Homo sapiens
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PROVIDER: PRJDB20798 | ENA |
REPOSITORIES: ENA
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Project description:In recent years gene expression profiling with microarrays has become an important tool in genomic research. Its usefulness in diagnosis and disease classification is now well documented. In many cases routine access to tissues primarily involved in pathophysiological processes is not possible. Attempts have therefore been made to use gene expression patterns in white blood cells (WBCs) as surrogate markers. We investigated if the analysis of gene expression profiles in whole white blood cells is sufficient or if improvements in reliability and sensitivity can be obtained by the analysis of sorted subtypes of WBCs. Using Affymetrix U133A gene chips we have determined gene expression profiles in WBCs, PBMCs, and T-cells. Changes in gene expression were induced in these cells by oxygen-consumption controlled treadmill exercise of healthy volunteers. We found that gene expression changes in T-cells, which indicated the presence of cell activation and apoptosis after exercise, were masked when mixed cell populations were analyzed. Of 157 genes that were found significantly differently expressed in T-cells when before and after exercise samples were compared, only 50 showed significant differences when PBMCs were analyzed; in WBCs only 20 of these genes showed significant differences. In the latter cells, some genes actually showed a significant change in the opposite direction. We conclude that the threshold for the detection of gene expression changes is lowered when the analysis is done in leukocyte subpopulations. In addition, knowledge about the cellular origin of an observed expression shift facilitates the interpretation of the obtained results. Keywords: T Lymphocytes, exercise, microarray analysis
2006-06-16 | GSE4251 | GEO
Project description:About 230 clinical trials currently explore the role of circulating tumor cell (CTC) analysis for therapy decisions, but no assays enable comprehensive molecular characterization of CTCs with diagnostic precision. We therefore combined a workflow for CTC enrichment and isolation with 100% purity with a non-random whole genome amplifiation method for single cells and applied it to 510 single CTCs and 189 leukocytes of 66 breast cancer patients. We defined a genome integrity index (GII) to identify cells suited for molecular chracterization by different molecular assay in more than 90% of single cells, such as diagnostic profiling for point mutations, gene amplifications and whole genomes of single cells. The high reliability on clinical samples enabled assessing the molecular heterogeneity of single CTCs of metastatic breast cancer patients. We readily identified therapeutically relevant genomic disparity between primary tumors and CTCs. Microheterogeneity analysis among individual CTCs uncovered preexisting cells reistsant to ERBB2 targeted therapies suggesting ongoing microevolution at late stage disease whose exploration may provide essential information for personalized treatment decisions. The analysis aimed to indentify profiles of copy number changes in genomic DNA of single circulating tumor cells (CTCs). For this, CTCs were enrched using the FDA approved CellSearch System and single-cell were isolated using the DEPArray System. Subsequently, single-cell DNA was amplified using the Ampli1 WGA Kits and subjected to single-cell aCGH analysis according to previously published protocol (Czyz ZT et al., PLoS One. 2014 Jan 21;9(1):e85907). The analysis included 38 single CTCs and 10 white blood cells (WBCs) obtained from 16 breast cancer patient. WBCs were used as controls for the analysis. In addition, four CTC cell pools were included in the analysis. This was done to show the discrepancies between the profiles of individual cells and corresponing average genomic profile of CTCs in a patient material (cell pools), thereby demonstrating the importance of the analysis on the cell-by-cell basis. The reference sample used for all aCGH experiments consisted of a pool of four single-cell WGA products generated from WBCs of a healthy female donor.
2014-11-05 | E-GEOD-58192 | biostudies-arrayexpress
Project description:In recent years gene expression profiling with microarrays has become an important tool in genomic research. Its usefulness in diagnosis and disease classification is now well documented. In many cases routine access to tissues primarily involved in pathophysiological processes is not possible. Attempts have therefore been made to use gene expression patterns in white blood cells (WBCs) as surrogate markers. We investigated if the analysis of gene expression profiles in whole white blood cells is sufficient or if improvements in reliability and sensitivity can be obtained by the analysis of sorted subtypes of WBCs. Using Affymetrix U133A gene chips we have determined gene expression profiles in WBCs, PBMCs, and T-cells. Changes in gene expression were induced in these cells by oxygen-consumption controlled treadmill exercise of healthy volunteers. We found that gene expression changes in T-cells, which indicated the presence of cell activation and apoptosis after exercise, were masked when mixed cell populations were analyzed. Of 157 genes that were found significantly differently expressed in T-cells when before and after exercise samples were compared, only 50 showed significant differences when PBMCs were analyzed; in WBCs only 20 of these genes showed significant differences. In the latter cells, some genes actually showed a significant change in the opposite direction. We conclude that the threshold for the detection of gene expression changes is lowered when the analysis is done in leukocyte subpopulations. In addition, knowledge about the cellular origin of an observed expression shift facilitates the interpretation of the obtained results. Experiment Overall Design: Genexpression profiles from 3 different probands before and after exhaustive exercise in White Blood Cells, Peripheral Blood Mononuclear Cells and T Lymphocytes, respectively, have been meassured on Affymetrix HG 133 A 2.0 GeneChips.
