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PAN-INTACT enables isolation of lineage-specific nuclei from fibrous tissues

ABSTRACT: PAN-INTACT method can be used to isolate cell type specific nuclei from fibrous mouse organs, which are particularly problematic. It is broadly applicable for profiling the transcriptional and epigenetic landscape of specific cell types. We envision that our method can be used to systematically probe mechanistic details of cell type-specific functions within individual organs of intact mice.

ORGANISM(S): Mus musculus

PROVIDER: GSE119792 | GEO | 2019/04/05

REPOSITORIES: GEO

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PAN-INTACT enables isolation of lineage-specific nuclei from fibrous tissues

Project description:PAN-INTACT enables isolation of lineage-specific nuclei from fibrous tissues

| PRJNA490328 | ENA

PAN-INTACT enables direct isolation of lineage-specific nuclei from fibrous tissues.

Project description: Not available

| S-EPMC6445515 | biostudies-literature

mini-INTACT reveals social isolation-induced epigenetic changes in Drosophila dopaminergic neurons

Project description:We introduce a more sensitive method for purifying specific cell-types from small numbers of fly heads for epigenomic analysis: a method we call ‘mini-INTACT’. We modified the INTACT method in Drosophila [Henry G. L. et al., Nucleic Acids Research, 2012, 1–14] to enable purification of genetically tagged rare cell types from Drosophila brain requiring ~50-100 fold less material. We used male fruit flies as a model to examine the effects of social-isolation vs. social-enrichment on the epigenome and transcriptome of dopaminergic neurons defined by expression of the TH-GAL4 driver. Using ChIP-seq on mini-INTACT purified nuclei, RNA-seq and bioinformatic analysis, we identify regulation of the transcriptome and behavior by Activity Related Genes who’s expression is induced by social enrichment.

2019-02-07 | GSE126186 | GEO

A farnesyl-dependent structural role for CENP-E in expansion of the fibrous corona

Project description:Correct chromosome segregation during cell division depends on proper connections between spindle microtubules and kinetochores. During prometaphase, kinetochores are temporarily covered with a dense protein meshwork known as the fibrous corona. Formed by oligomerization of ROD/ZW10/ZWILCH-SPINDLY (RZZ-S) complexes, the fibrous corona promotes spindle assembly, chromosome orientation and spindle checkpoint signaling. The molecular requirements for formation of the fibrous corona are not fully understood. Here we show that the fibrous corona depends on the mitotic kinesin CENP-E, and that poorly expanded fibrous coronas after CENP-E depletion are functionally compromised. This previously unrecognized role for CENP-E does not require its motor activity but instead is driven by its C-terminal microtubule-binding region and farnesyl modification thereof. The ‘birth’ of a farnesylation motif in CENP-E orthologs during Obazoa evolution closely aligns with presence of the full RZZ-S module, and we show that in cells CENP-E interacts with RZZ-S complexes in a farnesyl-dependent manner. CENP-E is recruited to kinetochores following RZZ-S, and - while not required for RZZ-S oligomerization per se - promotes subsequent fibrous corona expansion. Our results show that proper spindle assembly has a non-motor contribution from the kinesin CENP-E through stabilization of the fibrous corona meshwork during its formation.

2023-10-09 | PXD040338 | Pride

Solitary Fibrous Tumours gene profiling study

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Gene Expression Analysis of Soft Tissue Sarcomas: Characterization & Reclassification of Malignant Fibrous Histiocytoma

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Gene Expression Profile of Epiretinal Fibrous Membrane Associated with Proliferative Vitreoretinopathy

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2012-09-21 | E-GEOD-41019 | biostudies-arrayexpress

TU-tagging: cell type specific RNA isolation from intact complex tissues

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The fibrous cap of atherosclerotic lesions arise from multiple cellular origins by PDGFRB- and bioenergetic mechanisms

Project description:Stable atherosclerotic plaques are characterized by a thick extracellular matrix (ECM)-rich fibrous cap populated by protective ACTA2+ myofibroblast (MF)-like cells, assumed to be almost exclusively derived from smooth muscle cells (SMC). Herein, we show that in murine and human lesions, ~20-40% of ACTA2+ fibrous caps cells, respectively, are derived from non-SMC sources, including endothelial cells (EC) or macrophages that have undergone Endothelial-to-Mesenchymal (EndoMT) or Macrophage-to-Mesenchymal (MMT) transitions. In addition, weshow that SMC-specific knockout of the platelet-derived growth factor receptor beta (PDGFRB) in Apoe-/- mice fed a Western diet (WD) for 18 weeks results in brachiocephalic artery (BCA) lesions nearly devoid of SMC. While absence of SMCs does not affect lesion size, remodeling, or ACTA2+ fibrous cap cell content, prolonged WD feeding results in reduced indices of stability, indicating that EndoMT and MMT-derived MFs cannot compensate indefinitely for loss of SMC-derived MFs. Using RNA-seq analysis of the BCA region and in vitro models, we demonstrate that SMC to MF transitions (SMC-MFT) is induced by PDGF and TFGβ and is dependent on aerobic glycolysis, while EndoMT is induced by IL1β and TGFβ. Together, we provide the first quantitative evidence that the ACTA2+ fibrous cap originates from a tapestry of cell types, which transition to an MF state through distinct signaling pathways that are either dependent on or associated with extensive metabolic reprogramming.

2021-02-22 | GSE163519 | GEO

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