Isolation of Circulating Tumor Cells from Small Cell Lung Cancer patients using CD56+ as a marker
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 4000
ORGANISM(S): Homo sapiens
SUBMITTER:
PROVIDER: E-MTAB-10766 | biostudies-arrayexpress |
SECONDARY ACCESSION(S): ERP131166
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Human NK cells were sorted into CD56dim and CD56bright NK cell subpopulations. In order to define characteristics of both populations gene profiling was performed using Affymetrix arrays U133a and U133B.
2006-05-31 | E-MEXP-380 | biostudies-arrayexpress
Project description:Human Natural Killer (NK) cells comprise two main subsets, CD56bright and CD56dim cells, that differ in function, phenotype and tissue localization. To further dissect the heterogeneity of CD56dim cells, we have performed transcriptome analysis and functional ex vivo characterization of human NK cell subsets according to the expression of markers related to differentiation, migration or competence. Here, we show for the first time that the ability to respond to cytokines or to activating receptors is mutually exclusive in almost all NK cells with the exception of CD56dim CD62L+ cells. Indeed, only these cells combine the ability to produce interferon (IFN)-gamma after cytokines and proliferate in vivo during viral infection with the capacity to kill and produce cytokines upon engagement of activating receptors. Therefore, CD56dim CD62L+ cells represent a unique subset of polyfunctional NK cells. Ex vivo analysis of their function, phenotype, telomere length, frequencies during ageing as well as transfer experiments of NK cell subsets into immunodeficient mice suggest that CD56dim CD62L+ cells represent an intermediate stage of NK cell maturation, which after restimulation can accomplish multiple tasks and further develop into terminally differentiated effectors. Gene expression profiles of FACSAria sorted CD3- CD56bright CD62L+, CD3- CD56dim CD62L+ and CD3- CD56dim CD62L- NK cells from human peripheral blood of three donors were compared using Affymetrix GeneChip Human Genome HG-U133_Plus_2. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the three groups to the GeneChip arrays. Group1: CD3- CD56bright CD62L+,.Group2: CD3- CD56dim CD62L+, Group3: CD3- CD56dim CD62L-. Lists of differentially regulated genes were created using High Performance Chip Data Analysis (HPCDA) with Bioretis database (http://www.bioretis-analysis.de). Worldwide data sharing is possible via Bioretis, please ask the authors.
2010-05-28 | E-GEOD-21774 | biostudies-arrayexpress
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:Human NK cells from the decidua basalis of gravid uteri (dNK) and from cycling endometrium (eNK) of women undergoing hysterectomy were isolated and compared by gene expression profiling using Affymetrix microarrays with probes representing ~47,400 transcripts. Substantial differences indicate that these two types of NK cells represent distinct subsets. Freshly isolated NK cells were obtained by FACS sorting. 4 dNK and 5 eNK samples were obtained form independent donors. dNK cells were isolated from the decidua basalis of first trimester placentas and sorted as CD3-, CD16-, CD56+ cells. eNK cells were obtained from non-affected regions of cycling endometrium of donor women undergoing hysterectomy and were sorted as CD45+, CD56+, CD3- cells . The preliminary patient diagnoses included genital prolapse, fibroids, cervical dysplasia, or menorrhagia. All cycling endometrium samples were from the secretory phase of the cycle with exception of sample eNK_S6 that was from the proliferative phase.
2010-03-09 | E-GEOD-20499 | biostudies-arrayexpress
Project description:Inflammation leads the hypothalamus-pituitary-adrenal (HPA) axis activation and increased production of glucocorticoids, which produced by the adrenal cortex, exert potent anti-inflammatory effects. The use of omics, including proteomics revealed metabolic changes in steroidogenic adrenocortical cells, including downregulation of the tricarboxylic acid (TCA) cycle and oxidative phosphorylation, decreased ATP production and induction of oxidative stress after lipopolysaccharide (LPS)-induced inflammation.
