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Eldeeb D, Ikeda Y, Hojo H, Ohba S. Unraveling the hidden complexity: Exploring dental tissues through single-cell transcriptional profiling. Regen Ther 2024; 27:218-229. [PMID: 38596822 PMCID: PMC11002530 DOI: 10.1016/j.reth.2024.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/21/2024] [Accepted: 03/24/2024] [Indexed: 04/11/2024] Open
Abstract
Understanding the composition and function of cells constituting tissues and organs is vital for unraveling biological processes. Single-cell analysis has allowed us to move beyond traditional methods of categorizing cell types. This innovative technology allows the transcriptional and epigenetic profiling of numerous individual cells, leading to significant insights into the development, homeostasis, and pathology of various organs and tissues in both animal models and human samples. In this review, we delve into the outcomes of major investigations using single-cell transcriptomics to decipher the cellular composition of mammalian teeth and periodontal tissues. The recent single-cell transcriptome-based studies have traced in detail the dental epithelium-ameloblast lineage and dental mesenchyme lineages in the mouse incisors and the tooth germ of both mice and humans; unraveled the microenvironment, the identity of niche cells, and cellular intricacies in the dental pulp; shed light on the molecular mechanisms orchestrating root formation; and characterized cellular dynamics of the periodontal ligament. Additionally, cellular components in dental pulps were compared between healthy and carious teeth at a single-cell level. Each section of this review contributes to a comprehensive understanding of tooth biology, offering valuable insights into developmental processes, niche cell identification, and the molecular secrets of the dental environment.
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Affiliation(s)
- Dahlia Eldeeb
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Japan
- Department of Physiology, Division of Biomedical Sciences, Nihon University School of Medicine, Japan
- Department of Oral Biology, Faculty of Dentistry, Cairo University, Egypt
| | - Yuki Ikeda
- Department of Tissue and Developmental Biology, Graduate School of Dentistry, Osaka University, Japan
| | - Hironori Hojo
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Japan
| | - Shinsuke Ohba
- Department of Tissue and Developmental Biology, Graduate School of Dentistry, Osaka University, Japan
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2
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Eldeeb D, Okada H, Suzuki Y, Seki M, Tanaka J, Mishima K, Chung UI, Ohba S, Hojo H. Exploring the role of DNMT1 in dental papilla cell fate specification during mouse tooth germ development through integrated single-cell transcriptomics and bulk RNA sequencing. J Oral Biosci 2024; 66:530-538. [PMID: 38942194 DOI: 10.1016/j.job.2024.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/22/2024] [Accepted: 06/24/2024] [Indexed: 06/30/2024]
Abstract
OBJECTIVES This study aimed to investigate the regulatory mechanisms governing dental mesenchymal cell commitment during tooth development, focusing on odontoblast differentiation and the role of epigenetic regulation in this process. METHODS We performed single-cell RNA sequencing (scRNA-seq) of dental cells from embryonic day 14.5 (E14.5) mice to understand the heterogeneity of developing tooth germ cells. Computational analyses including gene regulatory network (GRN) assessment were conducted. We validated our findings using immunohistochemistry (IHC) and in vitro loss-of-function analyses using the DNA methyltransferase 1 (DNMT1) inhibitor Gsk-3484862 in primary dental mesenchymal cells (DMCs) isolated from E14.5 mouse tooth germs. Bulk RNA-seq of Gsk-3484862-treated DMCs was performed to identify potential downstream targets of DNMT1. RESULTS scRNA-seq analysis revealed diverse cell populations within the tooth germs, including epithelial, mesenchymal, immune, and muscle cells. Using single-cell regulatory network inference and clustering (SCENIC), we identified Dnmt1 as a key regulator of early odontoblast development. IHC analysis showed the ubiquitous expression of DNMT1 in the dental papilla and epithelium. Bulk RNA-seq of cultured DMCs showed that Gsk-3484862 treatment upregulated odontoblast-related genes, whereas genes associated with cell division and the cell cycle were downregulated. Integrated analysis of bulk RNA-seq data with scRNA-seq SCENIC profiles was used to identify the potential Dnmt1 target genes. CONCLUSIONS Dnmt1 may negatively affect odontoblast commitment and differentiation during tooth development. These findings contribute to a better understanding of the molecular mechanisms underlying tooth development and future development of hard-tissue regenerative therapies.
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Affiliation(s)
- Dahlia Eldeeb
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Japan; Department of Oral Biology, Faculty of Dentistry, Cairo University, Egypt
| | - Hiroyuki Okada
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Japan; Department of Orthopaedic Surgery, Graduate School of Medicine, The University of Tokyo, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Japan
| | - Junichi Tanaka
- Division of Pathology, Department of Oral Diagnostic Sciences, School of Dentistry, Showa University, Japan
| | - Kenji Mishima
- Division of Pathology, Department of Oral Diagnostic Sciences, School of Dentistry, Showa University, Japan
| | - Ung-Il Chung
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Japan
| | - Shinsuke Ohba
- Department of Tissue and Developmental Biology, Graduate School of Dentistry, Osaka University, Japan.
| | - Hironori Hojo
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Japan.
