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Differential LncRNA/mRNA expression profiling and functional network analyses in BMP2 deletion of mouse dental papilla cells

ABSTRACT: Differential LncRNA/mRNA expression profiling and functional network analyses in BMP2 deletion of mouse dental papilla cells

PROVIDER: PRJNA729791 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14530581.fastq.gz	Fastqsanger.gz
	SRR14530582.fastq.gz	Fastqsanger.gz
	SRR14530583.fastq.gz	Fastqsanger.gz
	SRR14530584.fastq.gz	Fastqsanger.gz
	SRR14530585.fastq.gz	Fastqsanger.gz

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Differential LncRNA/mRNA expression profiling and functional network analyses in BMP2 deletion of mouse dental papilla cells

Project description:We examined the transcriptional changes of the dental papilla mesenchymal cells of Bmp2 floxed/floxed and knock out mice by performing global transcriptome analysis. Total RNAs were isolated from the Bmp2 floxed/floxed and knock out cells for 8h, 48h and 72h and were utilized for RNA-seq. Our results showed that different gene expression of coding RNAs and non-coding RNAs was observed and involved in cell cycle, transcriptional regulation and developmentally relevant signaling pathways.

2022-01-12 | GSE174429 | GEO

Differential lncRNA/mRNA Expression Profiling and Functional Network Analyses in Bmp2 Deletion of Mouse Dental Papilla Cells.

Project description:Bmp2 is essential for dentin development and formation. Bmp2 conditional knock-out (KO) mice display a similar tooth phenotype of dentinogenesis imperfecta (DGI). To elucidate a foundation for subsequent functional studies of cross talk between mRNAs and lncRNAs in Bmp2-mediated dentinogenesis, we investigated the profiling of lncRNAs and mRNAs using immortalized mouse dental Bmp2 flox/flox (iBmp2fx/fx) and Bmp2 knock-out (iBmp2ko/ko) papilla cells. RNA sequencing was implemented to study the expression of the lncRNAs and mRNAs. Quantitative real-time PCR (RT-qPCR) was used to validate expressions of lncRNAs and mRNAs. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to predict functions of differentially expressed genes (DEGs). Protein-protein interaction (PPI) and lncRNA-mRNA co-expression network were analyzed by using bioinformatics methods. As a result, a total of 22 differentially expressed lncRNAs (16 downregulated vs 6 upregulated) and 227 differentially expressed mRNAs (133 downregulated vs. 94 upregulated) were identified in the iBmp2ko/ko cells compared with those of the iBmp2fx/fx cells. RT-qPCR results showed significantly differential expressions of several lncRNAs and mRNAs which were consistent with the RNA-seq data. GO and KEGG analyses showed differentially expressed genes were closely related to cell differentiation, transcriptional regulation, and developmentally relevant signaling pathways. Moreover, network-based bioinformatics analysis depicted the co-expression network between lncRNAs and mRNAs regulated by Bmp2 in mouse dental papilla cells and symmetrically analyzed the effect of Bmp2 during dentinogenesis via coding and non-coding RNA signaling.

| S-EPMC8727545 | biostudies-literature

Gene expression profiles of dental follicle cells after 7 days of differentiation in vitro with BMP2, IGF2 and dexamethasone

Project description:We analysed gene expression profiles in dental follicle cells after 7 days of osteogenic differentiation with different inducers. Total RNAs were isolated from dental follicle cells after 7 days of differentiation with dexamethasone, BMP2, IGF2 and for control with standard cell culture medium

2010-11-10 | E-GEOD-20963 | biostudies-arrayexpress

Comparative gene expression profiles of dental follicleand and papilla tissues at E17 and PN2

Project description:The aim of this study was to determine the differences in dental follicle and papilla tissues of mouse first lower molar between E17 and PN2 at the molecular level by combinational use of laser microdissection and microarray. Two-condition experiment

