Single cell transcriptional profiling of mouse molar and incisor tooth assembloids
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Mus musculus
SUBMITTER: Florian Hermans
PROVIDER: E-MTAB-12544 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Knowledge on tooth epithelial stem cells and corresponding biology in humans is sparse. Here, we developed an organoid model, typically replicating epithelial tissue stem cell biology, starting from human tooth. Dental follicle (DF), isolated from extracted wisdom teeth, efficiently generated long-term expandable epithelial organoids. The organoids displayed a tooth stemness phenotype as present in DF’s Epithelial Cell Rests of Malassez, a compartment deemed to contain tooth epithelial stem cells. To further decode the organoids in more granular detail, we applied scRNA-seq analysis on DF-derived organoids (passage 1 (P1) and P4) together with their primary tissue. Additionally, to decipher the amelogenesis-resembling process that takes place in the tooth organoids upon differentiation, we performed scRNA-seq analysis of P4 organoids switched to mineralization-inducing medium for 8 days.
2022-04-01 | E-MTAB-10596 | biostudies-arrayexpress
Project description:Embryologically the tooth is derived from both the ectoderm and neural crest (ectomesenchyme). It is often used as a model to study how epithelialmesenchymal interactions can control differentiation and morphogenesis. During early development organs of ectodermal origin share both a set of signalling molecules and exhibit common morphological features, subsequently proceeding along separate developmental programs.<br><br>Tooth development is a continuous process that can be divided into the initiation -, bud -, cap -, and bell-stages. In mice, tooth development begins at embryonic day 11.5 (E11.5), by thickening of the dental epithelium, while mineralization of enamel and dentin in first molar starts at postnatal day 0 (P0) (5). A multistep and complex process of the gene expression are involved in the early stage of tooth development. So far expression of more than 1300 genes and/or proteins have been detected during tooth germ development by microarrays/immunocytochemistry/in situ hybridization. Studies with mutant mice have identified a number of genes that regulate tooth development and morphology. For example, deficiency of Lef-1 or P63 arrests tooth development at early stages. Deficiency of Msx1 or Pax9 results in arrest of tooth development at the bud stage , while deficiency of Runx2/Cbfa1 or Sp3 inhibits cyto-differentiation of ameloblasts and/or odontoblasts. Shh is required for normal growth and morphogenesis, but is not essential for cyto-differentiation of the ameloblast and odontoblast populations. Ameloblastin and amelogenin knock-out mice develop severe enamel hypoplasia with abnormal ameloblast differentiation. <br><br>Recently, new connections between retinoid metabolism and PPAR responses have been identified. It has also been shown that endogenous retinoic acid is necessary for the initiation of odontogenesis , and that some of the genes that catalyze the oxidation of retinaldehyde into retinoic acid, exhibit distinct patterns of expression in developing murine teeth. Little is known about functions of PPAR-a as regards tooth germs or mature teeth. It is, however, likely that mitochondrial oxidative metabolism well as fatty acid metabolism is enhanced in late odontogenesis. These are metabolic activities which in other tissues are stimulated by PPAR-a agonists.<br><br>For this reason it was of interest to carry out comparative gene expression profiling of the first molar tooth germs of PPAR-a knock-out mouse and of the corresponding wild-type mice. The results suggest marked differences in gene expression, parts of which may be associated with an observed hypomineralization of enamel in the mature PPAR-a knock-out murine tooth.
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Project description:The global gene expression of murine tooth germs dissected at various stages of tooth development was investigated. A list of genes differentialy expressed throughout the various time points was submitted to bioinformatic analysis using Ingenuity Pathway Analysis (IPA) to identify significant associations between clusters of genes found to be differentially expressed and signalling or canonical pathways or molecular/cellular functions. This approach was also used with clusters of genes isolated using the profile search function of Spotfire.). The study entailed a total of 58 dual-labeled/two-chanel microarrays.The results, encompassing at least triplicate microarray data at each time-point, were treated as single colored arrays. The resulting expression data was subsequently assembled into a single data file, facilitating analysis of the time-course of expression profiles of expressed genes.
