Alginate-based 3D culture of human induced pluripotent stem cells and their differentiation to functional dopaminergic neurons
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA740008 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Human induced pluripotent stem cells (hiPSCs) represent an unlimited cell source for the generation of in vitro models of patient-specific dopaminergic (DA) neurons, posing a possibility to overcome the restricted accessibility to disease-affected tissue for mechanistic studies on Parkinson’s disease (PD). However, the complexity of the human brain is not fully recapitulated by existing monolayer culture methods. Consequently, neurons differentiated in a three dimensional (3D) in vitro culture system might better mimic the in vivo cellular environment for basic mechanistic studies and represent better predictors of drug responses in vivo. Thus, in this work we established a new in vitro cell culture model based on the microencapsulation of hiPSCs in small alginate/fibronectin beads and their differentiation to DA neurons. Optimisation of hydrogel matrix concentrations and composition resulted in high viability of embedded iPSCs. Neural differentiation capacity and DA neuronal yield, analyzed by qRT-PCR, immunofluorescence, and western blot analyses, were increased in the 3D neuronal cultures compared to neurons generated using the conventional 2D culture system. Additionally, electrophysiological parameters and metabolic switching profile supported the increased functionality and an anticipated metabolic resetting of neurons grown in alginate scaffolds with respect to the 2D neurons. We also report long-term maintenance of neuronal cultures and mature functional properties. Furthermore, our findings indicate that our 3D model system can recapitulate mitochondrial superoxide production as an important mitochondrial phenotype observed in PD patients’-derived neurons and that this phenotype might be detectable earlier during neuronal differentiation. Taken together, these results indicate that our alginate-based 3D culture system offers an advantageous strategy for the reliable and rapid derivation of mature and functional DA neurons from iPSCs.
2021-08-20 | GSE178683 | GEO
Project description:The goal of this study was to investigate differences in the transcriptome of control CPCs and CPCs carrying a homozygous deletion of RAB5C upon induction of chondrogenesis by in vitro 3D alginate culture. CPCs samples were taken on day 0 in 2D culture, and on days 3 and 28 of chondrogenic differentiation in 3D alginate culture.
2021-03-30 | GSE158463 | GEO
Project description:Human intestinal organoids were grown in a typical 3D matrigel culture environment, or in an alginate gel, then a subset from each condition were xenotransplanted to vascularized and mature in vivo. Epithelium was isolated and epithelial only organoids (enteroids) were then grown from each condition prior to sequencing bulk RNA-sequencing.
2019-06-27 | E-MTAB-7000 | biostudies-arrayexpress
Project description:Dopaminergic neurons located in the ventral midbrain can be broadly subdivided into two distinct subpopulations. Substantia nigra (SN) dopaminergic neurons are highly sensitive to toxic insults and selectively degenerate in Parkinson’s disease, while ventral tegmental area (VTA) dopaminergic neurons are associated with other neurological disorders. Access to enriched cultures of SN and VTA dopaminergic neuronal subpopulations will facilitate disease modelling and give insight in the differential vulnerability, but it is unclear how the differentiation of human ES cells can be directed towards these distinct lineages. We found that overexpression of the lineage specifying transcription factors Sox6 and Otx2 can direct the differentiation of human ES cells into enriched populations of respectively SN or VTA neurons. Proteomic analysis of these cultures resulted in the identification of several differential expressed proteins and provided insight in pathways contributing to the selective vulnerability of SN.
2021-11-03 | PXD028639 | Pride
Project description:D1 multipotent mesenchymal stromal cells (D1‐MSCs,ATCC® CRL 12424TM) and genetically modified with the lentiviral vector pSIN‐EF2‐Epo‐Pur to express erythropoietin (EPO). D1‐MSCs genetically modified to release EPO were immobilized into 3D alginatepoly‐ L‐lysine‐alginate (APA) microcapsules. Since different formulations of alginate 1.5%, poly‐L‐lysine 0.05%, alginate 0.1% and washings were designed, two types of APA microcapsules were obtained: Biological microcapsules (made of Biological formulations) and Technological microcapsules (made of Technological formulations). The expression of the cells under different conditions of these two types of microcapsules have been analyzed. The present analysis proved that the mechanical properties of the matrix in which cells are enclosed influences drastically gene expression
2017-10-30 | E-MTAB-5786 | biostudies-arrayexpress
Project description:We have generated isogenic induced pluripotent stem cell lines by reprogramming human fibroblasts from patients carrying the LRRK2 G2019S mutation with subsequent zinc finger nuclease - mediated targeted correction of the diseased allele. These iPS cell lines were differentiated for 30 days using a direct differentiation protocol towards midbrain dopaminergic neurons (mDANs). Isogenic human iPS cells carrying the LRRK2 WT and G2019S locus were differentiated to dopaminergic neurons to detect gene expression changes associated with mutated LRRK2.
