The long non-coding RNA, miRNA, and mRNA landscapes of cementoblasts during cementogenesis
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE207259 | GEO | 2025/06/01
REPOSITORIES: GEO
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Project description:Cementoblasts are cells that line the surface of the tooth root and produce a mineralized tissue known as cementum. Cementum is critical for attachment of the tooth to the adjacent periodontal ligament and has a similar biochemical composition to bone, however it differs in that it lacks vasculature and innervation, and does not undergo remodelling. It has been difficult to define markers that specifically identify cementoblasts. In order to compare the transcriptome of fully developed cementoblasts with neural crest derived (calvarial) osteoblasts in vivo, we used osteocalcin-GFP (OC-GFP) mice. Cells were isolated by digestion of calvaria (osteoblasts) or extracted molars (cementoblasts) and purified by FACS sorting for GFP positive cells before RNA extraction and microarray analysis.
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2013-02-15 | E-GEOD-29898 | biostudies-arrayexpress
Project description:Background: Long non-coding RNAs (lncRNAs) are increasingly implicated as gene regulators and may ultimately be more numerous than protein-coding genes in the human genome. Despite large numbers of reported lncRNAs, reference annotations are likely incomplete due to their lower and tighter tissue-specific expression compared to mRNAs. An unexplored factor potentially confounding lncRNA identification is inter-individual expression variability. Here, we characterize lncRNA natural expression variability in human primary granulocytes. Results: We annotate granulocyte lncRNAs and mRNAs in RNA-seq data from ten healthy individuals, identifying multiple lncRNAs absent from reference annotations, and use this to investigate three known features (higher tissue-specificity, lower expression, and reduced splicing efficiency) of lncRNAs relative to mRNAs. Expression variability was examined in seven individuals sampled three times at one or more than one month intervals. We show that lncRNAs display significantly more inter-individual expression variability compared to mRNAs. We confirm this finding in 2 independent human datasets by analyzing multiple tissues from the GTEx project and lymphoblastoid cell lines from the GEUVADIS project. Using the latter dataset we also show that including more human donors into the transcriptome annotation pipeline allows identification of an increasing number of lncRNAs, but minimally affects mRNA gene number. Conclusions: A comprehensive annotation of lncRNAs is known to require an approach that is sensitive to low and tight tissue-specific expression. Here we show that increased inter-individual expression variability is an additional general lncRNA feature to consider when creating a comprehensive annotation of human lncRNAs or proposing their use as prognostic or disease markers. We used PolyA+ RNA-seq data from human primary granulocytes of 10 healthy individuals to de novo annotate lncRNAs and mRNAs in this cell type and ribosomal depleted (total) RNA-seq data from seven of these individuals sampled three times to analyze lncRNA amd mRNA expression variability
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Project description:Cementum is a specialized mineralized tissue that covers the tooth root surface and anchors the tooth to the surrounding periodontal ligament. The coronal acellular cementum (AC) is indispensable for periodontal attachment and represents a key target for periodontal regenerative therapies. However, the developmental origin and molecular identity of AC-forming cementoblasts remain poorly understood. Here, through an integrated spatial and single-cell transcriptomic analysis, we identify AC-forming cementoblasts as a distinct population of noncanonical mineralizing cells enriched for cell-matrix organization and Wnt signaling signatures, distinguishing them from cellular cementum-forming cementoblasts localized in the apical portion. Lineage tracing using a Wnt inhibitory factor 1 (Wif1-creER) demonstrates that AC-forming cementoblasts originate exclusively from peri-epithelial apical Wif1+ cells of the elongating tooth root via canonical Wnt signaling activation. Collectively, our findings uncover the unique ontogeny and molecular signature of acellular cementum, providing insights into the formation and maintenance of the periodontal attachment apparatus.
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Project description:Aberrant expression of LncRNAs might be responsible for the HCC invasion and metastasis. we employed the LncRNAs microarray technology to study the LncRNAs expression profiles at genome-wide in hepatocellular carcinoma (HCC)tissue samples with early recurrence (less than 1 year, with invasion and metastasis out of liver) and late recurrence (longer than 2 years, without invasion and metastasis out of liver), which had different recurrent/metastatic potentials, by using normal liver tissue as control to screen the dysregulated LncRNAs which are potentially involved in the recurrence, invasion and metastasis process of HCC
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Project description:Cementum is a specialized mineralized tissue that covers the tooth root surface and anchors the tooth to the surrounding periodontal ligament. The coronal acellular cementum (AC) is indispensable for periodontal attachment and represents a key target for periodontal regenerative therapies. However, the developmental origin and molecular identity of AC-forming cementoblasts remain poorly understood. Here, through an integrated spatial and single-cell transcriptomic analysis, we identify AC-forming cementoblasts as a distinct population of noncanonical mineralizing cells enriched for cell-matrix organization and Wnt signaling signatures, distinguishing them from cellular cementum-forming cementoblasts localized in the apical portion. Lineage tracing using a Wnt inhibitory factor 1 (Wif1-creER) demonstrates that AC-forming cementoblasts originate exclusively from peri-epithelial apical Wif1+ cells of the elongating tooth root via canonical Wnt signaling activation. Collectively, our findings uncover the unique ontogeny and molecular signature of acellular cementum, providing insights into the formation and maintenance of the periodontal attachment apparatus.
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