Single cell RNA-seq analysis of TBX18-driven reprogramming of ventricular myocytes to cardiac pacemaker cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA784583 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To understand the transcriptional landscape of Tbx18-induced cardiac pacemaker cells. The control cells were ventricular myocytes expressing GFP.
2022-08-25 | GSE129545 | GEO
Project description:Background: Embryonic trancription factor TBX18 re-expression has been demonstrated to be capable of converting ventricular myocytes to pacemakers cells. The goals of this study are to investigate the effects of TBX18 on myocytes and non-myocytes at day 3, day 6 and day 14, as well as tracking the key node of reprogramming process and mechanism. Methods: Neonatal rat ventricular myocytes (NRVC) were treated by adeno-TBX18 or GFP for 3 days to investigate the early effects of TBX18 on myocytes and non-myocytes. Except for these 2 treatments, Adeno-TBX18 with one specific Tgfβ inhibitor, A83-01 (0.2uM) was treated for NRVC for 14 days for explore the effects of Tgfβ inhibition on fibroblast activation and myocyte reprogramming process. Attached NRVC monolayers were digested with 0.25% trypsin (Cat# LS003707, Corning, NY) for 5 min at 37 °C, and filtered through a 100-μm cell strainer (Fischer Scientific, Waltham, MA) to generate a single-cell suspension. Single cells were resuspended to a concentration of 700-2,000 cells per microliter. Gel beads-in-emulsion (GEMs) were generated with Chromium X (10X Genomics, Pleasanton, CA) and RNA libraries were prepared using the Chromium Next GEM Single Cell 3' GEM kit, v3.1 (10X Genomics Inc., Pleasanton, CA) with a targeted cell recovery of 4,000-10,000 cells per reaction. Quality control of cDNA and scRNA-seq libraries were performed using the Bioanalyzer High Sensitivity kit (Agilent Technologies Inc., CA). Libraries were sequenced using Novaseq 6000 (Illumina Inc., CA) with a minimum depth of 50,000–65,000 read pairs per cell. Result: Upon QA/QC filtering, 13,437 cells met the quality thresholds for subsequent analysis. We focused on three cell types: cardiomyocytes (CMs, Tnni3-positive), total FBs (Pdgfrb and Tcf21-positive) with 2 subpopulations, including myoFBs (Pdgfrb, Tcf21, Acta2-high) and quiescent FBs (Pdgfrb, Tcf21, Acta2-low). Pathway analysis further revealed that upregulated DEGs by TBX18 are involved in fibroblast activation and ECM remodeling. Among those, Tgfβ signaling, which is one of the major molecular mediators of fibrosis in the heart, figured prominently in TBX18-transduced CMs and FBs. This was evidenced by upregulated expression of Tgfβ ligands and profibrotic genes such as Tgfb1, Tgfb2, and Acta2 in TBX18-NRVCs. Accordingly, higher proportion of activated myofibroblasts (39.3% vs. 25.4%) and lower proportion of quiescent FBs were observed in TBX18-NRVCs compared to control (Fig. 2F). To test the causative role of Tgfβ signaling in triggering fibrosis upon TBX18 re-expression, monolayers of NRVCs were treated with a small molecule inhibitor of type I Tgfβ receptors, A83-01. Treatment with A83-01 significantly decreased the population of myoFBs from 68.0% in TBX18-NRVC to 49.5% of total cell population at d14. Heat map analysis of all genes indicated that TBX18-CMs show upregulation of fibroblast-related genes, which is mitigated with A83-01 treatment. The upregulated DEGs in TBX18-FBs pointed to ECM remodeling as well as inflammatory response involving Tgfβ and other cytokines. Again, treatment with A83-01 abrogated the rise of these pathways. Profibrotic genes such as Tgfb2, Tgfb3, Acta2, and inflammatory genes were upregulated in FBs transduced with Ad-TBX18, which was mitigated by A83-01 treatment. The upregulated gene clusters in TBX18-FBs were also upregulated in TBX18-CMs, particularly, interferon signaling, interleukin-4 regulation of apoptosis, which may have led to the loss of TBX18-CMs over time. The inflammatory and profibrotic pathways were suppressed by treatment with A83-01 and may explain the higher population of TBX18-CMs with A83-01 at d14.We also quantified the number of de novo iPMs based on: Tnni3high, Hcn4+, Nkx2-5low, Gja1low through our scRNA-seq analysis and demonstrated the proportions of Hcn4+ iPMs was similar in TBX18-CMs regardless of Tgfβ inhibition but was higher compared to control. Conclusion: Tgfβ signaling inhibition with a83-01 prevents against myofibroblast activation, cardiomyocytes apoptosis and inflammatory response induced by TBX18, and short term treatment of A8301 does not strongly interfere the reprogramming process and efficiency.
