Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE57199 | GEO | 2014/05/01
SECONDARY ACCESSION(S): PRJNA245896
REPOSITORIES: GEO
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Project description:Different fibroblast cells (eight in total) with different inhibitory capacity were analyzed and compared for their gene expression profile by whole genome microarray. Different fibroblast cells (eight in total) were analyzed with Affymetrix Whole Target (WT) Assay (GeneTitan plate format Gene ST 1.1) in order to find out gene expression differences.
2014-05-01 | E-GEOD-57199 | biostudies-arrayexpress
Project description:There is growing evidence that emerging malignancies in solid tissues might be kept under control by physical intercellular contacts with normal fibroblasts.Here we characterize transcriptional landscapes of fibroblasts that confronted cancer cells. We studied four pairs of in vitro and ex vivo fibroblast lines which, within each pair, differed in their capacity to inhibit cancer cells. The natural process was modeled in vitro by confronting the fibroblasts with PC-3 cancer cells. Fibroblast transcriptomes were recorded by Affymetrix microarrays and then investigated using network analysis.The network enrichment analysis allowed us to separate confrontation- and inhibition-specific components of the fibroblast transcriptional response. Confrontation-specific differences were stronger and were characterized by changes in a number of pathways, including Rho, the YAP/TAZ cascade, NF-kB, and TGF-beta signaling, as well as the transcription factor RELA. Inhibition-specific differences were more subtle and characterized by involvement of Rho signaling at the pathway level and by potential individual regulators such as IL6, MAPK8, MAP2K4, PRKCA, JUN, STAT3, and STAT5A.We investigated the interaction between cancer cells and fibroblasts in order to shed light on the potential mechanisms and explain the differential inhibitory capacity of the latter, which enabled both a holistic view on the process and details at the gene/protein level. The combination of our methods pointed to proteins, such as members of the Rho pathway, pro-inflammatory signature and the YAP1/TAZ cascade, that warrant further investigation via tools of experimental perturbation. We also demonstrated functional congruence between the in vitro and ex vivo models. The microarray data are made available via the Gene Expression Omnibus as GSE57199.
| S-EPMC4472614 | biostudies-literature
Project description:Somatic cell nuclear transfer (SCNT) into an enucleated oocyte can reprogram a differentiated nucleus to a totipotent state. However, the time course of transcriptional reprogramming has not been determined. To monitor the inactivation of somatic genes after SCNT in the bovine model system, we determined transcript levels of 159 genes highly expressed in fetal fibroblast nuclear donor cells, but not in metaphase II recipient oocytes. For 18 of these genes significantly higher transcript levels were found in four-cell SCNT embryos compared with four-cell embryos derived by in vitro fertilization (IVF), indicating incomplete silencing of somatic genes at this stage. RNA sequencing revealed that nearly 600 genes with no transcripts in oocytes were activated in eight-cell IVF embryos, in agreement with major embryonic genome activation (EGA). De novo transcription in SCNT embryos was delayed (16 genes before the 16-cell stage, 300 and >800 genes at the 16-cell and blastocyst stages). Intron-containing primary transcripts as another option to detect embryonic gene transcription revealed activation of >2,200 genes in IVF embryos at the eight-cell stage, while only 828 genes were activated in SCNT embryos. At the 16-cell stage, a higher number of activated genes was found in SCNT (1,917) than in IVF embryos (738). Self-organizing tree algorithm clustering confirmed that in SCNT embryos transcription of genes that are normally activated during major EGA is delayed. Our study provides detailed insight into the timing of genome activation in cloned embryos that is substantially different from IVF embryos in spite of similar developmental kinetics.
2021-05-31 | GSE125828 | GEO
Project description:Children with autosomal recessive deficiency suffer from life-threatening, often recurrent viral or bacterial infections. We have profiled transcriptional responses of fibroblast cell lines derived from patients deficient for key regulators of immune responses such as MYD88, IRAK4, UNC93B, STAT1 or NEMO. This systems immunology approach revealed distinct patterns or responsiveness to stimuli activating the Toll-like/IL1 Receptor pathway in either an MYD88-dependent (IL1B) or independent (poly(I:C)) fashion, or activating the TNF pathway. The prototypic signatures in cell lines derived from patients were as follows: NEMO-deficient cells were unresponsive to all three stimuli, UNC-93B-deficient cells did not respond to poly(I:C), and STAT1-deficient cells responded only weakly to poly(I:C) after eight hours (not shown). MyD88- and IRAK-4-deficient cells had indistinguishable phenotypes, both being unresponsive to IL-1B at both time points. The signatures obtained in response to TNF and poly(I:C) (via TLR3) in these cells were similar to that of control fibroblasts.
2009-07-15 | GSE12124 | GEO
Project description:The morphogen Indian Hedgehog is expressed by the intestinal epithelium and signals in paracrine manner to fibroblasts by activating trascription factor Gli1. ZsGreen is used to track Gli1+ cells. To describe different fibroblast subpopulations we used gp38 as a general marker and Sca1 as a marker expressed in some of gp38+ cells.
2018-10-27 | GSE105069 | GEO
Project description:The effect at long term (15 days) of leukemia inhibitory factor (LIF), TGFβ or TGFβ + anti-Lif stimulation on the human primary dermal fibroblast (hDF) transcriptome was analyzed by whole genome microarray expression profiling.
2016-12-06 | GSE81997 | GEO
Project description:The effect at short term (48 hours) of leukemia inhibitory factor (LIF), TGFβ or TGFβ + anti-Lif stimulation on the human primary dermal fibroblast (hDF) transcriptome was analyzed by whole genome microarray expression profiling.