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Project description:Study of changes in gene expression in mouse tooth germs between E15.5 and 21.5dpc
2007-04-01 | E-MEXP-947 | biostudies-arrayexpress
Project description:The goals of this study are to identify in vivo downstream targets of Yap through NGS-derived tooth germ transcriptome profiling. The mRNA profiles of wild-type, Yap conditional knockout (CKO) and YAP transgenic (Tg) mouse tooth germs at embryonic day 14.5 were generated by deep sequencing using Illumina Hiseq2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level via DNAnexus. The validation was performed through qRT–PCR and in situ hybrydization. A set of Hox genes were differentially expression in Yap CKO and YAP Tg mouse tooth germs, demonstating concurrent expression changes with Yap transcripts. This study provides a platform to systematically identify in vivo downstream targets of genes of interest. The mRNA profiles of wild type, Yap CKO and YAP Tg mouse tooth germs at embryonic day 14.5 were generated by deep sequencing using Illumina Hiseq.
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Project description:Sex of individuals, estimated on human remains, is important information in anthropological, archaeological and forensic researches. In forensic anthropology, this is one of the key points for identifying a person. In archeology and paleoanthropology, information about sex is important for reconstructing the social and biological structure of a group, lifestyle, and for modeling demographic and growth processes in the past. Sex estimation of adult individuals is possible according to morphological criteria when metric and descriptive features are used. In case of poor preservation of the adult skeletons, as well as on children's remains, sex estimation by morphological criteria has some limitations. Therefore regular attempts are made to attract alternative methods for sexing human remains. As one of such methods a liquid chromatography-mass spectrometry analysis of tooth enamel peptides can be used. The result of this analysis is the identification of certain fragments of amelogenins - the main structural proteins of the organic matrix of tooth enamel, which make up more than 90% of its protein content. Amelogenin genes are located on both the X- and Y-chromosomes and the products of these genes have structural differences that allow them to be differentiated from each other. In the process of maturation of tooth enamel, its protein matrix undergoes proteolytic degradation, as a result enamel already contains proteins in the form of their peptide fragments. Reliable and reproducible detection of unique peptide fragments of amelogenins encoded on the X- and Y-chromosomes in human enamel will make it possible to estimate sex of human remains. The work presents a peptidomic analysis of tooth enamel using chromatography-mass spectrometry. Experiments were carried out on a series of teeth of various archaeological data, tafonomic condition of crown and different biological generations of teeth (deciduous and permanent ones).
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Project description:The RSK2 gene is responsible for Coffin-Lowry syndrome, an X-linked monogenic disease associating severe learning deficit andassociated to typical facial and digital abnormalities and skeletal changes. Craniofacial and dental anomalies encountered in this rare disease have been poorly characterized. In this study we explore, through X-Ray microtomographic analysis, the variable craniofacial dysmorphism and dental anomalies present in Rsk2 knockout mice, an animal model of Coffin-Lowry syndrome, as well as in triple Rsk1,2,3 knockout mutants. We report in these mutants the occurrence of a surpernumerary tooth mesial to the first molar. This highly penetrant phenotype is considered as a remnant of evolutionary lost teeth. This possibly leads to the significant reduction of the maxillary diastema. Abnormalities of molar shape were almost restricted to the mesial part of both upper and lower first molars (M1). We also report an expression analysis of the four Rsk genes (Rsk1, 2, 3 and 4) at various stages of odontogenesis in wild-type (WT) mice. Rsk2 was mainly expressed in the mesenchymal, neural crest derived compartment, correlating with proliferative areas of the developing teeth and consistent with a biological function of RSK2 in cell cycle control and cell growth, which when invalidated could be responsible for the dental phenotype. In an attempt to unravel the molecular pathways involved in the genesis of these dental defects, we performed a comparative transcriptomic (DNA microarray) analysis of mandibular wild-type versus Rsk2-/Y molars, and further demonstrated a misregulation of selected genes, using a Rsk2 shRNA knock-down strategy in molar tooth germs cultured in vitro.
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