2024-09-27 | GSE189815 | GEO
Project description:In this study, we performed two-dimensional liquid chromatography coupled to tandem mass spectrometry (2D-LC-MS/MS) to characterize the global transcriptome and proteome changes in Tbx18-iPMs compared to control, GFP-overexpressing neonatal rat ventricular myocytes (NRVMs). 67% of protein abundances changed significantly (4,475 of 6,661 proteins; p<0.05) at a false discovery rate of 1.6%. Downregulation was broad among metabolic pathways, such as TCA cycle, oxidative phosphorylation, glycolysis and fatty acid oxidation. Ion channels associated with ventricular excitation-contraction coupling (sodium, calcium, and potassium channels, Connexin 43, among others) were likewise downregulated. Pacemaker phenotype was characterized by upregulation of the pacemaker current channel (HCN4) but also mechnosensitive Piezo1, Trp channels Trpp2 (PKD2) and TrpM7, and Connexin45. Consistent with emergent pacemaker morphology, there was broad upregulation of cytoskeletal proteins and their small GTPase regulators. Extracellular matrix and growth factor/cytokine/interferon genes were also dynamically upregulated, indicating that Tbx18-iPMs are primed for sinoatrial node integration.
2022-08-26 | PXD013351 | Pride
Project description:Transcriptome analysis of Tbx18-induced pacemaker cells (TBX18-iPMs) in comparison to ventricular cardiomyocytes
| PRJNA531698 | ENA
Project description:Study of the effects of interleukin 1 beta on transcript expression in ventricular cardiac myocytes
2010-04-01 | E-MEXP-1960 | biostudies-arrayexpress
Project description:Gene expression changes in neonatal rat ventricular myocytes plated in fibronectin (2 samples) or uncoated plates (2 samples).
2008-06-11 | E-GEOD-1055 | biostudies-arrayexpress
Project description:Title: Changes in gene expression affected by H2O2 in cardiac myocytes.<br/> Description: We aim to identify the changes in gene expression in response to <br/> oxidative stress in rat neonatal ventricular myocytes.<br/> Oxidative stress will be induced by dosing neonatal ventricular myocyte<br/> cultures with 0.2, 0.1 and 0.04mM hydrogen peroxide at 2, 4 and 8 hr time<br/> points using unstimulated myocytes as control.
2011-11-08 | E-MIMR-12 | biostudies-arrayexpress
Project description:Study of the effect of interleukin 33 (IL33) on transcript expression in neonatal rat ventricular cardiac myocytes at 0.5, 1 or 2 h
2010-04-01 | E-MEXP-1912 | biostudies-arrayexpress
Project description:Neonatal rat ventricular myocytes cultured for 48 hours without stimulation, in the presence of twenty micromolar phenylephrine, or in the presence of one micromolar PAMH. Keywords = Rattus Keywords = Ventricular Myocytes Keywords = Cardiomyocytes Keywords = Hypertrophy Keywords = Phenylephrine Keywords = PAMH Keywords = 5-hydroxytryptamine Keywords = Pyridine Keywords: repeat sample
2004-03-02 | GSE925 | GEO
Project description:Title: Regulation of gene expression through mitogen-activated protein kinase cascades in cardiac myocytes.<br/> Description: The aim of this study is to identify the changes in gene expression induced in rat neonatal <br/> ventricular myocytes, a well-established cell culture model, by endothelin-1, <br/> a known hypertrophic agonist, and to determine which of the changes are <br/> mediated through the ERK cascade. This continues TKAC^Ys previous study of the <br/> effects of oxidative stress, which induces cardiac myocyte apoptosis.<br/>
2006-10-01 | E-MIMR-3 | biostudies-arrayexpress