Ontology highlight
ABSTRACT:
PROVIDER: PRJNA954770 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24143500.fastq.gz | Fastqsanger.gz | |||
| SRR24143501.fastq.gz | Fastqsanger.gz | |||
| SRR24143502.fastq.gz | Fastqsanger.gz | |||
| SRR24143503.fastq.gz | Fastqsanger.gz | |||
| SRR24143504.fastq.gz | Fastqsanger.gz |
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Project description:Fibrosis refers to the abnormal proliferation and excessive accumulation of fibrous tissue in an organ or tissue, typically caused by chronic injury or inflammation. Fibroblasts play a crucial role in the initiation and progression of fibrosis, with their excessive activation and overproduction of ECM being key mechanisms in fibrotic diseases. In this study, we constructed decellularized lung scaffolds from normal mice and bleomycin-induced lung decellularized scaffolds to analyze and compare the differential gene expression in control human fibroblasts, TGFβ-induced human fibroblasts, fibroblasts co-cultured with normal lung decellularized scaffolds, and fibroblasts co-cultured with bleomycin-induced lung decellularized scaffolds. This investigation aims to explore the impact of ECM on fibroblast activation and its underlying mechanisms.
2025-08-20 | GSE275625 | GEO
Project description:Rationale: Stem cell-based tracheal replacement represents an emerging therapeutic option for patients with otherwise untreatable airway diseases including long-segment congenital tracheal stenosis and upper airway tumors. Clinical experience suggests an urgent need to restore mucociliary function in the lungs following transplantation of tissue-engineered grafts, while pre-clinical studies show that seeding scaffolds with autologous mucosa improves regeneration. Recent data suggest that high epithelial cell seeding densities are required in regenerative medicine and existing techniques are inadequate to achieve coverage of clinically suitable grafts. Objectives: To define a scalable airway epithelial cell culture system to deliver airway epithelial cells to clinical grafts. Methods: Human respiratory epithelial cells derived from endobronchial biopsies were cultured using a combination of mitotically inactivated fibroblasts and Rho-kinase (ROCK) inhibition. Cells were analyzed using immunofluorescence, qPCR and flow cytometry to assess airway stem cell marker expression. Differentiation capacity and ciliary beat were assessed in air-liquid interface cultures. Karyotyping and an in vivo tracheal xenograft model were used to investigate the suitability of expanded cells for tracheal reconstruction. Measurements and Main Results: 3T3 feeder cells and ROCK inhibition allowed rapid expansion of airway basal stem cells. These cells were capable of multipotent airway differentiation in vitro, forming epithelia containing both ciliated and goblet lineages. Cilia were functional with normal beat frequency and pattern. Cultured cells repopulated a decellularized tracheal scaffold in a heterotopic tracheal transplantation xenograft model. Conclusions: Our method addresses the clinical need to generate large numbers of airway basal epithelial cells in the time window demanded by clinical transplantation.
2015-10-01 | GSE69005 | GEO
Project description:The objective of this study was to evaluate primary, human AT2 cells following seeding into decellularized lung scaffolds.
2025-12-18 | GSE306714 | GEO
Project description:The brain extracellular matrix (ECM) regulates myelin repair and regeneration after demyelination by interacting with neuronal progenitors and immune cells. Therefore, generating and characterizing ECM scaffolds in regions with distinct neuroregenerative capacities is crucial to identify factors that modulate cellular regenerative behavior. We established an effective decellularization protocol for the human neural stem cell (NSC)-rich subventricular zone (SVZ), frontal cortex (FC), and white matter (WM), and defined region-specific matrisomes using comparative proteomics. As proof of concept, we investigated the survival and differentiation of NSCs and monocytes within the decellularized scaffolds. NSCs cultured in WM and FC acquired an astrocytic phenotype, while both astrocytic and oligodendrocytic phenotypes were promoted by SVZ scaffolds. Additionally, monocytes seeded on SVZ and WM scaffolds exhibited an anti-inflammatory differentiation. This model is suitable for investigating ECM properties and assessing cell-matrix interactions.
