Small RNA-seq analysis of E10.5 Tbx18-expressing peri-wolffian duct stroma
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ABSTRACT:
PROVIDER: PRJNA729438 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14509093.fastq.gz | Fastqsanger.gz | |||
| SRR14509094.fastq.gz | Fastqsanger.gz | |||
| SRR14509095.fastq.gz | Fastqsanger.gz | |||
| SRR14509096.fastq.gz | Fastqsanger.gz |
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Project description:The overall goal of this project is to characterize the repertoire of miRNAs in E10.5 Tbx18-expressing peri-wolffian duct stroma cells during development. To achieve this, E10.5 peri-wolffian ducts were dissected from timed-mated Tbx18-Cre;CAG-tdTomato embryos, followed by FACS sorting based on RFP expression to enrich for Tbx18-expressing cells.
2024-05-07 | GSE174322 | GEO
Project description:The T-box transcription factor TBX18 is essential to mesenchymal cell differentiation in several tissues and Tbx18 loss-of-function results in dramatic organ malformations and perinatal lethality. Here we demonstrate for the first time that Tbx18 is required for the normal development of periductal smooth muscle stromal cells in prostate, particularly in the anterior lobe, with a clear impact on prostate health in adult mice. Prostate abnormalities are only subtly apparent in Tbx18 mutants at birth; to examine postnatal prostate development we utilized a relatively long-lived hypomorphic mutant and a novel conditional Tbx18 allele. Similar to the ureter, cells that fail to express Tbx18 do not condense normally into smooth muscle cells of the periductal prostatic stroma. However, in contrast to ureter, the periductal stromal cells in mutant prostate assume a hypertrophic, myofibroblastic state and the adjacent epithelium becomes grossly disorganized. To identify molecular events preceding the onset of this pathology, we compared gene expression in the urogenital sinus (UGS), from which the prostate develops, in Tbx18-null and wild type littermates at two embryonic stages. Genes that regulate cell proliferation, smooth muscle differentiation, prostate epithelium development, and inflammatory response were significantly dysregulated in the mutant urogenital sinus around the time that Tbx18 is first expressed in the wild type UGS, suggesting a direct role in regulating those genes. Together, these results argue that Tbx18 is essential to the differentiation and maintenance of the prostate periurethral mesenchyme and that it indirectly regulates epithelial differentiation through control of stromal-epithelial signaling.
2016-04-26 | GSE80083 | GEO
Project description:Breast cancers display a high degree of diversity between and within tumors due to variations in both tumor cells and non-malignant cells of the tumor microenvironment (TME). While most studies on the TME have focused on stroma located within the tumor mass, few studies have examined the peri-tumoral microenvironment, which extends beyond the tumor margins and includes the surrounding, benign-appearing tissues. Here, we examined the heterogeneity in tumors and peri-tumoral stroma from 10 ER+PR+HER2- invasive breast carcinomas, through multi-region transcriptomic profiling. Tumor samples were obtained from the center, superior, inferior, medial, and lateral (C, S, Inf, M, L) regions of each tumor. Peritumoral samples were obtained from four radial directions corresponding to the regions the tumor samples were collected from (S, Inf, M, L) and from three zones of increasing distances from the tumor margins (Zone 1: 1-3 cm, Zone 2: 3-5 cm, Zone 3: 5-7 cm). To represent the normal breast transcriptomic state, 5 non-directional samples were each obtained from 3 non-tumor bearing breasts (NTB) - 1 patient had undergone cosmetic reduction mammoplasty and 2 patients were germline BRCA2-mutation carriers who had undergone risk-reducing mammoplasties. Total RNA was isolated and microarray was performed using the human Clariom™ S Assay (ThermoFisher Scientific). In total, 144 transcriptomic profiles (47 Tumor, 82 peri-tumoral stroma, 15 NTB) were analyzed. Heterogeneity was observed both within and between the tumor samples, highlighting that unlike the histological classification, an individual tumor is often comprised of several molecular sub-types. Similarly, the peri-tumoral stroma was also heterogeneous, albeit independent of the tumor heterogeneity. Four distinct stromal clusters were noted, which differed in their molecular pathways and cell type composition. Among these, the adipose-enriched stroma that had inflammatory cancer-associated fibroblasts and innate immune cells was significantly associated with poorer overall survival, in contrast to the myofibroblast-enriched stroma. These data together suggest that the peri-tumoral heterogeneity may be an important determinant of the evolution and treatment of breast cancers.
2022-08-22 | GSE211729 | GEO
Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. HoxB7-GFP transgenic mice were utilized to isolate the ureteric duct cells from E10.5 embryonic kidneys. The ureteric duct cells were isolated from embryos using microdissection, trypsin treatment and FACS. The RNA was isolated from purified ureteric duct cells and the gene expression profiles were determined by microarrays.
2010-05-27 | E-GEOD-21584 | biostudies-arrayexpress
Project description:Adipose-enriched peri-tumoral stroma, in contrast to myofibroblast-enriched stroma, prognosticates poorer survival in breast cancers.
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Project description:Evaluation of the transcriptional changes in E11.5 ureter mesenchyme cells upon loss of Tbx18 or overexpression of an activator version of Tbx18, respectively.
2023-03-13 | GSE198129 | GEO
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:The evolutionarily conserved transcription factor, Tbx18, is expressed in a dynamic pattern throughout embryonic and early postnatal life and plays crucial roles in the development of multiple organ systems. Previous studies have indicated that this dynamic function is controlled by an expansive regulatory architecture, extending far upstream and downstream of the gene. With the goal of identifying elements that interact with the Tbx18 promoter in developing prostate, we coupled chromatin conformation capture (4C) and ATAC-seq from embryonic day 18.5 (E18.5) mouse urogenital sinus (UGS), where Tbx18 is highly expressed. The data revealed dozens of active chromatin elements distributed throughout a 1.5 million base pair topologically associating domain (TAD). To identify cell types contributing to this chromatin signal, we used lineage tracing methods with a Tbx18 Cre “knock-in” allele; these data show clearly that Tbx18-expressing precursors differentiate into wide array of cell types in multiple tissue compartments, most of which have not been previously reported. We also used a 209 kb Cre-expressing Tbx18 transgene, to partition enhancers for specific precursor types into two rough spatial domains. Within this central 209 kb compartment, we identified ECR1, previously described to regulate Tbx18 expression in ureter, as an active regulator of UGS expression. Together these data define the diverse fates of Tbx18+ precursors in prostate-associated tissues for the first time, and identify a highly active TAD controlling the gene’s essential function in this tissue.
2018-12-29 | GSE123102 | 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:Transcriptome analysis of Tbx18-induced pacemaker cells (TBX18-iPMs) in comparison to ventricular cardiomyocytes
| PRJNA531698 | ENA