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Genome wide analysis of the changes in gene expression following co-culture of A431 cancer cells and stromal fibroblasts

ABSTRACT: This experiment tested the hypothesis that distinct changes in gene expression are triggered in response to direct contact between cancer cells and fibroblasts, as opposed to co-cultures in which the cells are physically separated by membrane that permits diffusion

ORGANISM(S): Homo sapiens

PROVIDER: GSE121058 | GEO | 2020/03/31

REPOSITORIES: GEO

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scRNAseq of co-culture of primary human oligodendrocytes and IL-23 polarized human CD4 T cells in direct contact (contact) versus separated by a porous membrane (insert, no contact)

Project description:Multiple sclerosis (MS) is characterized by the loss of myelin and of myelin-producing oligodendrocytes (OLs) in the central nervous system (CNS). Pro-inflammatory CD4+ Th17 cells are considered pathogenic in MS and are harmful to OLs. We investigated the mechanisms driving human CD4+ T cell-mediated OL cell death. Using single cell RNA sequencing, we assessed the transcriptomic profile of primary human OLs and Th17 cells in direct contact or separated by an insert. We showed that upon close interaction, OLs upregulate the expression of mRNA coding for chemokines and antioxidant/anti-apoptotic molecules, while Th17 cells upregulate the expression of mRNA coding for chemokines and pro-inflammatory cytokines such as IL-17A, IFN-γ and granzyme B. We found that secretion of CCL3, CXCL10, IFN-γ, TNFα and granzyme B is induced upon direct contact in co-cultures of human Th17 cells with human OLs. In addition, we validated by flow cytometry and immunofluorescence that granzyme B levels are upregulated in Th17 compared to Th2 cells, and are even higher in Th17 cells upon direct contact with OLs or MO3.13 cells compared to Th17 cells separated from OLs by an insert.

2022-02-28 | GSE196953 | GEO

Single Cell Sequencing Reveals Gene Expression Signatures Associated with Bone Marrow Stromal Cell Subpopulations and Time in Culture [microarray]

Project description:Background Bone marrow stromal cells (BMSCs) are a heterogeneous population that participates in wound healing, immune modulation and tissue regeneration. Next generation sequencing was used to analyze transcripts from single BMSCs in order to better characterize BMSC subpopulations. Methods Cryopreserved passage 2 BMSCs from one healthy subject were cultured through passage 10. The transcriptomes of bulk BMSCs from designated passages were analyzed with microarrays and RNA sequencing (RNA-Seq). For some passages, single BMSCs were separated using microfluidics and their transcriptomes were analyzed by RNA-Seq. Results Transcriptome analysis microarray and RNA-Seq of unseparated BMSCs from passages 2, 4, 6, 8, 9 and 10 yielded similar results; both data sets grouped passages 4 and 6 and passages 9 and 10 together and genes differentially expressed among these early and late passage BMSCs were similar. 3D Diffusion map visualization of single BMSCs from passages 3, 4, 6, 8 and 9 clustered passage 3 and 9 into two distinct groups, but there was considerable overlap for passage 4, 6 and 8 cells. Markers for early passage, FGFR2, and late passage BMSCs, PLAT, were able to identify three subpopulations within passage 3 BMSCs; one that expressed high levels of FGFR2 and low levels of PLAT; one that expressed low levels of FGFR2 and high levels of PLAT and one that expressed intermediate levels of FGFR2 and low levels of PLAT. Conclusions Single BMSCs can be separated by microfluidics and their transcriptome analyzed by next generation sequencing. Single cell analysis of early passage BMSCs identified a subpopulation of cells expressing high levels of FGFR2 that might include skeletal stem cells.