2017-03-30 | GSE97180 | GEO

A fine-tuned regulation of Bmp2 by Nodal/TGFβ signalling induced lncRNA-Smad7

Project description:The transforming growth factor beta (TGF-β) superfamily proteins are potent regulators of cellular development and differentiation. Long non-coding RNAs (lncRNAs) play widespread roles in spatial-temporal regulation of early development. However, the roles of lncRNAs regulated by nodal/TGF-β signaling is still elusive. Here, we showed a nodal-driven Smad induced lncRNA in mouse embryonic stem cells (mESCs), lncRNA-Smad7, which is divergently transcribed to Smad7, regulates cell fate determination through repressing Bmp2. Depletion of lncRNA-Smad7 dramatically impairs cardiomyocyte differentiation in mESCs. Moreover, LncRNA-Smad7 represses Bmp2 expression and binds at the promoter region of Bmp2. Importantly, knock-down Bmp2 rescues the defect of cardiomyocyte differentiation. Hence, we showed that lncRNA-Smad7 is antagonistic to BMP signaling in mESCs. Furthermore, lncRNA-Smad7 regulates cell fate determination between osteocytes and myocytes formation in C2C12 cells by repressing Bmp2. Thus, we provide new insights regarding the antagonistic effects between nodal/TGF-β and BMP signaling via lncRNA-Smad7.

2022-10-19 | GSE178136 | GEO

The human dental apical papilla promotes spinal cord repair through a paracrine mechanism

Project description:Traumatic spinal cord injury is an overwhelming condition that strongly and suddenly impacts the patient’s life and her/his entourage. There are currently no predictable treatments to repair the spinal cord, while many strategies are proposed and evaluated by researchers throughout the world. One of the most promising avenues is the transplantation of stem cells, although its therapeutic efficiency is limited by several factors, among which cell survival at the lesion site. In our previous study, we showed that the implantation of a human dental apical papilla, residence of stem cells of the apical papilla (SCAP), supported functional recovery in a rat model of spinal cord hemisection.

2021-12-20 | GSE191140 | GEO

Expression data from human dental follicle cells

Project description:We analysed the genexpression of dental follicle cells (DFCs) after 3 days osteogenic differentiation with BMP2 after transfection with a DLX3 plasmid (pDLX3) and after transfection with an empty plasmid (pEV) Total RNAs were isolated from dental follicle cells after transfection with pDLX3 and pEV and osteogenic induction with BMP2 at day 3

2014-08-01 | E-GEOD-59949 | biostudies-arrayexpress

Expression data from human dental follicle cells

2014-08-01 | GSE59949 | GEO

BCOR-regulated genes in human oculo-facio-cardio-dental syndrome

Project description:Oculo-facio-cardio-dental syndrome (OFCD) is a rare genetic disorder characterized by teeth with extremely long roots (radiculomegaly), and craniofacial, eye and cardiac abnormalities. The mutation of the transcriptional co-repressor BCOR has been identified as being responsible for oculo-facio-cardio-dental (OFCD) syndrome. Mesenchymal stem cells (MSCs) is isolated from the root apical papilla of an OFCD patient. Gene expression profiling is performed and compared between mutant MSCs and wild type MSCs. Total RNA were extracted from normal MSCs (MSCWT) and mutant MSCs (MSCO).

2009-07-23 | E-GEOD-15214 | biostudies-arrayexpress

Immortalized mouse floxed Bmp2 dental papilla mesenchymal cell lines preserve odontoblastic phenotype and respond to BMP2.

Project description:Bone morphogenetic protein 2 (Bmp2) is essential for odontogensis and dentin mineralization. Generation of floxed Bmp2 dental mesenchymal cell lines is a valuable application for studying the effects of Bmp2 on dental mesenchymal cell differentiation and its signaling pathways during dentinogenesis. Limitation of the primary culture of dental mesenchymal cells has led to the development of cell lines that serve as good surrogate models for the study of dental mesenchymal cell differentiation into odontoblasts and mineralization. In this study, we established and characterized immortalized mouse floxed Bmp2 dental papilla mesenchymal cell lines, which were isolated from 1st mouse mandibular molars at postnatal day 1 and immortalized with pSV40 and clonally selected. These transfected cell lines were characterized by RT-PCR, immunohistochemistry, and analyzed for alkaline phosphatase activity and mineralization nodule formation. One of these immortalized cell lines, iBmp2-dp, displayed a higher proliferation rate, but retained the genotypic and phenotypic characteristics similar to primary cells as determined by expression of tooth-specific markers as well as demonstrated the ability to differentiate and form mineralized nodules. In addition, iBmp2-dp cells were inducible and responded to BMP2 stimulation. Thus, we for the first time described the establishment of an immortalized mouse floxed Bmp2 dental papilla mesenchyma cell line that might be used for studying the mechanisms of dental cell differentiation and dentin mineralization mediated by Bmp2 and other growth factor signaling pathways.

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