2025-05-27 | PXD062743 | Pride
Project description:In this study we developed highly proliferative and lineage restricted lung endothelial derived progenitor-like cells using the transient expression of Yamanaka factors via doxycycline inducible system combined with LIF-supplemented media. We investigate the potential of these induced progenitor-like cells for the vascular engineering of the lungs. Our results show that these cells recapitulate the segment specific heterogeneity in the decellularized lung scaffolds and show immediate recovery of endothelial genes after recellularization.
2020-06-23 | E-MTAB-8394 | biostudies-arrayexpress
Project description:Full osteochondral regeneration remains a major clinical challenge. Among other experimental cartilage regenerative approaches, decellularized cartilage (DCC) is considered a promising material for generating potentially implantable scaffolds useful as cartilage repair strategy. Bibliography is extensive, but decellularization methods are multiple and cartilage regenerative properties are limited. In this work, we focus on screening and comparing different decellularization methods, aiming to generate DCC potentially useful in biomedical context, and therefore, with biological activity and functional properties in terms of induction of differentiation and regeneration. Data indicate that enzymatic and detergents-based decellularization methods differentially affect ECM components, and that it has consequences in further biological behavior. SDS-treated DCC powder are not useful to be further processed in 2D or 3D structures, because these structures tend to rapidly solubilize, or disaggregate, in physiologic media conditions. Conversely, Trypsin-treated DCC powders processed to mechanically stable 2D films and 3D porous scaffolds, presumably due to partial digestion of collagens during decellularization. In vitro cell culture studies indicate that these structures are biocompatible and induce and potentiate chondrogenic differentiation. In vivo implantation of DCC derived 3D porous scaffolds in rabbit osteochondral defects induce subchondral bone regeneration and fibrocartilage tissue formation after implantation. Therefore, this work defines an optimal cartilage tissue decellularization protocol able to generate DCC powders processable to biocompative and bioactive 2D and 3D structures. These structures are useful for in vitro cartilage research and in vivo subchondral bone regeneration, while hyaline cartilage regeneration with DCC as implantable material remains elusive.
2025-05-13 | PXD050583 | Pride
Project description:In this study, we used a recellularization method of perfusing cells into biological scaffolds through vascular pedicles. ASCs and L6 cells were co-seeded into adipose decellularized extracellular matrix (adECM) biological scaffolds. On one hand, this strategy ensures uniform distribution of seeded cells in the scaffold and avoids the formation of non-functional "muscle islands" later. On the other hand, co-seeding of L6 cells and ASCs addresses the issue of low myogenic differentiation potential of ASCs. Subsequently, the recellularized biological scaffold treatment of VML animal experiments showed that the combined recellularization strategy had significantly better muscle regeneration and angiogenesis than the single ASCs recellularization strategy, and the former had better functional recovery of tibialis anterior muscle (TA). Further single cell sequencing analysis found that compared to singly seeded ASCs in biological scaffolds, L6 cells in the combined recellularization induced ASCs to transform into a new subpopulation of cells highly expressing Mki67, CD34 and CDK1 genes, which had stronger ability of oriented myogenic differentiation and formed more mature and larger muscle fibers, significantly restoring TA muscle function.