2019-01-10 | GSE124860 | GEO

Single Cell Sequencing Reveals Gene Expression Signatures Associated with Bone Marrow Stromal Cell Subpopulations and Time in Culture [scRNA-seq]

2019-01-10 | GSE124858 | GEO

Single Cell Sequencing Reveals Gene Expression Signatures Associated with Bone Marrow Stromal Cell Subpopulations and Time in Culture [NGS_bulk cell RNA-seq]

2019-01-10 | GSE124859 | GEO

scRNAseq of co-culture of primary human oligodendrocytes and IL-23 polarized human CD4 T cells in direct contact (contact) versus separated by a porous membrane (insert, no contact)

Project description:scRNAseq of co-culture of primary human oligodendrocytes and IL-23 polarized human CD4 T cells in direct contact (contact) versus separated by a porous membrane (insert, no contact)

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Gene expression changes induced in the stromal cell line EL08-1D2 by co-culture with leukemic B cells (CLL)

Project description:Tumor cell survival critically depends on heterotypic communication with benign cells in the microenvironment. Here we describe a novel survival signaling pathway activated in stromal cells by contact to B-cells from chronic lymphocytic leukemia (CLL) patients. The expression of PKC-M-NM-2II and the subsequent activation of NF-M-NM-:B in bone marrow stromal cells is a prerequisite to support the survival of malignant B-cells. PKC-M-NM-2 knockout mice are insusceptible to CLL-transplantations, underscoring the in vivo significance of the PKC-M-NM-2II- NF-M-NM-:B signaling pathway in the tumor microenvironment. Upregulated stromal PKC-M-NM-2II in biopsies from CLL, breast- and pancreatic- cancer patients suggest that this pathway may commonly be activated in a variety of malignancies. We used microarrays to determine gene expression changes induced by co-culturing with leukemic B-cells (CLL) in EL08-1D2 cells. We compared EL08-1D2 cells co-cultured for 5 days with leukemic B-cells to EL08-1D2 mono-cultured cells by microarray analysis on Affymetrix MG-430_2.0 arrays.

2013-03-08 | E-GEOD-36414 | biostudies-arrayexpress

Transcriptional changes on lymphatic endothelial cells upon co-culture with human melanoma cells

Project description:The aim was to study transcriptional changes on the primary human lymphatic endothelial cells when they have been in contact with a human melanoma cell line

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Gene expression changes induced in the stromal cell line EL08-1D2 by co-culture with leukemic B cells (CLL)

Project description:Tumor cell survival critically depends on heterotypic communication with benign cells in the microenvironment. Here we describe a novel survival signaling pathway activated in stromal cells by contact to B-cells from chronic lymphocytic leukemia (CLL) patients. The expression of PKC-βII and the subsequent activation of NF-κB in bone marrow stromal cells is a prerequisite to support the survival of malignant B-cells. PKC-β knockout mice are insusceptible to CLL-transplantations, underscoring the in vivo significance of the PKC-βII- NF-κB signaling pathway in the tumor microenvironment. Upregulated stromal PKC-βII in biopsies from CLL, breast- and pancreatic- cancer patients suggest that this pathway may commonly be activated in a variety of malignancies. We used microarrays to determine gene expression changes induced by co-culturing with leukemic B-cells (CLL) in EL08-1D2 cells.

2013-03-08 | GSE36414 | GEO

Effects of co-culture of Endothelial Cells with Mesenchymal Stem Cells on Gene Expression

Project description:Study designed to explore the effects of endothelial cell/MSC co-culture on individual gene expression profile of each cell type 4 independent samples from each of 4 groups: MSCs cultured alone; Pulmonary endothelial cells cultured alone; MSCs co-cultured with PECs then FACS separated; PECs co-cultured with MSCs then FACS separated

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A diffusion-based microfluidic device for single-cell RNA-seq

Project description:Microfluidic devices provide a low-input and efficient platform for single-cell RNA-seq (scRNA-Seq). Here we present microfluidic diffusion-based RNA-seq (MID-RNA-seq) for conducting scRNA-seq with a diffusion-based reagent swapping scheme. This device incorporates cell trapping, lysis, reverse transcription and PCR amplification all in one microfluidic chamber. MID-RNA-Seq provides high data quality that is comparable to existing scRNA-seq methods while implementing a simple device design that permits multiplexing. The robustness and scalability of MID-RNA-Seq device will be important for transcriptomic studies of scarce cell samples.

2019-02-25 | GSE119271 | GEO

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