Massively parallel whole-organism lineage tracing using CRISPR/Cas9 induced genetic scars
Ontology highlight
ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE81533 | GEO | 2019/05/17
REPOSITORIES: GEO
Similar Datasets
Project description:A key goal of developmental biology is to understand how a single cell transforms into a full-grown organism consisting of many different cell types. Single-cell RNA-sequencing (scRNA-seq) has become a widely-used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However, a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here, we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses, LINNAEUS (LINeage tracing by Nuclease-Activated Editing of Ubiquitous Sequences) can be used as a systematic approach for identifying the lineage origin of novel cell types, or of known cell types under different conditions.
2018-04-04 | GSE106121 | GEO
Project description:We hypothesize that, the mTOR pathway is a dominant pathway in cultured keloid and hypertrophy scar fibriblasts compared to normal skin cells. Certain pathway changes can be detected after medication treatment. Global gene expression in RNA samples from rapamycin and tacrolimus treated fibroblasts (from normal skin and hypertrophic scars, keloid scars) is assayed to study the possibility to use mTOR inhibitors as potential drug to treat abnormal scarring. We investigated the difference between normal wound healing and hypertrophic scars and keloids as well.
2014-05-20 | E-MTAB-2509 | biostudies-arrayexpress
Project description:Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars
| PRJNA415636 | ENA
Project description:Fibrosis is vaguely described as connective tissue deposition that can be excessive in pathological conditions. This suggests a quantitative spectrum of fibrosis wherein there can be more or less extracellular matrix (ECM), which in the context of a repairing skin wound could reflect the range from normal scar to keloid. This depiction, however, does not encompass the potential qualitative differences between normal and pathological scars. In keloids, the markedly different physical (hard and dense) and histological (hyalinization) characteristics compared to normal scars indicate an altered and inappropriate matrix, rather than simply too much. With this quantitative discovery-based proteomics we provide a thorough molecular description of keloid lesions relative to normal scars, which is an essential step towards our understanding of this problem.
2019-12-03 | PXD015057 | Pride
Project description:It is well accepted that elevated mechanical tension of the skin surrounding a healing wound stimulates a fibrotic cascade of events and contributes to an increased size of scars. A laxity paradox in the field of hair transplantation describes a phenomenon opposing this view. During Strip Follicular Unit Transplantation (Strip FUT), surgeons remove a strip of scalp skin (approximately 5 cm x 10 cm, depending on the number of hair follicles required) from the occipital scalp, which is then used to harvest hair follicles that will be transplanted into the balding frontal scalp. Most patients with normal scalp skin laxity heal with narrow normotrophic scars, while a small number of patients (14%) with very loose scalp skin, and so low residual skin tension, heal with post operating scar widening (4 - 12 mm). These scars, referred to as stretched scars in the hair transplantation field, often require revision surgery or secondary hair grafting into the scar. We hypothesise that stretched scars present a unique transcriptional signature different from other types of scars. To determine the gene expression profile of stretched scars, we used Affymetrix microarrays to perform profiling of fibrotic dermis and the surrounding patient-matched healthy dermis.
2022-12-31 | GSE162904 | GEO
Project description:Cardiac fibroblasts convert to myofibroblasts with injury to mediate healing after acute myocardial infarction and to mediate long-standing fibrosis with chronic disease. Myofibroblasts remain a poorly defined cell-type in terms of their origins and functional effects in vivo. Methods: Here we generate Postn (periostin) gene-targeted mice containing a tamoxifen inducible Cre for cellular lineage tracing analysis. This Postn allele identifies essentially all myofibroblasts within the heart and multiple other tissues. Results: Lineage tracing with 4 additional Cre-expressing mouse lines shows that periostin-expressing myofibroblasts in the heart derive from tissue-resident fibroblasts of the Tcf21 lineage, but not endothelial, immune/myeloid or smooth muscle cells. Deletion of periostin+ myofibroblasts reduces collagen production and scar formation after myocardial infarction. Periostin-traced myofibroblasts also revert back to a less activated state upon injury resolution. Conclusions: Our results define the myofibroblast as a periostin-expressing cell-type necessary for adaptive healing and fibrosis in the heart, which arises from Tcf21+ tissue-resident fibroblasts. Fluidigm C1 whole genome transcriptome analysis of lineage mapped cardiac myofibroblasts
2016-06-14 | E-GEOD-83337 | biostudies-arrayexpress
Project description:Although pigment synthesis is well understood, relevant mechanisms of psychologically debilitating dyspigmentation in nascent tissue after cutaneous injuries are still unknown. Here, differences in genomic transcription of hyper- and hypopigmented tissue relative to uninjured skin were investigated using a red Duroc swine scar model. Transcription profiles differed based on pigmentation phenotypes with a trend of more upregulation or downregulation in hyper- or hypopigmented scars, respectively. Ingenuity Pathway Analysis of significantly modulated genes in both pigmentation phenotypes showed pathways related to redox, metabolic, and inflammatory responses were more present in hypopigmented samples, while those related to stem cell development differentiation were found mainly in hyperpigmented samples. Cell-cell and cell-extracellular matrix interactions and inflammation responses were predicted (z-score) active in hyperpigmented and inactive in hypopigmented. The proinflammatory high-mobility group box 1 pathway showed the opposite trend. Analysis of differentially regulated mutually exclusive genes showed an extensive presence of metabolic, proinflammatory, and oxidative stress pathways in hypopigmented scars, while melanin synthesis, glycosaminoglycans biosynthesis, and cell differentiation pathways were predominant in hyperpigmented scar. Several potential therapeutic gene targets have been identified.
2020-09-17 | GSE158155 | GEO
Project description:Massively parallel whole-organism lineage tracing using CRISPR/Cas9 induced genetic scars
| PRJNA321866 | ENA
Project description:Human hair follicles undergo repetitive cycles of growth throughout their lifetime. During the hair follicle cycle, functional and structural changes occur within the surrounding skin environment. However, skin that experienced a deep injury lacks cycling hair follicles and turns into a mass of unremodelled scar tissue. We hypothesise that re-introducing cycling hair follicles into human scars will stimulate skin remodelling improving fibrotic tissue. To determine the transcriptional events underlying remodelling of scar dermis after hair follicle transplantation, we used Affymetrix microarrays to perform profiling of scar dermis before (0 mo), and at three time points after hair transplantation transplantation: 2, 4, and 6 months.
2022-12-31 | GSE145470 | GEO
Project description:Injury in mammals induces a connective tissue response to either regenerate as before, or to scar. The fibroblastic actions and mechanisms that underlie these connective tissue responses remain obscure, as direct observation in animals is too difficult and current assays do not faithfully reproduce physiology. Here, we developed a skin explant technique termed scar-in-a-dish (SCAD) that faithfully recapitulates uniform scars with contraction and reveals how scarring occurs in unprecedented detail. By growing mouse SCADs, with a traceable scar-progenitor fibroblast lineage, we observed previously unseen intercellular connections form between scar-progenitors that then collectively swarm into the nascent wound in highly regular periodic movements that progressively contract the skin and form scars. Swarming is exclusive to scar progenitors and absent from oral cavity fibroblasts that regenerate scarless. By testing a panel of adhesion molecules that might instigate intercellular connections, we found swarming was induced by the upregulation of N-cadherin in scar progenitors. Impeding N-cadherin binding inhibited swarming and contraction, and led to reduced scarring in SCAD and in mice. Blocking N-cadherin and scar-progenitor swarming thus provides a novel therapeutic space to curtail pathological fibrotic responses across a range of medical settings.
2020-10-26 | PXD016068 | Pride