2013-03-07 | E-GEOD-43364 | biostudies-arrayexpress
Project description:Background: Three-dimensional (3D) in vitro culture systems using human induced pluripotent stem cells (hiPSCs) represent impactful platforms to model neurodegenerative disease biology in physiologically relevant microenvironments. Though many successful biomaterials-based 3D model systems have been established for other neurogenerative diseases, such as Alzheimer’s Disease, relatively few exist for Parkinson’s Disease (PD) research. Methods: We employed tissue engineering approaches to construct a 3D silk scaffold-based platform for the culture of hiPSC-dopaminergic (DA) neurons derived from healthy individuals and PD patients harboring LRRK2 G2019S or GBA N370S mutations. We then compared results from protein, gene expression and metabolic analyses obtained from two-dimensional (2D) and 3D culture systems. Results: The 3D platform enabled the formation of dense dopamine neuronal network architectures and developed biological profiles both similar and distinct from 2D culture systems in healthy and PD disease lines. 3D PD cultures showed elevated levels of α-synuclein and alterations in purine metabolite profiles. Furthermore, computational network analysis of transcriptome networks nominated several novel molecular interactions occurring in neurons from patients with mutations in LRRK2 and GBA. Conclusion: The brain-like 3D system presented here is a realistic platform to interrogate molecular mechanisms underlying PD biology. The key advantages of silk-based bioengineering technology include long-term culture and the ability to incorporate multiple brain-relevant cell types to parse cell-cell interactions in development, disease, and aging.
2022-03-16 | GSE172409 | GEO
Project description:Studies of underlying neurodegenerative processes in Parkinson’s Disease (PD) have traditionally utilized cell cultures grown on two-dimensional (2D) surfaces. Biomimetic three-dimensional (3D) cell culture platforms have been developed to better emulate features of the brain’s natural microenvironment. We here use our bioengineered brain-like tissue model, composed of a silk-hydrogel composite, to study the 3D microenvironment’s contributions on the development and performance of dopaminergic-like neurons (DLNs). Compared with 2D culture, SH-SY5Y cells differentiated in 3D microenvironments were enriched for DLNs concomitant with a reduction in proliferative capacity during the neurodevelopmental process. Additionally, the 3D DLN cultures were more sensitive to oxidative stresses elicited by the PD-related neurotoxin 1-methyl-4-phenylpyridinium (MPP). MPP induced transcriptomic profile changes specific to 3D-differentiated DLN cultures, replicating the dysfunction of neuronal signaling pathways and mitochondrial dynamics implicated in PD. Overall, this physiologically-relevant 3D platform resembles a useful tool for studying dopamine neuron biology and interrogating molecular mechanisms underlying neurodegeneration in PD.
2022-10-17 | GSE203522 | GEO
Project description:modENCODE_submission_467 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: BY200 (engineered, target gene dat-1 tagged by GFP); Tissue: dopaminergic neurons (embryonic); Developmental Stage: Mixed stage of embryos 20dC; Genotype: dat-1::GFP (pRN2003); Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Strain BY200 (engineered, target gene dat-1 tagged by GFP); temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue dopaminergic neurons (embryonic)
2010-08-04 | E-GEOD-23257 | biostudies-arrayexpress
Project description:Identification of new small molecules that regulate the step-wise differentiation of hPSC into dopaminergic neurons population. Furthermore, the naturally occurring steroid, guggulsterone, was found to be the most effective inducer of neural stem cells into dopaminergic neurons. Total RNA extracted at different stages of neural differentiation from human pluripotent stem cells
2013-04-24 | E-GEOD-42265 | biostudies-arrayexpress