2007-11-02 | E-GEOD-4251 | biostudies-arrayexpress
Project description:Outcomes for pediatric brain tumor patients remain poor, yet there is optimism that chimeric antigen receptor (CAR) T cell therapy can improve prognosis. Here, we present interim results from the first six patients treated on an ongoing phase I clinical trial (NCT04510051) of IL13BBζ-CAR T cells delivered weekly into the lateral cerebral ventricles. Our preliminary clinical findings suggest CAR T cell therapy is safe and well tolerated in both lymphodepleted and nonlymphodepleted patients, and may offer modest clinical benefit. In addition to our clinical findings, we carried out a series of correlative analyses leveraging single cell genomics and orthogonal methods to profile PBMCs, mononuclear cells in the cerebrospinal fluid (CSF) and post-treatment tumors. leveraging both single cell genomics and more traditional approaches. These studies identified important interactions between CAR T infusions and the endogenous immune system. Notably, we identified and characterized a population of expanding CAR- CD8+ T cells identified in the CSF. Furthermore, we found these and other immune changes observed in the CSF were not well captured by PBMCs. Conversely, we provide evidence of clonally expanded TCRs shared between CSF and post-treatment tumor. While these data are limited, our findings suggest T cell dynamics observed in the CSF are reflected in the tumor, but not in PBMCs. Taken together, these initial findings provide support for continued investigation into locoregionally-delivered IL13BBζ-CAR T cells for children and young adults with brain tumors, and provide important insights into endogenous immune response during therapy.
2025-03-14 | GSE261235 | GEO
Project description:single cell analysis of PBMCs and kidney cells from SSc patients
| PRJDB18660 | ENA
Project description:We performed a systematic analysis of differential gene expression in a wide set of peripheral human immune cells of MPO-deficient patients using single cell RNA-sequencing (scRNAseq) of peripheral blood mononuclear cells (PBMCs) in stable disease state.
2021-08-20 | GSE182244 | GEO
Project description:Purpose: We report the application of single-cell RNA sequencing for profiling the genexpression of different monocyte types in order to characterize monocytes that differentiate into macrophages under danger signal in comparison to conventional GM-CSF and M-CSF macrophages Methods: Monocytes freshly isolated from PBMCs were differentiated into GM-CSF, M-CSF, and danger-signal induced macrophages. Two million cells of each macrophage population were tagged accordingly with TotalSeq™‑B Hashtags. Single cell RNA sequencing was performed on all macrophage populations in order to characterize cells from each population. ScRNAseq analysis was performed with the R package Seurat on 16470 barcodes after filtering. Results: Cluster analysis reveals distinct separation of all three macrophage populations. Conclusion: The clear difference in overall gene expression profile suggests that macrophages exposed to danger signal differentiate into a novel macrophage type in contrast to conventional GM-CSF and M-CSF monocytes.
2022-01-11 | GSE180113 | GEO
Project description:Patients suffering from Coronavirus disease 2019 (COVID-19) can develop neurological sequelae, such as headache, neuroinflammatory or cerebrovascular disease. These conditions - here termed Neuro-COVID - are more frequent in patients with severe COVID-19. To understand the etiology of these neurological sequelae, we utilized single-cell sequencing and examined the immune cell profiles from the cerebrospinal fluid (CSF) of Neuro-COVID patients compared to patients with non-inflammatory and autoimmune neurological diseases or with viral encephalitis. The CSF of Neuro-COVID patients exhibited an expansion of dedifferentiated monocytes and of exhausted CD4+ T cells. Neuro-COVID CSF leukocytes featured an enriched interferon signature; however, this was less pronounced than in viral encephalitis. Repertoire analysis revealed broad clonal T cell expansion and curtailed interferon response in severe compared to mild Neuro-COVID patients. Collectively, our findings document the CSF immune compartment in Neuro-COVID patients and suggest compromised antiviral responses in this setting.
2020-12-11 | GSE163005 | GEO