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Zhang X, Zhou S, Zhan Y, Mei Z, Qian A, Yuan Y, Zhang X, Fu T, Ma S, Li J. Molecular insights into the proteomic composition of porcine treated dentin matrix. Mater Today Bio 2024; 25:100990. [PMID: 38371466 PMCID: PMC10873736 DOI: 10.1016/j.mtbio.2024.100990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/23/2024] [Accepted: 02/03/2024] [Indexed: 02/20/2024] Open
Abstract
Background Human-treated dentin matrix (hTDM) has recently been studied as a natural extracellular matrix-based biomaterial for dentin pulp regeneration. However, porcine-treated dentin matrix (pTDM) is a potential alternative scaffold due to limited availability. However, there is a dearth of information regarding the protein composition and underlying molecular mechanisms of pTDM.Methods: hTDM and pTDM were fabricated using human and porcine teeth, respectively, and their morphological characteristics were examined using scanning electron microscopy. Stem cells derived from human exfoliated deciduous teeth (SHEDs) were isolated and characterized using flow cytometry and multilineage differentiation assays. SHEDs were cultured in three-dimensional environments with hTDM, pTDM, or biphasic hydroxyapatite/tricalcium phosphate. The expression of odontogenesis markers in SHEDs were assessed using real-time polymerase chain reaction and immunochemical staining. Subsequently, SHEDs/TDM and SHEDs/HA/TCP complexes were transplanted subcutaneously into nude mice. The protein composition of pTDM was analyzed using proteomics and compared to previously published data on hTDM.Results: pTDM and hTDM elicited comparable upregulation of odontogenesis-related genes and proteins in SHEDs. Furthermore, both demonstrated the capacity to stimulate root-related tissue regeneration in vivo. Proteomic analysis revealed the presence of 278 protein groups in pTDM, with collagens being the most abundant. Additionally, pTDM and hTDM shared 58 identical proteins, which may contribute to their similar abilities to induce odontogenesis. Conclusions Both hTDM and pTDM exhibit comparable capabilities in inducing odontogenesis, potentially owing to their distinctive bioactive molecular networks.
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Affiliation(s)
- Xiya Zhang
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
| | - Sha Zhou
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
| | - Yuzhen Zhan
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
| | - Ziyi Mei
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
| | - Aizhuo Qian
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
| | - Yu Yuan
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
| | - Xiaonan Zhang
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
| | - Tiwei Fu
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
| | - Shiyong Ma
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, The Ministry of Education, Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Jie Li
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
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Chen X, Li G, Zhang J, Hu L, Zhao G, Wu B, Wei F, Xiong F. The temporal protein signature analyses of developing human deciduous molar tooth germ. Proteomics 2024:e2300396. [PMID: 38522031 DOI: 10.1002/pmic.202300396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/31/2024] [Accepted: 03/05/2024] [Indexed: 03/25/2024]
Abstract
The tooth serves as an exemplary model for developmental studies, encompassing epithelial-mesenchymal transition and cell differentiation. The essential factors and pathways identified in tooth development will help understand the natural development process and the malformations of mineralized tissues such as skeleton. The time-dependent proteomic changes were investigated through the proteomics of healthy human molars during embryonic stages, ranging from the cap-to-early bell stage. A comprehensive analysis revealed 713 differentially expressed proteins (DEPs) exhibiting five distinct temporal expression patterns. Through the application of weighted gene co-expression network analysis (WGCNA), 24 potential driver proteins of tooth development were screened, including CHID1, RAP1GDS1, HAPLN3, AKAP12, WLS, GSS, DDAH1, CLSTN1, AFM, RBP1, AGO1, SET, HMGB2, HMGB1, ANP32A, SPON1, FREM1, C8B, PRPS2, FCHO2, PPP1R12A, GPALPP1, U2AF2, and RCC2. Then, the proteomics and transcriptomics expression patterns of these proteins were further compared, complemented by single-cell RNA-sequencing (scRNA-seq). In summary, this study not only offers a wealth of information regarding the molecular intricacies of human embryonic epithelial and mesenchymal cell differentiation but also serves as an invaluable resource for future mechanistic inquiries into tooth development.
