Comparative transcriptomics of epithelial cells grown under static and microfluidic gut-on-chip conditions and benchmarked against human in vivo intestinal cells
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ABSTRACT:
PROVIDER: PRJNA657247 | ENA |
REPOSITORIES: ENA
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Project description:Gut-on-chip devices enable exposure of cells to a continuous flow of culture medium, inducing shear stresses and could thus better recapitulate the in vivo human intestinal environment in an in vitro epithelial model compared to static culture methods. We aimed to study if dynamic culture conditions affect the gene expression of Caco-2 cells cultured statically or dynamically in a gut-on-chip device and how these gene expression patterns compared to that of intestinal segments in vivo. For this we applied whole genome transcriptomics. Dynamic culture conditions led to a total of 5927 differentially expressed genes (3280 upregulated and 2647 downregulated genes) compared to static culture conditions. Gene set enrichment analysis revealed upregulated pathways associated with the immune system, signal transduction and cell growth and death, and downregulated pathways associated with drug metabolism, compound digestion and absorption under dynamic culture conditions. Comparison of the in vitro gene expression data with transcriptome profiles of human in vivo duodenum, jejunum, ileum and colon tissue samples showed similarities in gene expression profiles with intestinal segments. It is concluded that both the static and the dynamic gut-on-chip model are suitable to study human intestinal epithelial responses as an alternative for animal models.
2021-02-08 | GSE156269 | GEO
Project description:Transcriptome profiling of human peritoneal mesothelial cells grown in static and stretching conditions
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Project description:Transcriptome profiling of WT and Cav-1- mouse peritoneal mesothelial cells grown in static and stretching conditions
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Project description:Due to the widespread application of food-relevant inorganic nanomaterials, the gastrointestinal tract is potentially exposed to these materials. Gut-on-chip in vitro model systems are proposed for the investigation of compound toxicity as they better recapitulate the in vivo human intestinal environment than static models, due to the added shear stresses associated with the flow of medium in line with what cells experience in vivo. We aimed to compare the cellular responses of intestinal epithelial Caco-2 cells at the gene expression level upon TiO2 (E171) and ZnO (NM110) nanomaterial exposure when cultured under dynamic and static conditions. For this, we applied whole genome transcriptome analyses. Differentially expressed genes and related biological processes revealed culture condition specific responses upon exposure to TiO2 and ZnO nanomaterials. The materials had more effects on cells cultured in the gut-on-chip when compared to the static model, indicating that shear stress might be a major factor in cell susceptibility. This is the first report on application of a gut-on-chip system to evaluate cellular responses upon TiO2 and ZnO nanomaterials compared to a static system and extends current knowledge on nanomaterial-cell interactions and toxicity assessment. Dynamically cultured cells appear to be more sensitive and the gut-on-chip might thus be an attractive model to be used more extensively in the toxicological hazard characterization.
2022-01-26 | GSE158620 | GEO
Project description:Introduction: Inflammatory bowel disease (IBD) is a complex multi-factorial disease for which physiologically relevant in vitro models are lacking. Existing models are often a compromise between biological relevance and scalability. Here, we integrated intestinal epithelial cells (IEC) derived from human intestinal organoids from 3 different donors in a gut-on-a-chip platform to model the human intestine and key aspects of IBD. The goal of our transcriptomics experiment was to compare microfluidic-grown IEC to donor-paired HIO cultures in standard Matrigel droplets used for gut-on-a-chip seeding. Methods: For the microfluidic gut-on-a-chip, IEC cells were seeded in the top channel of a 3-lane OrganoPlate on top of a Collagen I gel embedded in the middle channel. Cells were kept in HISC medium devoid of A83-01 for 2 days, before medium was switched back to HISC medium. 6 days after seeding, cells were triggered with LPS 100ng/mL, IFN-γ 20ng/mL for 24 hours. RNA was isolated with TRI-reagent followed by a phenol-chloroform extraction. For the static Matrigel-grown HIO, RNA was isolated of confluent cultures with TRI-reagent followed by a phenol-chloroform extraction. Library preparations, sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). rRNA depletion was performed using Ribozero rRNA Removal Kit (Illumina, San Diego, CA, USA). RNA sequencing library preparation used NEBNext Ultra RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (Applied Biosystems, Carlsbad, CA, USA). The sequencing libraries were multiplexed and clustered on one lane of a flowcell and loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a HiSeq 2x150 Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
2020-06-25 | GSE153191 | GEO
Project description:Giantsos-Adams2013 - Growth of glycocalyx
under static conditions
This model is described in the article:
Heparan Sulfate Regrowth
Profiles Under Laminar Shear Flow Following Enzymatic
Degradation.
