Expression Profiling of Fibroblasts in Chronic and Acute Disease Models
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA496051 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Mouse models of acute and chronic liver damage
| PRJNA702143 | ENA
Project description:Gene expression patterns among populations of kidney fibroblasts at different stages of injury or repair were analyzed by Affymetrix arrays.
2018-10-13 | GSE121190 | GEO
Project description:Whole blood transcriptional profiling of pediatric idiopathic thrombocytopenic purpura (ITP) patients comparing self-limited acute ITP patients with chronic ITP patients or progression-to-chronic ITP patients. Patient samples were collected during 3 different disease states: 8 samples from acute ITP pts (within 6 months of dx, during active disease), 4 samples from progression-to-chronic ITP pts (within 6 months of dx), and 14 samples from chronic ITP (after 6 months of dx).
2011-07-31 | E-GEOD-23754 | biostudies-arrayexpress
Project description:Though there has been extensive investigation of the kidney's acute cellular and molecular responses following cisplatin treatment, the mechanisms of progression from acute to chronic disease have not been explored. In this study, we use functional and morphological metrics to establish a time point when the transition from acute repairable kidney injury to chronic irreparable disease is clearly established. We then used microarray and western blot analysis to investigate the molecular changes (i.e., gene expression, pathway activity, signaling) associated with the transition from acute to chronic cisplatin-induced kidney disease.
2017-12-13 | GSE107976 | GEO
Project description:We characterized the transcriptional landscape of acute and chronic models of dextran sodium sulfate (DSS) and adoptive transfer (AT) colitis murine models to derive novel temporal gene expression and splicing signatures in blood and colonic tissue in order to capture dynamics of colitis remission and relapse. We show that colitis induces robust expression of minor isoforms and using machine learning, demonstrate that specific temporal gene expression and splicing signatures are highly predictive of tissue histopathology spanning blood and colonic tissue as well as various experimental sites and protocols. Finally, we identified sub networks of patient-derived causal networks that were enriched in these temporal signatures to distinguish acute and chronic disease components within the broader molecular landscape of IBD.
2022-12-31 | GSE214600 | GEO
Project description:Background: Peyronie’s disease (PD) is an acquired fibrotic process affecting the tunica albuginea (TA) of the penis. The development of fibrotic plaques can lead to penile curvature/deformities, shortening and erectile dysfunction. Medical treatments are lacking due to limited understanding of disease pathophysiology. Elucidation of molecular pathways and cell types involved could lead to the development of novel disease models and conservative therapeutics. Objective: To characterise the transcriptomic signature of plaques from PD patients and compare it to normal TA using RNA sequencing (RNAseq) and network analysis. Design, setting and participants: We collected surgical TA samples from 6 PD patients and 6 control patients where RNAseq was performed, followed by functional analysis. Our findings were validated through RT-qPCR and immunohistochemistry in other patient samples (biological validation) and tested in an in vitro PD model derived from patient samples. Results and limitations: These findings are the first report of using human samples for transcriptome-wide analysis of genital tract fibrosis. Differential gene expression identified 1294 differentially expressed genes in PD patients. Functional analysis reveals an active inflammatory component in the chronic PD plaque. Moreover, nearly half of all overexpressed genes were regulated by NF-kB and STAT. Further analysis shows that NF-kB is TNFα and TLR-activated and JAK/STAT-signalling occurs through interleukins (IL2/IL6) /interferons (Type I/II)). This data suggests an important macrophage-related response. We validated genes from enriched pathways using RT-qPCR both in the RNAseq samples and 5 additional samples. Immunohistochemical staining for macrophages (CD68) corroborated these findings. Stimulation of PD-derived fibroblasts and myofibroblasts with TNFα revealed expression of macrophage chemoattractant protein-1 (CCL2/MCP-1). Conclusions: Our analysis suggests that, even in an established, chronic PD-plaque, acute inflammatory pathways are still active. We show for the first time that TNFα and TLR-activation could be an important pathway in PD-pathophysiology. Additionally, we suggest that this process is potentially maintained through macrophages. Release of TNFα induce chemoattraction of more macrophages by CCL2 production of (myo)fibroblasts. Both could lead to development of novel druggable targets and more representative disease models.
2022-01-24 | GSE126005 | GEO
Project description:Deep sequencing reveals an acute inflammatory signature in chronic Peyronie’s disease
| PRJNA518887 | ENA
Project description:The lack of suitable animal models reflecting chronically relapsing inflammation and tissue remodeling have hindered fibrosis research in inflammatory bowel diseases (IBD). This study investigated changes in connective tissue in a chronic murine model using different cycles of dextran sodium sulphate (DSS) to mimic the relapsing nature of the disease. We used whole gene expression arrays to study differences in colonic gene expression levels between acute and more chronic DSS colitis, Acute and chronic relapsing colonic inflammation was induced in C57BL6 female mice using several cycles of exposure to DSS in drinking water, followed by recovery phases. Total RNA, extracted from snap frozen colon from five mice per condition was used to analyze mRNA expression via Affymetrix Mouse Gene 1.0 ST arrays.
2013-09-03 | E-GEOD-42768 | biostudies-arrayexpress
Project description:Molecular characterization of chronic liver disease dynamics: from liver fibrosis to acute-on-chronic liver failure
| PRJNA580468 | ENA
Project description:Adult zebrafish are capable of photoreceptor (PR) regeneration following acute phototoxic lesion (AL). We developed a chronic low light (CLL) exposure model that more accurately reflects chronic photoreceptor degeneration observed in many human retinal diseases. Here, we characterize the morphological and transcriptomic changes associated with acute and chronic models of PR degeneration at 8 time points over a 28-day window using immunohistochemistry and 3’mRNA-seq. We first observed a differential sensitivity of rod and cone PRs to CLL. Next, we found no evidence for Müller glia (MG) gliosis or regenerative cell-cycle reentry in the CLL model, which is in contrast to the robust gliosis and proliferative response from resident MG in the AL model. Differential responses of microglia between the models was also observed. Transcriptomic comparisons between the models revealed gene-specific networks of PR regeneration and degeneration, including genes that are activated under conditions of chronic PR stress. Finally, we showed that CLL is at least partially reversible, allowing for rod and cone outer segment outgrowth and replacement of rod cell nuclei via an apparent upregulation of the existing rod neurogenesis mechanism. Collectively, these data provide a direct comparison of the morphological and transcriptomic photoreceptor degeneration and regeneration models in zebrafish.
2023-08-28 | GSE233896 | GEO