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Widespread Changes in Transcriptome Profile of Human Mesenchymal Stem Cells Induced by Two-Dimensional (2D) Nanosilicates

ABSTRACT: Widespread Changes in Transcriptome Profile of Human Mesenchymal Stem Cells Induced by Two-Dimensional (2D) Nanosilicates

PROVIDER: PRJNA427920 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6431450.fastq.gz	Fastqsanger.gz
	SRR6431451.fastq.gz	Fastqsanger.gz
	SRR6431452.fastq.gz	Fastqsanger.gz
	SRR6431453.fastq.gz	Fastqsanger.gz

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Widespread Changes in Transcriptome Profile of Human Mesenchymal Stem Cells Induced by Two-Dimensional (2D) Nanosilicates

Project description:Two-dimensional (2D) nanomaterials, an ultrathin class of materials such as graphene, nanoclays, transition metal dichalcogenides (TMDs), and transition metal oxides (TMOs), have emerged as a new generation of materials due to their unique properties relative to macroscale counterparts. However, little is known about the transcriptome dynamics following exposure to these nanomaterials. Here we investigate the interactions of 2D nanosilicates, a layered clay, with human mesenchymal stem cells (hMSCs) at the whole transcriptome level by high-throughput sequencing (RNA-seq). Analysis of cell-nanosilicate interactions by monitoring change in transcriptome profile uncovers key biophysical and biochemical cellular pathways triggered by nanosilicates. A widespread alteration of genes is observed due to nanosilicate exposure as more than 4,000 genes are differentially expressed. The change in mRNA expression levels reveal clathrin-mediated endocytosis of nanosilicates. Nanosilicate attachment to cell membrane and subsequent cellular internalization activate stress-responsive pathways such as mitogen activated protein kinase (MAPK), which subsequently directs hMSC differentiation towards osteogenic and chondrogenic lineages. This study provides transcriptomic insight on the role of surface-mediated cellular signaling triggered by nanomaterials and enables development of nanomaterials-based therapeutics for regenerative medicine. This approach in understanding nanomaterial-cell interactions, illustrates how change in transcriptomic profile can predict downstream effects following nanomaterial treatment.

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The differences in miRNA expression with miRNA microarrays of two-dimensional (2D)- and three-dimensional (3D)-SNP cells

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Gene expression analysis of MCF7 breast cancer cells cultured as xenografts, in two dimensional cultures, in polyHEMA anchorage independent three dimansional cell culture models and in Matrigel three dimensional cultures.

Project description:The traditional method for studying cancer in vitro is to grow immortalized cancer cells in two-dimensional (2D) monolayers on plastic. However, many cellular features are impaired in these unnatural conditions and big alterations in gene expression in comparison to tumors have been reported. Three-dimensional (3D) cell culture models have become increasingly popular and are suggested to be better models than 2D monolayers due to improved cell-to-cell contacts and structures that resemble in vivo architecture. The aim of this study was to compare gene expression patterns of MCF7 breast cancer cells when grown as xenografts, in 2D, in polyHEMA coated anchorage independent 3D models and in Matrigel on-top 3D cell culture models. Surprisingly small variations in gene expression patterns were observed between the models indicating that 3D and xenograft are not always that different from 2D cell cultures. Gene expression analysis of MCF7 breast cancer cells cultured as xenografts for 43 days, in two dimensional cultures for seven days (2D7d), in polyHEMA three dimensional cell culture models for four and seven days (PH7d and PH7d), and in Matrigel three dimensional cultures for four and seven days (MG4d and MG7d). Two biological replicates was included for each sample.

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Project description:3D cultivation of cells lead to changes in morphology of the cells. This is likely to explain the higher radioresistance of cells growing in 3D compared to cells growing in 2D cell culture. Whole genome gene expression is performed to determine genes involved in changes of cell moroholgy and radioresistance. Keywords: comparison of 2D vs. 3D cell culture RNA of cells was isolated four days after growing in the two different cell culture systems

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Gene expression profile of A549 cells cultured with normal 2D condition and xenografted tumor tissue

Project description:Preclinical cancer drug discovery efforts have employed two-dimensional (2D)-cell-based assay models, which fail to forecast in vivo efficacy and contribute to a lower success rates of clinical approval. Three-dimensional (3D) cell culture models are recently expected to bridge the gap between 2D and in vivo models. We compared between A549 cells cultured in ordinal 2D condition and xenografted tumor tissue. Gene microarrays were used to observe the global gene expression in A549 cells cultured with petri dish (2D, control) or xenografted tumor tissue and identified distinct classes of up or down-regulated genes.

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Expression data of two human cancer cell lines cultivated in 2-dimensional (2D) vs. 3-dimensional (3D) cell culture

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Project description:Canine mammary gland tumors can be used as predictive models for human breast cancer. There are several types of microRNAs common in human breast cancer and canine mammary gland tumors. The functions of microRNAs in canine mammary gland tumors are not well understood. In the present study, we compared the characterization of microRNA expression in two-dimensional and three-dimensional canine mammary gland tumor cell models. The expression of microRNA-210 in the three-dimensional-SNP cells was 10.19 times higher than that in the two-dimensional-SNP cells.

2022-07-07 | GSE203410 | GEO

Widespread changes in transcriptome profile of human mesenchymal stem cells induced by two-dimensional nanosilicates.

Project description:Two-dimensional nanomaterials, an ultrathin class of materials such as graphene, nanoclays, transition metal dichalcogenides (TMDs), and transition metal oxides (TMOs), have emerged as a new generation of materials due to their unique properties relative to macroscale counterparts. However, little is known about the transcriptome dynamics following exposure to these nanomaterials. Here, we investigate the interactions of 2D nanosilicates, a layered clay, with human mesenchymal stem cells (hMSCs) at the whole-transcriptome level by high-throughput sequencing (RNA-seq). Analysis of cell-nanosilicate interactions by monitoring changes in transcriptome profile uncovered key biophysical and biochemical cellular pathways triggered by nanosilicates. A widespread alteration of genes was observed due to nanosilicate exposure as more than 4,000 genes were differentially expressed. The change in mRNA expression levels revealed clathrin-mediated endocytosis of nanosilicates. Nanosilicate attachment to the cell membrane and subsequent cellular internalization activated stress-responsive pathways such as mitogen-activated protein kinase (MAPK), which subsequently directed hMSC differentiation toward osteogenic and chondrogenic lineages. This study provides transcriptomic insight on the role of surface-mediated cellular signaling triggered by nanomaterials and enables development of nanomaterials-based therapeutics for regenerative medicine. This approach in understanding nanomaterial-cell interactions illustrates how change in transcriptomic profile can predict downstream effects following nanomaterial treatment.

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Madin-Darby Canine Kidney (MDCK) cells grown in 2-dimensional and 3-dimensional type I collagen culture.

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