2016-12-06 | GSE81996 | GEO
Project description:Fibroblasts are a main player in the tumor-inhibitory microenvironment. Upon tumor initiation and progression, fibroblasts can lose their tumor-inhibitory capacity and promote tumor growth. The molecular mechanisms that underlie this switch have not been defined completely. Previously, we identified four proteins overexpressed in cancer-associated fibroblasts and linked to Rho GTPase signaling. Here, we show that knocking out the Ras homolog family member A (RhoA) gene in normal fibroblasts decreased their tumor-inhibitory capacity, as judged by neighbor suppression in vitro and accompanied by promotion of tumor growth in vivo. This also induced PC3 cancer cell motility and increased colony size in 2D cultures. RhoA knockout in fibroblasts induced vimentin intermediate filament reorganization, accompanied by reduced contractile force and increased stiffness of cells. There was also loss of wide F-actin stress fibers and large focal adhesions. In addition, we observed a significant loss of α-smooth muscle actin, which indicates a difference between RhoA knockout fibroblasts and classic cancer-associated fibroblasts. In 3D collagen matrix, RhoA knockout reduced fibroblast branching and meshwork formation and resulted in more compactly clustered tumor-cell colonies in coculture with PC3 cells, which might boost tumor stem-like properties. Coculturing RhoA knockout fibroblasts and PC3 cells induced expression of proinflammatory genes in both. Inflammatory mediators may induce tumor cell stemness. Network enrichment analysis of transcriptomic changes, however, revealed that the Rho signaling pathway per se was significantly triggered only after coculturing with tumor cells. Taken together, our findings in vivo and in vitro indicate that Rho signaling governs the inhibitory effects by fibroblasts on tumor-cell growth.
| S-EPMC5338371 | biostudies-literature
Project description:Inflammation of synovial tissue (synovitis) is a hallmark of osteoarthritis (OA) pathogenesis and is pronounced in obese individuals. The aim of this study was therefore to perform scRNA-seq analysis of synovial fibroblast from hip OA patients who were either obese or normal-weight to identify specific fibroblast subsets that exhibit disease-associated inflammatory functions. : scRNA-seq identified eight OA synovial fibroblast clusters, with distinct differences between obese and normal-weight patients. Fibroblast clusters in obese OA patients highly expressed gene signatures related to immune cell regulation, fibrosis and inflammatory signalling, including Chitinase3-like 1 (CHI3L1), CXCL12, osteonectin (SPARC), SMOC2 and Galectin-1 (LGALS1). Pseudotemporal expression dynamics demonstrated a transition in the expression of the transcriptional regulator MYC and Inhibin A in normal-weight clusters, and the expression of FOS and CHI3L1 in obese fibroblast clusters. Analysis of fibroblast conditioned media showed that obese OA fibroblasts secreted significantly greater amounts of CHI3L1, whilst normal-weight fibroblasts secreted greater amounts of Inhibin.
2020-10-31 | GSE152815 | GEO
Project description:PurposeTo synthesize a ternary cationic copolymer called CS-g-(PEI-b-mPEG) and characterize its features as a non-viral siRNA carrier; in turn, to investigate the influence of small interfering RNA (siRNA) targeting IkappaB kinase subunit beta (IKKbeta) on the proliferation of human Tenon's capsule fibroblasts (HTFs) in vitro.MethodsFirst, a novel cationic copolymer composed of low molecular weight, linear poly(ethyleneimine) [PEI] blocked with polyethylene glycol (PEG) and grafted onto a chitosan (CS) molecule was synthesized. CS-g-(PEI-b-mPEG) was then compacted with 21nt siRNA at various copolymer/siRNA charge (N/P) ratios, and the resulting complexes were characterized by dynamic light scattering, gel electrophoresis, and serum incubation. Cell Titer 96 AQ(ueous) One Solution cell proliferation assay was used to investigate the cytotoxicity of this cationic copolymer. Second, siRNAs targeting IKKbeta (IKKBeta-siRNAs) were delivered into the HTFs using CS-g-(PEI-b-mPEG) as the vehicle. Real-time reverse transcription polymerase chain reaction (RT-PCR) subsequently assessed the mRNA level of IKKbeta, and western blot assay was used to determine protein expression. After IKKB-siRNA transfection, Cell Titer 96 AQ(ueous) One Solution cell proliferation assay was used to evaluate the proliferation of HTFs.ResultsThe diameter of the CS-g-(PEI-b-mPEG)/siRNA complexes tended to decrease whereas their zeta potential tended to increase as the N/P ratio increased. The CS-g-(PEI-b-mPEG) copolymer showed good siRNA binding ability and high siRNA protection capacity. Furthermore, the copolymer presented remarkable transfection efficiency and showed much less cytotoxicity than 25 kDa PEI. IKKB-siRNAs were successfully delivered into HTFs using CS-g-(PEI-b-mPEG) as a vector. As a result, the expression of IKKbeta was downregulated at both the mRNA and protein levels, and the activation of nuclear factor-kappaB (NF-kappaB) in the HTFs was subsequently inhibited. Most impressively, the proliferation of HTFs was also effectively suppressed through the blocking of the NF-kappaB pathway.ConclusionsAll the results demonstrate that CS-g-(PEI-b-mPEG) is a promising candidate for siRNA delivery, featuring excellent biocompatibility, biodegradability, and transfection efficiency. The RNA interference (RNAi) strategy using cationic copolymers as siRNA carriers will be a safe and efficient anti-scarring method following glaucoma filtration surgery.
| S-EPMC2613073 | biostudies-literature