Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Discerning Biomaterials-driven Transcriptome Dynamics to Induce Mesenchymal Stem Cell Differentiation

ABSTRACT: Bioactive materials harness the body’s innate regenerative potential by directing endogenous progenitor cells to facilitate tissue repair. Dissolution products of inorganic biomaterials provide unique biomolecular signaling for tissue-specific differentiation. We demonstrate the role of the inorganic biomaterial synthetic two-dimensional (2D) nanosilicates, and its ionic dissolution products on human mesenchymal stem cell differentiation. We utilize whole transcriptome sequencing (RNA-seq), to characterize the contribution of nanosilicates and its ionic dissolution products on endochondral differentiation. Our study highlights the modulatory role of ions in stem cell transcriptome dynamics by regulating lineage-specific gene expression patterns.

ORGANISM(S): Homo sapiens

PROVIDER: GSE193172 | GEO | 2022/05/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Biomaterials direct functional B cell response in a material specific manner

Project description:B cells are an adaptive immune target of biomaterials development in vaccine research but despite their role in wound healing have not been studied tissue engineering and regenerative medicine. We evaluated the B cell response to biomaterial scaffold materials implanted in a muscle wound; a biological extracellular matrix (ECM) and synthetic polyester polycaprolactone. In the local muscle tissue, small numbers of B cells are recruited in response to tissue injury and biomaterial implantation. ECM materials induced plasmablasts in lymph nodes and antigen presentation in the spleen while the synthetic PCL implants delayed B cell migration and induced an antigen presenting phenotype. In muMt- mice lacking B cells, the fibrotic response to the synthetic biomaterials decreased. Immunofluorescence confirmed antigen presenting B cells in fibrotic tissue surrounding silicone breast implants. In sum, the adaptive B cell immune response to biomaterial depends on composition and induces local, regional and systemic immunological changes.

2021-12-01 | GSE182633 | GEO

Discerning Biomaterials-driven Transcriptome Dynamics to Induce Mesenchymal Stem Cell Differentiation

Project description:Discerning Biomaterials-driven Transcriptome Dynamics to Induce Mesenchymal Stem Cell Differentiation

| PRJNA795176 | ENA

Transcription profiling by array of MG-63 cells grown on different biomaterials used in bone grafts

Project description:During the past decades, there have been major advances in the field of biomaterials, thereby generating a vast variety of materials for a broad range of tissue engineering and regeneration applications. Although gene expression profiling has been used occasionally in biomaterial research, its usefulness for understanding cell-biomaterial interactions should be further explored for it to fulfill its promise as a tool to assess and improve material properties. Here, the transcriptional landscape induced by 23 materials is explored with a variety of properties within the scope of bone regeneration. An osteoblast cell line is used to identify the gene expression profiles that can be adopted in response to biophysical and chemical cues. It is shown that TGF-beta and WNT signaling may be involved in the cellular response to osteoinductive materials along with differential cell adhesion kinetics via attenuated FAK signaling. The previously reported effect of calcium and phosphate on BMP2 and TGF-beta signaling is confirmed and the biological effect of the addition of nanohydroxyapatite in poly (d,l-lactic acid) polymer particles is studied. Together with future applications, this approach will help researchers understand cellular responses in relation to material properties, which will promote the development of more effective biomaterials for applications in tissue regeneration.

2018-10-05 | E-MTAB-7219 | biostudies-arrayexpress

A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [bulk RNA-seq]

Project description:The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra–/¬– knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses.

2021-08-01 | GSE175888 | GEO

A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq]

2021-08-01 | GSE175889 | GEO

A Comparative Proteomic Study of Decellularized Extracellular Matrix Biomaterials Derived from Porcine Vocal Fold and Small Intestinal Submucosa Tissue Source

Project description:Decellularized extracellular matrix (dECM) is used to make regenerative biomaterials. As the ECM markups vary across organs, derived dECM products may possess different molecular and biological profiles as well. This study aims to compare the proteomic profiles of dECM biomaterials derived from small intestinal submucosa (SIS) and vocal fold (VF) tissue using mass spectrometry-based proteomics.

2023-02-01 | PXD033621 | Pride

Sparse feature selection methods identify unexpected global cellular response to strontium-containing materials

Project description:Despite the increasing sophistication of biomaterials design and functional characterization studies, little is known regarding cells' global response to biomaterials. Here, we combined nontargeted holistic biological and physical science techniques to evaluate how simple strontium ion incorporation within the well-described biomaterial 45S5 bioactive glass (BG) influences the global response of human mesenchymal stem cells. Our objective analyses of whole gene-expression profiles, confirmed by standard molecular biology techniques, revealed that strontium-substituted BG up-regulated the isoprenoid pathway, suggesting an influence on both sterol metabolite synthesis and protein prenylation processes. This up-regulation was accompanied by increases in cellular and membrane cholesterol and lipid raft contents as determined by Raman spectroscopy mapping and total internal reflection fluorescence microscopy analyses and by an increase in cellular content of phosphorylated myosin II light chain. Our unexpected findings of this strong metabolic pathway regulation as a response to biomaterial composition highlight the benefits of discovery-driven nonreductionist approaches to gain a deeper understanding of global cell-material interactions and suggest alternative research routes for evaluating biomaterials to improve their design.

2018-11-25 | E-MTAB-7384 | biostudies-arrayexpress

RNA-Seq analysis used to explore the bone-froming mechanism of microbially catalyzed biomaterials

Project description:We developed a microbial catalytic concept and strategy to prepare calcium carbonate with micro/nanostructures on the surface of bioceramics to improve bone-forming bioactivity. It involves three processes: bacterial adhesion on biomaterials, production of carbonate assisted with bacteria, nucleation and growth of calcium carbonate nano-crystals on the surface of bioceramics. The microbially catalyzed biominerals exhibited relatively uniform micro/nanostructures on both 2D and 3D CaSiO3 bioceramics. The descriptive analysis of RNA-sequencing revealed that the topographic and chemical cues presented by microbially catalyzed micro/nanostructures could stimulate the biological processes including adhesion, proliferation and differentiation. The study offers a microbially catalytic concept and strategy of fabricating micro/nanostructured biomaterials for tissue regeneration.

2020-11-26 | GSE162127 | GEO

Gene expression microrarray of MSC grown on bone inducing scaffolds

Project description:Mesenchymal Stem Cells have been seeded on calcium based biomaterials. Gene expression is evaluated at day 0 (unseeded cells), day 5, and day 10, in order to study differential expressions at different time points and infer if biomaterial induced gene expression variation able to differentiate stem cells towards the osteoblasts lineage.

2016-01-29 | E-MTAB-3440 | biostudies-arrayexpress

miRNA expression microrarray of MSC grown on bone inducing scaffolds

Project description:Mesenchymal Stem Cells have been seeded on calcium based biomaterials. miRNA expression is evaluated at day 0 (unseeded cells), day 5, and day 10, in order to study miRNA differential expressions at different time points and infer if biomaterial induced miRNA expression variation able to differentiate stem cells towards the osteoblasts lineage.

2016-01-29 | E-MTAB-3441 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data