancer (SCLC) and non-small cell lung cancer which account for 20% and 80% of lung carcinomas, respectively. NSCLCs, which are divided into the three major subtypes adenocarcinoma, squamous cell carcinoma and dedifferentiated large cell carcinoma, show different characteristics such as the expression of certain keratins or production of mucin and lack of neuroedocrine differentiation. The molecular pathogenesis of lung cancer involves the accumulation of genetic und epigenetic alterations including the activation of proto-oncogenes and inactivation of tumor suppressor genes which are different for lung cancer subgroups. The development of microarray technologies opened up the possibility to quantify the expression of a large number of genes simultaneously in a given sample. There are several recent reports on expression profiling on lung cancers but the analysis interpretation of the results might be difficult because of the heterogeneity of cellular components. The methods used for sample selection and processing can have a strong influence on the expression values obtained through microarray profiling. Laser capture microdissection (LCM) provides higher specificity in the selection of target cells compared to traditional bulk tissue selection methods, but at an increased processing cost. Here we describe the use of an expression microarray study on NSCLC samples and surrounding tissue, comparing macroscopic lung tumor and tissue samples (“grind and bind”), versus tumor and alveolar compartment cells laser capture microdissected (LCM) from the same macroscopic lung samples. In this study, a set of 31 pairs and one non-paired sample of macroscopic tumor and non-tumor samples (10 pairs and 1 non-paired sample squamous-cell carcinoma, 19 pairs and one non-paired samples adenocarcinoma, 2 pairs adeno-squamous-cell carcinoma) was selected for bulk/macro sampling. Of these 31 pairs and 2 non-paired samples, 16 pairs plus 15 non paired samples were reanalyzed using laser capture microdissection (LCM) for sampling the cells (7 pairs and 3 non-paired samples squamous-cell carcinoma, 8 pairs and 11 non-paired samples adeno carcinomas, 1 pair and 1 non paired sample Adeno-squamous-cell carcinoma). For macroscopic samples, 50 to 80 µg of tissue was used to isolate total RNA. Gene expression profile was determined using Affymetrix Human Genome Gene 1.0 ST genechip. For the LCM samples, from representative slides histologically confirmed and mapped by a pathologist, approximately 1000 cells/sample were collected by LCM;. cDNA was amplified using Nugen WT-Ovation One-Direct amplification system. Here we describe the use of an expression microarray study on NSCLC samples and surrounding tissue, comparing macroscopic lung tumor and tissue samples (“grind and bind”), versus tumor and alveolar compartment cells laser capture microdissected (LCM) from the same macroscopic lung samples.
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