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Affiliation(s)
- Xiaohang Chen
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, China
- Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Gaochi Li
- Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Jian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Liang Hu
- Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Guoqiang Zhao
- Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Buling Wu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, China
| | - Fengxiang Wei
- Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College), Shenzhen, China
| | - Fu Xiong
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
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Hu X, Li H, Yang M, Chen Y, Zeng A, Wu J, Zhang J, Tian Y, Tang J, Qian S, Wu M. Effect of Long Non-coding RNA and DNA Methylation on Gene Expression in Dental Fluorosis. Biol Trace Elem Res 2024; 202:221-232. [PMID: 37059921 DOI: 10.1007/s12011-023-03660-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/04/2023] [Indexed: 04/16/2023]
Abstract
In the process of tooth development, the interaction between genetic information, epigenetic inheritance, and environment jointly affects the teeth formation. At present, the mechanism of dental fluorosis is rarely studied from transcriptomics, and there is no report on epigenetic perspective. In the study, SD rats were randomly divided into dental fluorosis group and control group fed with NaF (150 mg/L) or distilled water for 8 weeks. After 3.5 days of birth, the RNAs or DNA of rat mandibular molars were detected by RNA-seq or MethylTarget, respectively. The results demonstrated that a total of 1723 differentially expressed genes (DEGs) and 2511 differential expression lncRNAs (DE-lncRNAs) were mainly involved in the ion channels, calcium ion transport, and immunomodulatory signaling pathways. ATP2C1 and Nr1d1, which were related to Ca2+ transport, cellular calcium homeostasis, endoplasmic reticulum stress and immunity, may be the key genes in the formation of dental fluorosis. Notably, we also found that the immune response plays an important role in the formation of dental fluorosis, and a large amount of DEGs was enriched in immune regulation and NF-κB signaling pathways. Furthermore, the methylation levels of 13 sites were increased in Ago4, Atf3, Atp2c1, Dusp1, Habp4, and Mycl, while methylation levels of 5 CpG sites decreased in Ago4, Atp2c1, Habp4, and Traf6, and conformably, the expression of these genes have been significantly changed. This study comprehensively analyzed the occurrence mechanism of dental fluorosis from transcriptomics and epigenetics, so as to provide theoretical reference for further research.
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Affiliation(s)
- Xiaoyan Hu
- Hospital of Stomatology, Zunyi Medical University, Zunyi, 563099, China
| | - Huiru Li
- Hospital of Stomatology, Zunyi Medical University, Zunyi, 563099, China
| | - Minzhi Yang
- Hospital of Stomatology, Zunyi Medical University, Zunyi, 563099, China
| | - Yujiong Chen
- Hospital of Stomatology, Zunyi Medical University, Zunyi, 563099, China
| | - Ailin Zeng
- Hospital of Stomatology, Zunyi Medical University, Zunyi, 563099, China
| | - Jiayuan Wu
- Hospital of Stomatology, Zunyi Medical University, Zunyi, 563099, China
- Special Key Laboratory of Oral Disease Research, Higher Education Institution in Guizhou Province, Zunyi, 563006, China
| | - Jian Zhang
- Hospital of Stomatology, Zunyi Medical University, Zunyi, 563099, China
- Special Key Laboratory of Oral Disease Research, Higher Education Institution in Guizhou Province, Zunyi, 563006, China
| | - Yuan Tian
- Hospital of Stomatology, Zunyi Medical University, Zunyi, 563099, China
- Special Key Laboratory of Oral Disease Research, Higher Education Institution in Guizhou Province, Zunyi, 563006, China
| | - Jing Tang
- Hospital of Stomatology, Zunyi Medical University, Zunyi, 563099, China
- Special Key Laboratory of Oral Disease Research, Higher Education Institution in Guizhou Province, Zunyi, 563006, China
| | - Shengyan Qian
- Hospital of Stomatology, Zunyi Medical University, Zunyi, 563099, China
- Special Key Laboratory of Oral Disease Research, Higher Education Institution in Guizhou Province, Zunyi, 563006, China
| | - Mingsong Wu
- Hospital of Stomatology, Zunyi Medical University, Zunyi, 563099, China.
- Special Key Laboratory of Oral Disease Research, Higher Education Institution in Guizhou Province, Zunyi, 563006, China.
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Rao P, Jing J, Fan Y, Zhou C. Spatiotemporal cellular dynamics and molecular regulation of tooth root ontogeny. Int J Oral Sci 2023; 15:50. [PMID: 38001110 PMCID: PMC10673972 DOI: 10.1038/s41368-023-00258-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Tooth root development involves intricate spatiotemporal cellular dynamics and molecular regulation. The initiation of Hertwig's epithelial root sheath (HERS) induces odontoblast differentiation and the subsequent radicular dentin deposition. Precisely controlled signaling pathways modulate the behaviors of HERS and the fates of dental mesenchymal stem cells (DMSCs). Disruptions in these pathways lead to defects in root development, such as shortened roots and furcation abnormalities. Advances in dental stem cells, biomaterials, and bioprinting show immense promise for bioengineered tooth root regeneration. However, replicating the developmental intricacies of odontogenesis has not been resolved in clinical treatment and remains a major challenge in this field. Ongoing research focusing on the mechanisms of root development, advanced biomaterials, and manufacturing techniques will enable next-generation biological root regeneration that restores the physiological structure and function of the tooth root. This review summarizes recent discoveries in the underlying mechanisms governing root ontogeny and discusses some recent key findings in developing of new biologically based dental therapies.
