ABSTRACT: MIXL1-GFP reporter lines (HESC3MIXL1-GFP/w and MEL1MIXL1-GFP/w, referred to as HES3 and MEL1 in this submission) were differentiated as spin embryonic bodies (Ebs) supplemented with mesodermal inducing growth factors (BMP4,SCF, VEGF based). Methylcellulose hematopoietic colony forming assays were performed by culturing dissociated day 4 EBs in the presence of hematopoietic growth factors (VEGF, SCF, IL3, IL6, TPO, EPO and FLT3L) for 7-9 days. Addition of WNT3a to the methylcellulose lead to the formation of compact, mesodermal colonies, which we term 'mesosphere' (Meso-balls). We demonstrated that the inclusion of WNT3a in the methylcellulose could be replaced with BIO, a GSK3 inhibitor, acting as a canonical WNT signaling agonist. Mesospheres formed in the culture supplemented with BIO molecules were termed 'BIO-balls'. Expression profiling between 'meso-balls' and 'BIO-balls' were compared and analyzed for markers assisiting in defining their phenotypes.
Project description:MIXL1-GFP reporter lines were differentiated as Spin EBs in APEL medium supplemented with Wnt3a alone, BMP4 alone or Wnt3a/BMP4 in combination. EBs induced in the absence of growth factors were used as control. EBs induced with BMP4 or Wnt3a/BMP4 were FACS sorted based on E-CADHERIN and GFP expression. Unsorted EBs and sorted fractions were subjected to Illumina microarray processing.
Project description:This study aimed to examine gene expression in human ES cells (the RUNX1C GFP reporter line) differentiated towrads hameatopoietic mesoderm in a defined serum free medium. At day 7 of differentiation, the cells were sorted into fractions based on CD34 and CD41 expression and the four fractions analysed by microarray. The total number of samples analysed was 13. Undifferentiated hESC (RUNX1C GFP/w, based on the HES3 cell line) plus samples from d1 to d8 of differentiation comprised one experiment (9 samples) and four flow sorted fractions from d7 differentiated cells (CD34-CD41-, CD34lo CD41-, CD34hi CD41- and CD34lo CD41lo) comprised the second experiment. The parent cell line was maintained on mouse feeder cells in KOSR containing medium supplemented with 10 ng/ml FGF2. Differentiation was performed as spin EBs in APEL medium (Ng et al Nature Protocols 2008). For the first 4 days, medium was supplemented with BMP4, VEGF, SCF and Activin. Medium was changed at d4 to fresh APEL medium supplemented with BMP4, VEGF, SCF, FGF2 and IGF2.
Project description:The HSC niche factor SCF is required for HSC maintenance. Using an Scf-GFP knockin mouse, we have identified a perivascular cell type in the bone marrow expressing high level of Scf. To characterize the novel Scf-GFP+ cells from the bone marrow, we performed microarray analysis on these cells.
Project description:Wild-type (WT) and Etv2-overexpressing (OE) mouse embryonic stem cells (mESC) were cultured and differentated to embryoid bodies (EBs) in mesodermal conditions. Induction of Etv2 in OE EBs was achieved by the addition of doxycycline. Cells were collected at different time points (i.e., D2, D3, D4 for WT and D3, D4 for OE EBs) following FACS based on the presence or absence of two surface markers: Flk1 (F+/-) and Pdgfrα (P+/-). We performed single-cell RNA sequencing (scRNA-seq) on the FACS sorted cells at different time points. The transcriptomic profiles revealed that ETV2 overexpression promotes HE lineage specification while repressing cardiac and skeletal muscle programs.
Project description:The HSC niche factor SCF is required for HSC maintenance. Using an Scf-GFP knockin mouse, we have identified a perivascular cell type in the bone marrow expressing high level of Scf. To characterize the novel Scf-GFP+ cells from the bone marrow, we performed microarray analysis on these cells. Total RNA were isolated from 3 independent, freshly aliquots of FACS sorted 5,000 SCF-GFP+ cells or whole bone marrow cells isolated from young adult mice. Purified RNA was amplified using the WT-OvationM-bM-^DM-" Pico RNA Amplification system (NuGEN Technologies). Sense strand cDNA was generated using WT-OvationM-bM-^DM-" Exon Module (NuGEN), then fragmented and labeled using the FL-OvationM-bM-^DM-" cDNA Biotin Module V2 (NuGEN). 2.5M-BM-5g of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 1.0 microarrays.
Project description:The best assay for confirmation of pluripotency for mouse embryonic stem cells (ESCs) is blastocyst chimerism and for human ESCs the production of teratomas in immunodeficient mice that contain lineages from all three primordial germ layers. However, the latter assay has been interpreted by some as one type of human-animal chimera and studies involving human-animal chimerism present a wide range of ethical issues with restrictive legislation in some countries. The need for teratoma assays is compelling because unproven differentiation may suggest a dangerously flawed cell resource for use in future therapies. We find that a three dimensional anchorage independent growth protocol for hESCs using methylcellulose and matrigel encourages prolonged growth of embryoid bodies (EBs) leading onto formation of teratomas in vitro. Our late EBs are a miniature form of teratomas containing lineages from all three germ layers, do not show embryonal carcinoma cells and allows integration of microinjected cancer cells (HepG2-GFP). Additional data files are linked below as supplementary files: [1] Beadstudio_Controls_non-normalized.txt: Control Probe Profile intensity data exported from Beadstudio. [2] Beadstudio_background_removed_non-normalized.txt: Background corrected intensity data exported from Beadstudio using the default Beadstudio background correction setting. No normalization carried out on the data. [3] VST_quantile_filterp0.01_normalized.txt: Data after VST transformation, quantile normalized and filtered with detection p-value 0.01. This data set was used for analysis in the accompanying publication.
