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Single cell RNA sequencing reveals mesenchymal heterogeneity and critical functions of Cd271 in tooth development

BACKGROUND: Accumulating evidence suggests that the maxillary process, to which cranial crest cells migrate, is essential to tooth development. Emerging studies indicate that Cd271 plays an essential role in odontogenesis. However, the underlying mechanisms have yet to be elucidated. AIM: To establi...

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Autores principales: Zhang, Yan-Yan, Li, Feng, Zeng, Xiao-Ke, Zou, Yan-Hui, Zhu, Bing-Bing, Ye, Jia-Jia, Zhang, Yun-Xiao, Jin, Qiu, Nie, Xin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Baishideng Publishing Group Inc 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10324503/
https://www.ncbi.nlm.nih.gov/pubmed/37424952
http://dx.doi.org/10.4252/wjsc.v15.i6.589
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author Zhang, Yan-Yan
Li, Feng
Zeng, Xiao-Ke
Zou, Yan-Hui
Zhu, Bing-Bing
Ye, Jia-Jia
Zhang, Yun-Xiao
Jin, Qiu
Nie, Xin
author_facet Zhang, Yan-Yan
Li, Feng
Zeng, Xiao-Ke
Zou, Yan-Hui
Zhu, Bing-Bing
Ye, Jia-Jia
Zhang, Yun-Xiao
Jin, Qiu
Nie, Xin
author_sort Zhang, Yan-Yan
collection PubMed
description BACKGROUND: Accumulating evidence suggests that the maxillary process, to which cranial crest cells migrate, is essential to tooth development. Emerging studies indicate that Cd271 plays an essential role in odontogenesis. However, the underlying mechanisms have yet to be elucidated. AIM: To establish the functionally heterogeneous population in the maxillary process, elucidate the effects of Cd271 deficiency on gene expression differences. METHODS: p75NTR knockout (Cd271(-/-)) mice (from American Jackson laboratory) were used to collect the maxillofacial process tissue of p75NTR knockout mice, and the wild-type maxillofacial process of the same pregnant mouse wild was used as control. After single cell suspension, the cDNA was prepared by loading the single cell suspension into the 10x Genomics Chromium system to be sequenced by NovaSeq6000 sequencing system. Finally, the sequencing data in Fastq format were obtained. The FastQC software is used to evaluate the quality of data and CellRanger analyzed the data. The gene expression matrix is read by R software, and Seurat is used to control and standardize the data, reduce the dimension and cluster. We search for marker genes for subgroup annotation by consulting literature and database; explore the effect of p75NTR knockout on mesenchymal stem cells (MSCs) gene expression and cell proportion by cell subgrouping, differential gene analysis, enrichment analysis and protein-protein interaction network analysis; understand the interaction between MSCs cells and the differentiation trajectory and gene change characteristics of p75NTR knockout MSCs by cell communication analysis and pseudo-time analysis. Last we verified the findings single cell sequencing in vitro. RESULTS: We identified 21 cell clusters, and we re-clustered these into three subclusters. Importantly, we revealed the cell–cell communication networks between clusters. We clarified that Cd271 was significantly associated with the regulation of mineralization. CONCLUSION: This study provides comprehensive mechanistic insights into the maxillary- process-derived MSCs and demonstrates that Cd271 is significantly associated with the odontogenesis in mesenchymal populations.
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spelling pubmed-103245032023-07-07 Single cell RNA sequencing reveals mesenchymal heterogeneity and critical functions of Cd271 in tooth development Zhang, Yan-Yan Li, Feng Zeng, Xiao-Ke Zou, Yan-Hui Zhu, Bing-Bing Ye, Jia-Jia Zhang, Yun-Xiao Jin, Qiu Nie, Xin World J Stem Cells Basic Study BACKGROUND: Accumulating evidence suggests that the maxillary process, to which cranial crest cells migrate, is essential to tooth development. Emerging studies indicate that Cd271 plays an essential role in odontogenesis. However, the underlying mechanisms have yet to be elucidated. AIM: To establish the functionally heterogeneous population in the maxillary process, elucidate the effects of Cd271 deficiency on gene expression differences. METHODS: p75NTR knockout (Cd271(-/-)) mice (from American Jackson laboratory) were used to collect the maxillofacial process tissue of p75NTR knockout mice, and the wild-type maxillofacial process of the same pregnant mouse wild was used as control. After single cell suspension, the cDNA was prepared by loading the single cell suspension into the 10x Genomics Chromium system to be sequenced by NovaSeq6000 sequencing system. Finally, the sequencing data in Fastq format were obtained. The FastQC software is used to evaluate the quality of data and CellRanger analyzed the data. The gene expression matrix is read by R software, and Seurat is used to control and standardize the data, reduce the dimension and cluster. We search for marker genes for subgroup annotation by consulting literature and database; explore the effect of p75NTR knockout on mesenchymal stem cells (MSCs) gene expression and cell proportion by cell subgrouping, differential gene analysis, enrichment analysis and protein-protein interaction network analysis; understand the interaction between MSCs cells and the differentiation trajectory and gene change characteristics of p75NTR knockout MSCs by cell communication analysis and pseudo-time analysis. Last we verified the findings single cell sequencing in vitro. RESULTS: We identified 21 cell clusters, and we re-clustered these into three subclusters. Importantly, we revealed the cell–cell communication networks between clusters. We clarified that Cd271 was significantly associated with the regulation of mineralization. CONCLUSION: This study provides comprehensive mechanistic insights into the maxillary- process-derived MSCs and demonstrates that Cd271 is significantly associated with the odontogenesis in mesenchymal populations. Baishideng Publishing Group Inc 2023-06-26 2023-06-26 /pmc/articles/PMC10324503/ /pubmed/37424952 http://dx.doi.org/10.4252/wjsc.v15.i6.589 Text en ©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved. https://creativecommons.org/licenses/by-nc/4.0/This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial.
spellingShingle Basic Study
Zhang, Yan-Yan
Li, Feng
Zeng, Xiao-Ke
Zou, Yan-Hui
Zhu, Bing-Bing
Ye, Jia-Jia
Zhang, Yun-Xiao
Jin, Qiu
Nie, Xin
Single cell RNA sequencing reveals mesenchymal heterogeneity and critical functions of Cd271 in tooth development
title Single cell RNA sequencing reveals mesenchymal heterogeneity and critical functions of Cd271 in tooth development
title_full Single cell RNA sequencing reveals mesenchymal heterogeneity and critical functions of Cd271 in tooth development
title_fullStr Single cell RNA sequencing reveals mesenchymal heterogeneity and critical functions of Cd271 in tooth development
title_full_unstemmed Single cell RNA sequencing reveals mesenchymal heterogeneity and critical functions of Cd271 in tooth development
title_short Single cell RNA sequencing reveals mesenchymal heterogeneity and critical functions of Cd271 in tooth development
title_sort single cell rna sequencing reveals mesenchymal heterogeneity and critical functions of cd271 in tooth development
topic Basic Study
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10324503/
https://www.ncbi.nlm.nih.gov/pubmed/37424952
http://dx.doi.org/10.4252/wjsc.v15.i6.589
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