2023-07-21 | PXD036542 | Pride
Project description:Osteosarcoma pretherapeutic biopsy samples of pediatric and adult patients (median 14 years, mean 16.5) years were analyzed using Affymetrix 10K2 high-density SNP arrays. Numerical aberrations and allelic imbalances were correlated with the histological degree of necrosis and clinical follow-up.
2010-08-01 | E-MEXP-2688 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2016-05-19 | E-GEOD-67123 | biostudies-arrayexpress
Project description:Plasma DNA and DNA from circulating tumour cells (CTCs) was extracted from Colon Cancer Patients and hybridized against a reference sample for CGH. We compared genetic abberrations of Plasma DNA against normal tissue and genetic aberrations of CTCs, tumour tissue and metastatic tissue.
2011-11-08 | E-MEXP-3416 | biostudies-arrayexpress
Project description:Systems biology is an approach to comprehensively study complex interactions within a biological system. Most published systems vaccinology studies have utilized whole blood or peripheral blood mononuclear cells (PBMC) to monitor the immune response after vaccination. Because human blood is comprised of multiple hematopoietic cell types, the potential for masking responses of under-represented cell populations is increased when analyzing whole blood or PBMC. To investigate the contribution of individual cell types to the immune response after vaccination, we established a rapid and efficient method to purify human T and B cells, natural killer (NK) cells, myeloid dendritic cells (mDC), monocytes, and neutrophils from fresh venous blood. Purified cells were fractionated and processed in a single day. RNA-Seq and quantitative shotgun proteomics were performed to determine expression profiles for each cell type prior to and after inactivated seasonal influenza vaccination. Our results show that transcriptomic and proteomic profiles generated from purified immune cells differ significantly from PBMC. Differential expression analysis for each immune cell type also shows unique transcriptomic and proteomic expression profiles as well as changing biological networks at early time points after vaccination. This cell type-specific information provides a more comprehensive approach to monitor vaccine responses. PBMC and six purified cell types from two vaccinated donors were isolated prior to (d0) and at days 1, 3, and 7 post-TIV vaccination for RNA-seq analysis
2015-01-06 | E-GEOD-64655 | biostudies-arrayexpress
Project description:We compared the cellular and molecular outcome following permanent LAD ligation in wildtype and T- and B cell deficient Rag2del mice. Our results demonstrate that the significant changes in the cardiac immune response following myocardial infarction (MI). 8-12 weeks old, male and female C57BL/6J mice (Charles River, Wilmington, MA, USA) and B6.Rag2del mice (Jackson laboratory, Bar Harbor, ME, USA) were used for this study. Seven days after MI, entire mouse ventricles were isolated and enzymatically digested. Cells were then labelled with CD45 magnetic beads (Miltenyi Biotec, Germany) and positively enriched using the AutoMACS instrument (Miltenyi Biotec, Germany). Viable macrophages/monocytes (CD45+CD11b+CD11c-DAPI-Lactadherinlo), dendritic cells (CD45+CD11b+CD11c+ DAPI-Lactadherinlo), and NK cells (CD45+CD11b-CD11c+NK1.1+ DAPI-Lactadherinlo) were then sorted on the BD FACSAriaTM IIIu (Becton Dickinson, Franklin Lakes, NJ, USA) roughly in a 1:1:1 ratio into DMEM containing 10% FCS before processing for 10× Genomics single-cell RNA sequencing (scRNA-Seq). Libraries for scRNA-Seq were constructed according to the 10× Genomics protocol using the GemCode Single-Cell 3′ Gel Bead and Library V3 Kit. Quality of amplified cDNA and final libraries were evaluated on the 2100 Bioanalyzer instrument (Agilent) using a High Sensitivity NGS Analysis Kit (Advanced Analytical). Subsequent sequencing was conducted on the HighSeq4000 Sequencing System using the HiSeq SBS and HiSeq PE Cluster Kit V4 (all Illumina, San Die-go, CA. USA).
2023-07-20 | E-MTAB-13147 | biostudies-arrayexpress