Project description:Precise control of gene expression during development is orchestrated by transcription factors and co-regulators including chromatin modifiers. How particular chromatin modifying enzymes affect specific developmental processes is not well defined. Here we report that Gcn5, a HAT essential for embryonic development, is largely required for c-MYC target gene transcription downstream of FGF signaling in early embryoid bodies (EBs). Gcn5 null EBs display deficient activation of ERK and p38, disorganized cytoskeletal networks, and compromised capacity to differentiate toward mesodermal and endodermal lineages. These findings establish a regulatory role for Gcn5 in execution of a critical signaling pathway during early development.
Project description:Precise control of gene expression during development is orchestrated by transcription factors and co-regulators including chromatin modifiers. How particular chromatin modifying enzymes affect specific developmental processes is not well defined. Here we report that Gcn5, a HAT essential for embryonic development, is largely required for c-MYC target gene transcription downstream of FGF signaling in early embryoid bodies (EBs). Gcn5 null EBs display deficient activation of ERK and p38, disorganized cytoskeletal networks, and compromised capacity to differentiate toward mesodermal and endodermal lineages. These findings establish a regulatory role for Gcn5 in execution of a critical signaling pathway during early development.
Project description:Introduction: Malignant pleural mesothelioma (MPM) is an aggressive malignancy with poor prognosis. Unlike many other cancers, MPM is mostly characterized by inactivation of tumor suppressor genes. Its highly malignant nature in absence of tumor driving oncogene mutations indicates an extrinsic supply of stimulating signals by cells of the tumor microenvironment (TME). Cancer-associated fibroblasts (CAFs) are an abundant cell type of the TME and have been shown to drive the progression of several cancer types. The aim of the current study was to isolate and characterize patient-derived mesothelioma-associated fibroblasts (Meso-CAFs), and evaluate their impact on MPM cells. Methods: Meso-CAFs were isolated from surgical specimens of MPM patients and analyzed by comparative genomic hybridization, transcriptomics and proteomics. Human MPM cell lines were retrovirally transduced with GFP. The impact of Meso-CAFs on tumor cell growth, migration, and response to pathway inhibitors and cisplatin was investigated in 2D and 3D co-culture models by videomicroscopy and automated image analysis. Results: Meso-CAFs possess normal genomes without gene copy number aberrations typical for MPM cells. They express CAF markers and lack MPM marker expression. Their proteome and secretome profiles clearly differ from normal lung fibroblasts with particularly strong differences in the fraction of actively secreted proteins. The presence of Meso-CAFs in co-culture resulted in increased proliferation and migration of MPM cells. A similar effect on cell growth was induced by conditioned medium. Met/PI3K or WNT signaling inhibition abolished the Meso-CAF-mediated growth stimulation. While Meso-CAFs reduced the efficacy of EGFR inhibition in co-cultures, they did not provide protection of tumor cells against cisplatin. Conclusion: Our study provides the first characterization of human patient-derived Meso-CAFs and demonstrates a strong impact of Meso-CAFs on tumor cell growth and migration, two key aspects of MPM aggressiveness, indicating a substantial role of Meso-CAFs in driving MPM progression. Moreover, we show that Meso-CAFs significantly influence drug response and identify signaling pathways required for Meso-CAF-mediated growth stimulation. These data could be relevant for improving therapeutic strategies in MPM.
Project description:Introduction: Malignant pleural mesothelioma (MPM) is an aggressive malignancy with poor prognosis. Unlike many other cancers, MPM is mostly characterized by inactivation of tumor suppressor genes. Its highly malignant nature in absence of tumor driving oncogene mutations indicates an extrinsic supply of stimulating signals by cells of the tumor microenvironment (TME). Cancer-associated fibroblasts (CAFs) are an abundant cell type of the TME and have been shown to drive the progression of several cancer types. The aim of the current study was to isolate and characterize patient-derived mesothelioma-associated fibroblasts (Meso-CAFs), and evaluate their impact on MPM cells. Methods: Meso-CAFs were isolated from surgical specimens of MPM patients and analyzed by comparative genomic hybridization, transcriptomics and proteomics. Human MPM cell lines were retrovirally transduced with GFP. The impact of Meso-CAFs on tumor cell growth, migration, and response to pathway inhibitors and cisplatin was investigated in 2D and 3D co-culture models by videomicroscopy and automated image analysis. Results: Meso-CAFs possess normal genomes without gene copy number aberrations typical for MPM cells. They express CAF markers and lack MPM marker expression. Their proteome and secretome profiles clearly differ from normal lung fibroblasts with particularly strong differences in the fraction of actively secreted proteins. The presence of Meso-CAFs in co-culture resulted in increased proliferation and migration of MPM cells. A similar effect on cell growth was induced by conditioned medium. Met/PI3K or WNT signaling inhibition abolished the Meso-CAF-mediated growth stimulation. While Meso-CAFs reduced the efficacy of EGFR inhibition in co-cultures, they did not provide protection of tumor cells against cisplatin. Conclusion: Our study provides the first characterization of human patient-derived Meso-CAFs and demonstrates a strong impact of Meso-CAFs on tumor cell growth and migration, two key aspects of MPM aggressiveness, indicating a substantial role of Meso-CAFs in driving MPM progression. Moreover, we show that Meso-CAFs significantly influence drug response and identify signaling pathways required for Meso-CAF-mediated growth stimulation. These data could be relevant for improving therapeutic strategies in MPM.