Project description:Lung cancer is the leading cause of cancer-related deaths world-wide. ~85% of lung carcinomas are non–small cell lung carcinoma (NSCLC). Tumor cell heterogeneity is very poorly defined. However, it is known to be important for tumor response to cancer therapy and cancer agressivenes. We subjected three NSCLC tumors resected from different patients to Drop-seq in order to 1) elucidate the capability of scRNA-seq analysis in identifying different tumor cell populations; and 2) ascertain the clinical value of the genes which distinguish cancer cells from other cells in the tissue. As anticipated, the tissue composition of independently collected samples varied. Despite deficient populations in some samples, both donor and patient samples contributed to the majority of cell populations. However, cancer cells were all patient-specific. These findings emphasize the utility of single cell gene expression data in identification of tumor cell populations. The collected data might be further used for predicting of drugs specific to the biology of activated pathways and patient outcome.
Project description:Non-small cell lung cancer (NSCLC) is a common lung disorder.Recent studies have shown that circRNA plays critical roles in a myriad of biological processes and human diseases,Since the roles of circRNA in NSCLC remain unknown,they were investigated in the study.Our findings indicate that the expression profiles of circRNAs have changed in NSCLC as compared with normal lung, and may provide novel insight into the molecular mechanism underlying the disease and potential novel diagnostic or therapeutic targets for NSCLC.
Project description:Differences in gene expression profiles regarding the expression of genes encoding for proteins with G protein-coupled receptor (GPCR) activity between SCLC and NSCLC and normal lung samples was successfully examined. In the present study, 8 SCLC, 16 NSCLC and 14 normal lung RNA samples (human) had been purchased from OriGene Technologies. Gene expression analysis was performed using Affymetrix microarrays (Human Exon 1.0 ST Array).
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.
Project description:Exosomes play important roles in intercellular communication through the delivery of their cargoes, which include proteins, lipids, and RNAs. Increasingly, multiple studies have reported the association between exosomal small non-coding RNAs and cancer, due to their regulatory functions in gene expression. Hence, analysis of the features of small non-coding RNA expression and their incorporation into exosomes is important for cancer research. Here, we performed deep sequencing to investigate the expression of small RNAs in plasma exosomes from lung adenocarcinoma patients, lung squamous cell carcinoma patients, and healthy controls. We found that 5’ YRNA hY4-derived fragments are significantly upregulated in non-small cell lung cancer (NSCLC) exosomes, and may serve as a novel class of circulating biomarkers for NSCLC diagnosis. We also identified that the RNY4P7 gene on chromosome 2 may not be a pseudogene, because the corresponding transcript hY4 reverse fragment was detected in exosomes and cells. Further, we demonstrated that a panel of small RNAs, including miR-451a and miR-122-5p, may be selectively sorted into NSCLC exosomes. Overall, our studies have indicated a wider range of biological effects in NSCLC that may be mediated by exosomal small RNAs than previously known.
Project description:Asparagine-linked glycosylation (N-glycosylation) of proteins in the cancer secretome has gained increasing attention as a potential biomarker for cancer detection and diagnosis. Small extracellular vesicles (sEVs) constitute a large part of the cancer secretome, yet little is known about whether their N-glycosylation status reflects cancer characteristics. Here we investigated the N-glycosylation of sEVs released from small-cell lung carcinoma (SCLC) and non-small-cell lung carcinoma (NSCLC) cells. The N-glycans of SCLC-sEVs were characterized by the presence of structural units found in the brain N-glycome, while NSCLC-sEVs were dominated by typical lung-type N-glycans with NSCLC-associated core fucosylation. We pulled down these glycoproteins from the detergent-solubilized sEVs with SSA-conjugated beads for H520-sEVs and WGA-conjugated beads for H446-sEVs, and the protein bands were subjected to shotgun proteomics. The analysis revealed that several integrin subunits were enriched in the sEVs: V, 6, 1, and 5 subunits in H520-sEVs and V and 1 subunits in H446-sEVs.
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.
Project description:Lung cancer is the leading cause of cancer-related death worldwide, and non-small cell lung cancer (NSCLC) accounts for approximately 85% of lung cancers. Lymphatic metastasis serves as a predominant NSCLC metastatic route and an essential predictor of patient prognosis. Recently, circular RNA (circRNA) has emerged as critical mediator in various tumor initiation and progression. To identify essential circRNA that involves in the lymphatic metastasis of NSCLC, Next generation sequencing (NSG) was performed in 6 paired NSCLC tissues and normal adjacent tissues (NAT).
Project description:Lung cancer is the leading cause of cancer-related deaths worldwide. Despite advancements and improvements in surgical and medical treatments, the survival rate of lung cancer patients remains frustratingly poor. Local control for early stage non-small cell lung cancer (NSCLC) has dramatically improved over the last decades for both operable and inoperable patients. However, the molecular mechanisms of NSCLC invasion leading to regional and distant disease spread remain poorly understood. Here we identify miR-224 to be significantly up-regulated in NSCLC tissues, in particular in resected NSCLC metastasis. Increased miR-224 expression promotes cell migration, invasion and proliferation by directly targeting the tumor suppressors, TNFAIP1 and SMAD4. In concordance with in vitro studies, mouse xenograft studies validated that miR-224 function as a potent oncomiR in NSCLC in vivo. Moreover, we found promoter hypomethylation and activated ERK signaling to be involved in the regulation of miR-224 expression in NSCLC. Up-regulated mir-224 thus facilitates tumor progression by shifting the equilibrium of the partially antagonist functions of SMAD4 and TNFAIP1 towards enhanced invasion and growth in NSCLC. Our findings indicate that targeting miR-224 could be effective in the treatment of certain lung cancer patients Oncogenic role of miR-224 in lung cancer