2024-03-26 | GSE247751 | GEO
Project description:The liver is the most common site for colorectal cancer (CRC) metastasis and new tissue culture models are needed to study hepatic metastasis from CRC as none of the current models mimic the biological, biochemical and structural characteristics of the metastatic microenvironment. Decellularization provides a novel approach for the study of cancer extracellular matrix (ECM) as decellularized scaffolds retained their tissue-specific features and biological properties. In the present study we created a 3D model of CRC and matched CRC liver metastasis (CRLM) using patient-derived decellularized ECM scaffolds seeded with HT-29 CRC cell line. Here we show increased HT-29 cell proliferation and migration capability when cultured in cancer-derived scaffolds compared to same-patient healthy colon and liver tissues. CRLM scaffolds also induced activation of epithelial-mesenchymal transition (EMT) with cancer cells showing loss of E-cadherin expression and increased Vimentin expression. EMT was confirmed by gene expression profiling, with the most represented biological processes in CRLM-seeded scaffolds involving demethylation, deacethylation, cellular response to stress metabolic processes, response to oxygen level and to starvation. The complex 3D culture environment reduced the HT-29 cell response to anti-CRC drug 5-FU when used at standard IC50 determined in 2D cultures. In conclusion, our 3D culture system with patient-derived tissue-specific decellularized ECM better recapitulates the metastatic microenvironment compared to conventional 2D culture conditions and represents a relevant approach for the study of liver CRC metastasis formation and progression. Transcriptomic analysis was performed comparing the global gene expression profiles of HT29 cells grown on CRLM and HL scaffolds. The transcriptomic profile of each 3D subtype was compared with HT29 cells grown in plastic. Hierarchical clustering analysis revealed that the gene expression signature of recellularized CRLM scaffolds was more comparable to recellularized HL scaffolds, than to HT29 cells grown in 2D. Gene set enrichment analysis (GSEA) of the differently expressed genes (DEG) up-regulated in recellularized CRLM scaffolds compared to HT29 grown in 2D revealed that genes involved in demethylation, deacethylation and metabolic process belong to the most enriched biological pathways in repopulated-CRLM scaffolds. Comparing the DEG between recellularized CRLM scaffolds vs HT29 grown in 2D with a series of a-priori defined gene-set, called Hallmark, we obtained concordant results with the “HYPOXIA” and “EPITHELIAL_MESENCHYMAL_TRANSITION” pathway, enriched in recellularized CRLM, supporting the idea that 3D culture models are the ability to re-create a complex environment in terms of oxygen tension, nutrients, and metabolic gradient, similarly to the in vivo environment.
2019-11-30 | GSE125404 | GEO
Project description:This study investigated early host reactions to implanted materials to predict successful tissue regeneration with implant. Three kinds of scaffold, i.e., non-coat, collagen-coated, and PMB-coated porous polystylene scaffolds were implanted subcutaneously in mice dorsal area. Those scaffolds were used as bio-incomopatible materials, appropriate materials for tissue regeneration (bio active), and inappropriate to regenration (bio-inert) scaffolds. Seven days after implantation, scaffolds were explanted and total RNA was isolated from infiltrated host cells into scaffold by laser microdissection. Gene expressions of cells in collagen- and PMB-coated scaffold were normalized using results of non coat scaffold. Genes with more than 2-fold difference between collagen and PMB were picked up and narrowed to related keywords; inflammation, angiogenesis, wound healing, and mcrophage polarization. Among those genes, interluekin (IL)-1beta which promote both inflammation and wound healing was up-regulated in collagen-coated scaffold. On the other hand, IL-10 which suppress both inflammation and wound healing was up-regulated in PMB-coated scaffold. Angiogenesis-promoting genes were up-regulated and angiogenesis suppressve genes were suppressed in collagen. Up-regulation of IL-1b and the angiogenesis-relating genes inside the porous scaffolds are the possibly important factors for controlling tissue regeneration. Three-condition experiment, host cells infiltrated in non coat (reference), collagen-coated, and PMB-coated scaffolds. Two-microarray condition experiments, collagen vs. non coat and PMB coat vs. non coat. Hybridization: 2 replicates. Scanning: 3 replicates. Biological experiments: once.
2014-01-23 | E-GEOD-52053 | biostudies-arrayexpress
Project description:Volumetric muscle loss (VML) resulting from extremity trauma presents chronic and persistent functional deficits which ultimately manifest disability. Acellular biological scaffolds, or decellularized extracellular matrices (ECMs), embody an ideal treatment platform due to their current clinical use for soft tissue repair, off-the-shelf availability, and zero autogenous donor tissue burden. ECMs have been reported to promote functional skeletal muscle tissue remodeling in small and large animal models of VML injury, and this conclusion was reached in a recent clinical trial that enrolled 13 patients. However, numerous other pre-clinical reports have not observed ECM-mediated skeletal muscle regeneration. The current study was designed to reconcile these discrepancies. The capacity of ECMs to orchestrate functional muscle tissue remodeling was interrogated in a porcine VML injury model using unbiased assessments of muscle tissue regeneration and functional recovery. Here, we show that VML injury incites an overwhelming inflammatory and fibrotic response that leads to expansive fibrous tissue deposition and chronic functional deficits, which ECM repair does not augment.
2018-05-23 | GSE114798 | GEO