Expression data from Neural Progenitor cells cultured on 2D flat surfaces and in 3D scaffolds
Ontology highlight
ABSTRACT: A genomic expression comparison was done among neural progenitor cells cultured on 2D substrates, 3D porous polystyrene scaffolds, and as 3D neural spheres (in vivo surrogate), with the goal of assessing the feasibility of establishing the meaning of 3D and associated physiological relevance at the molecular level Neural progenitor cells were cultured on 2D surfaces, in 3D scaffolds and as 3D neural spheres. Chemical cues are controlled by coating. Only spacial properties of the culture systems were compared.
Project description:A genomic expression comparison was done among neural progenitor cells cultured on 2D substrates, 3D porous polystyrene scaffolds, and as 3D neural spheres (in vivo surrogate), with the goal of assessing the feasibility of establishing the meaning of 3D and associated physiological relevance at the molecular level
Project description:A transcriptomic expression comparison was done among superior cervical ganglion (SCG) cells cultured on 2D substrates, 3D porous polystyrene scaffolds, and in freshly dissected tissue (in vivo surrogate), with the goal of assessing the feasibility of establishing the meaning of 3D and associated physiological relevance at the molecular level SCG cells were cultured on 2D surfaces and in 3D scaffolds. Chemical cues are controlled by coating. Only spacial properties of the culture systems were compared. Cells from freshly dissected tissue were used as in vivo surrogates for positive control of 3D cells.
Project description:A transcriptomic expression comparison was done among superior cervical ganglion (SCG) cells cultured on 2D substrates, 3D porous polystyrene scaffolds, and in freshly dissected tissue (in vivo surrogate), with the goal of assessing the feasibility of establishing the meaning of 3D and associated physiological relevance at the molecular level
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.
Project description:Microarray analysis was used to evaluate expression differences from a single donor human bone marrow stromal cells (hBMSCs) as a function of varied polymer-based tissue engineering scaffolds. These scaffolds include polycaprolactone (PCL) nanofibers (PCL_NF), films (PCL_SC), poly D,L-lactic acid (PDLLA) nanofibers (PDLLA_NF), films (PDLLA_SC), tissue culture polystyrene (TCPS) and TCPS with osteogenic supplements (TCPS_OS). The results revealed that scaffold structure was able to significantly affect gene expression, with nanofiber scaffolds inducing similar gene expression patterns to hBMCSs cultured with osteogenic media. A library of scaffolds prepared from polycaprolactone or poly D,L-lactic acid was sythesized and cultured with hBMSCs for 14 days with RNA extracted from cells on Day 1 and Day 14. Gene expression analysis was performed using BRB ArrayTools. SC = spun coat, BNF = big nanofiber, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements. This data forms is part of a pending publication: Baker et al. Ontology Analysis of Global Gene Expression Differences of Human Bone Marrow Stromal Cells Cultured on 3D Scaffolds or 2D Films and is a subset of the 72 array data referenced in ( Kumar et al. The determination of stem cell fate by 3D scaffold structures through the control of cell shape, Biomaterials (2011) 32, 9188-9196.) The 72 array data set is submitted separately to GEO as GSE50743.
Project description:Microarray analysis was used to evaluate expression differences from a single donor human bone marrow stromal cells (hBMSCs) as a function of varied polymer-based tissue engineering scaffolds. The results revealed that gene expression patterns of hBMSCs grouped according to scaffold. A library of scaffolds prepared from polycaprolactone (PCL) or poly D,L-lactic acid (PDLLA) was sythesized and cultured with hBMSCs for 14 days with RNA extracted from cells on Day 1 and Day 14. Gene expression analysis was performed using BRB ArrayTools. GF = gas foam, SC = spun coat, BNF = big nanofiber, SNF = small nanofiber, FFF = free-form fabricated, TCPS = tissue culture polystyrene, TCPS+OS = tissue culture polystyrene with osteogenic supplements. The 72 arrays data was used previously in the publication: Kumar et al. The determination of stem cell fate by 3D scaffold structures through the control of cell shape, Biomaterials (2011) 32, 9188-9196. A companion data set of 24 arrays was submitted separately to GEO as GSE50744 and will be referenced to Baker et al. Ontology Analysis of Global Gene Expression Differences of Human Bone Marrow Stromal Cells Cultured on 3D Scaffolds or 2D Films
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.
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.
Project description:In this study, RNA sequencing was employed to investigate the differences in gene expression levels and patterns of cells recruited into suture-bony combined calvarial injury following the implatation of distinct types of commonly used calvarial scaffolds including gelatin methacryloyl hydrogel (GelMA), porous chitosan scaffold (CTS), and polylactic acid eletrospinning membrane (PLA).