Giantsos-Adams KM, Koo AJ, Song S,
Sakai J, Sankaran J, Shin JH, Garcia-Cardena G, Dewey CF.
Cell Mol Bioeng 2013 Jun; 6(2):
160-174
Abstract:
The local hemodynamic shear stress waveforms present in an
artery dictate the endothelial cell phenotype. The observed
decrease of the apical glycocalyx layer on the endothelium in
atheroprone regions of the circulation suggests that the
glycocalyx may have a central role in determining
atherosclerotic plaque formation. However, the kinetics for the
cells' ability to adapt its glycocalyx to the environment have
not been quantitatively resolved. Here we report that the
heparan sulfate component of the glycocalyx of HUVECs increases
by 1.4-fold following the onset of high shear stress, compared
to static cultured cells, with a time constant of 19 h.
Cell morphology experiments show that 12 h are required
for the cells to elongate, but only after 36 h have the
cells reached maximal alignment to the flow vector. Our
findings demonstrate that following enzymatic degradation,
heparan sulfate is restored to the cell surface within
12 h under flow whereas the time required is 20 h
under static conditions. We also propose a model describing the
contribution of endocytosis and exocytosis to apical heparan
sulfate expression. The change in HS regrowth kinetics from
static to high-shear EC phenotype implies a differential in the
rate of endocytic and exocytic membrane turnover.
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2024-09-02 | BIOMD0000000830 | BioModels
Project description:We developed the microfluidic-oscillatory-washing-based ChIP-Seq (MOWChIP-Seq) protocol. We achieved genome-wide mapping of histone modifications (H3K4me3 and H3K27ac) with as few as 100 cells. Moreover, the automated microfluidic platform dramatically reduced assay time and has a potential for future scale-up.
2015-07-21 | GSE65516 | GEO
Project description:Gut-on-chip devices enable exposure of cells to a continuous flow of culture medium, inducing shear stresses and could thus better recapitulate the in vivo human intestinal environment in an in vitro epithelial model compared to static culture methods. We aimed to study if dynamic culture conditions affect the gene expression of Caco-2 cells cultured statically or dynamically in a gut-on-chip device and how these gene expression patterns compared to that of intestinal segments in vivo. For this we applied whole genome transcriptomics. Dynamic culture conditions led to a total of 5927 differentially expressed genes (3280 upregulated and 2647 downregulated genes) compared to static culture conditions. Gene set enrichment analysis revealed upregulated pathways associated with the immune system, signal transduction and cell growth and death, and downregulated pathways associated with drug metabolism, compound digestion and absorption under dynamic culture conditions. Comparison of the in vitro gene expression data with transcriptome profiles of human in vivo duodenum, jejunum, ileum and colon tissue samples showed similarities in gene expression profiles with intestinal segments. It is concluded that both the static and the dynamic gut-on-chip model are suitable to study human intestinal epithelial responses as an alternative for animal models.
| S-EPMC7864925 | biostudies-literature
Project description:Laminar shear stress due to constant blood flow is known to play a critical role in maintaining vascular health. In contrast, endothelial cell senescence appears to be closely associated with the incidence of vascular disorder. In an attempt to identify functional biomarkers for age-related vascular health/disease, the present study investigated differential gene expression of young and senescent human umbilical vein endothelial cells (HUVECs) under static and laminar shear stress. We used a cDNA microarray method to compare gene expression profiles of young and senescent HUVECs under static and laminar shear stress conditions. Keywords: stress response, age state analysis
2009-05-23 | GSE13712 | GEO