Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA448888 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In a stepwise approach, we evaluated available protocols before performing an analysis on circulating tumor cells of small cell lung cancer patients. We first compared 19 protocols on single MCF7 cells spiked miRExplore. Second, we analyzed MCF7 single cell equivalents of the eight best protocols. Third, we carried out single cell small RNA sequencing using the best performing protocol on 8 cell lines and 67 circulating tumor cells from seven small cell lung cancer patients.
2021-05-25 | GSE162514 | GEO
Project description:Early detection of small cell lung cancer crucially demands highly reliable markers. Growing evidence suggests that extracellular vesicles carry tumor cell-specific cargo suitable as protein markers in cancer. Therefore, we isolated plasma-derived exosomes from newly diagnosed small cell lung cancer patients and investigated proteome dynamics of these exosomes aiming at improving the detection of small cell lung cancer. A total of 1,016 proteins were initially identified. After data processing and statistical analysis, several proteins were found to be differentially expressed in comparing small cell lung cancer patients and healthy individuals, indicating that circulating exosomes may encompass specific proteins with potential diagnostic attributes for small cell lung cancer. Furthermore, our data may indicate a novel tumor-suppressing role of blood coagulation and involvement of complement activation in small cell lung cancer pathogenesis.
2022-04-04 | PXD028885 | Pride
Project description:MicroRNA-224 promotes tumor progression in non-small cell lung cancer
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Project description:Small cell lung cancer (SCLC) is a neuroendocrine tumor treated clinically as a single disease with poor outcomes. Distinct SCLC molecular subtypes have been defined based on expression of lineage-related transcription factors: ASCL1, NEUROD1, POU2F3 or YAP1, but their origins remain unknown. We developed an in vitro model of MYC-driven SCLC tumor cell progression, and performed a time-series analysis of single-cell transcriptome profiling to reveal that MYC drives the dynamic evolution of SCLC subtypes. Analyses of these single-cell RNA seq data reveal that MYC promotes a temporal shift from an ASCL1-to-NEUROD1-to-YAP1+ state from a neuroendocrine cell of origin. MYC activates Notch signaling to dedifferentiate tumor cells to non-neuroendocrine fates. Additional single-cell RNA sequencing of 4RPM tumors reveal individual tumors to consist of cells at nearly every stage of RPM tumor evolution modeled in vitro. With the single-cell RNA sequencing of this human SCLC liver biopsy, along with IHC on a panel of 21 human biopsies, we show that human SCLC exhibits intratumoral SCLC subtype heterogeneity, suggesting this dynamic evolution occurs in patient tumors. Together, these single-cell RNA sequencing data support our conclusions that genetics, cell of origin, and tumor cell plasticity determine SCLC subtype.
2020-05-28 | GSE150766 | GEO
Project description:Circulating tumor cells (CTCs) represent the molecular characteristics of tumor sites and travel in the blood for seeding distant metastases. "EpCAM+/pan-cytokeratin (CK)+/CD45-/DAPI+" has been widely accepted as a CTC definition, especially in breast cancer, prostate cancer and colorectal cancer. However, reports on CTC detection in non-small cell lung cancer are limited due to a lack of efficient CTC marker. We describe hexokinase 2 (HK2) that assays elevated glycolysis of cancer cells, called Warburg effect, as a new marker for CTC detection in lung adenocarcinoma (LUAD), especially the CK negative CTCs. Single-cell sequencing was used to confirm the malignancy of putative CTCs by detecting genome-wide copy number alternations characteristic of malignant cells. We employed this marker in a variety of liquid biopsies from LUAD patients, including peripheral blood, pleural effusion and cerebrospinal fluid.
2021-02-28 | E-MTAB-8767 | biostudies-arrayexpress
Project description:Lung cancer, of which more than 80% is non-small cell, is the leading cause of cancer-related death in the United States. Copy number alterations (CNAs) in lung cancer have been shown to be positionally clustered in certain genomic regions. However, it remains unclear whether genes with copy number changes are functionally clustered. Using a dense single nucleotide polymorphism array, we performed genome-wide copy number analyses of a large collection of non-small cell lung tumors (n = 301). We proposed a formal statistical test for CNAs between different groups (e.g., noninvolved lung vs. tumors, early vs. late stage tumors). We also customized the gene set enrichment analysis (GSEA) algorithm to investigate the overrepresentation of genes with CNAs in predefined biological pathways and gene sets (i.e., functional clustering). We found that CNAs events increase substantially from germline, early stage to late stage tumor. In addition to genomic position, CNAs tend to occur away from the gene locations, especially in germline, noninvolved tissue and early stage tumors. Such tendency decreases from germline to early stage and then to late stage tumors, suggesting a relaxation of selection during tumor progression. Furthermore, genes with CNAs in non-small cell lung tumors were enriched in certain gene sets and biological pathways that play crucial roles in oncogenesis and cancer progression, demonstrating the functional aspect of CNAs in the context of biological pathways that were overlooked previously. We conclude that CNAs increase with disease progression and CNAs are both positionally and functionally clustered. The potential functional capabilities acquired via CNAs may be sufficient for normal cells to transform into malignant cells. Copy number analysis was performed on 301 non-small cell lung cancer tumor samples using Affymetrix 250K Nsp GeneChip
2011-12-06 | E-GEOD-34140 | biostudies-arrayexpress
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:Tumorigenicity and genetic profiling of circulating tumor cells in small-cell lung cancer
| PRJNA248876 | ENA
Project description:Small cell lung cancer (SCLC) is a neuroendocrine tumor treated clinically as a single disease with poor outcomes. Distinct SCLC molecular subtypes have been defined based on expression of lineage-related transcription factors: ASCL1, NEUROD1, POU2F3 or YAP1, but their origins remain unknown. Here, we develop an in vitro model of MYC-driven SCLC tumor cell progression and perform a time-series analysis of single-cell transcriptome profiling to reveal that MYC drives the dynamic evolution of SCLC subtypes. Analyses of these single-cell RNA seq data reveal that MYC promotes a temporal shift from an Ascl1-to-Neurod1-to-Yap1+ state from a neuroendocrine cell of origin. They also support our findings that MYC activates Notch signaling to dedifferentiate tumor cells to non-neuroendocrine fates. Additional single-cell RNA sequencing of 4 bulk Rb1/Trp53/MycT58A (RPM) tumors reveal individual tumors to consist of cells at nearly every stage of RPM tumor evolution modeled in vitro. Together, these single-cell RNA sequencing data place 3 of 4 SCLC subtypes on a defined trajectory and suggest that genetics, cell of origin, and tumor cell plasticity determine SCLC subtype.
2020-05-28 | GSE149179 | GEO