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Affiliation(s)
- Pengcheng Rao
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Junjun Jing
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yi Fan
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chenchen Zhou
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China.
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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Yao S, Zhou X, Gu M, Zhang C, Bartsch O, Vona B, Fan L, Ma L, Pan Y. FGFR1 variants contributed to families with tooth agenesis. Hum Genomics 2023; 17:93. [PMID: 37833774 PMCID: PMC10576343 DOI: 10.1186/s40246-023-00539-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Tooth agenesis is a common dental anomaly that can substantially affect both the ability to chew and the esthetic appearance of patients. This study aims to identify possible genetic factors that underlie various forms of tooth agenesis and to investigate the possible molecular mechanisms through which human dental pulp stem cells may play a role in this condition. RESULTS Using whole-exome sequencing of a Han Chinese family with non-syndromic tooth agenesis, a rare mutation in FGFR1 (NM_001174063.2: c.103G > A, p.Gly35Arg) was identified as causative and confirmed by Sanger sequencing. Via GeneMatcher, another family with a known variant (NM_001174063.2: c.1859G > A, p.Arg620Gln) was identified and diagnosed with tooth agenesis and a rare genetic disorder with considerable intrafamilial variability. Fgfr1 is enriched in the ectoderm during early embryonic development of mice and showed sustained low expression during normal embryonic development of Xenopus laevis frogs. Functional studies of the highly conserved missense variant c.103G > A showed deleterious effects. FGFR1 (c.103G > A) was overexpressed compared to wildtype and promoted proliferation while inhibiting apoptosis in HEK293 and human dental pulp stem cells. Moreover, the c.103G > A variant was found to suppress the epithelial-mesenchymal transition. The variant could downregulate ID4 expression and deactivate the TGF-beta signaling pathway by promoting the expression of SMAD6 and SMAD7. CONCLUSION Our research broadens the mutation spectrum associated with tooth agenesis and enhances understanding of the underlying disease mechanisms of this condition.
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Affiliation(s)
- Siyue Yao
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, 136 Hanzhong Road, Nanjing, 210029, China
- The Affiliated Stomatology Hospital of Suzhou Vocational Health College, Suzhou, 215000, China
| | - Xi Zhou
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, 136 Hanzhong Road, Nanjing, 210029, China
| | - Min Gu
- Department of Stomatology, Affiliated Third Hospital of Soochow University, The First People's Hospital of Changzhou City, Changzhou City, 213003, Jiangsu Province, China
| | - Chengcheng Zhang
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, 136 Hanzhong Road, Nanjing, 210029, China
| | - Oliver Bartsch
- Institute of Human Genetics, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Liwen Fan
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, 136 Hanzhong Road, Nanjing, 210029, China
| | - Lan Ma
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, 136 Hanzhong Road, Nanjing, 210029, China.
| | - Yongchu Pan
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China.
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, 136 Hanzhong Road, Nanjing, 210029, China.
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.
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Hermans F, Bueds C, Hemeryck L, Lambrichts I, Bronckaers A, Vankelecom H. Establishment of inclusive single-cell transcriptome atlases from mouse and human tooth as powerful resource for dental research. Front Cell Dev Biol 2022; 10:1021459. [PMID: 36299483 PMCID: PMC9590651 DOI: 10.3389/fcell.2022.1021459] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Single-cell (sc) omics has become a powerful tool to unravel a tissue’s cell landscape across health and disease. In recent years, sc transcriptomic interrogation has been applied to a variety of tooth tissues of both human and mouse, which has considerably advanced our fundamental understanding of tooth biology. Now, an overarching and integrated bird’s-view of the human and mouse tooth sc transcriptomic landscape would be a powerful multi-faceted tool for dental research, enabling further decipherment of tooth biology and development through constantly progressing state-of-the-art bioinformatic methods as well as the exploration of novel hypothesis-driven research. To this aim, we re-assessed and integrated recently published scRNA-sequencing datasets of different dental tissue types (healthy and diseased) from human and mouse to establish inclusive tooth sc atlases, and applied the consolidated data map to explore its power. For mouse tooth, we identified novel candidate transcriptional regulators of the ameloblast lineage. Regarding human tooth, we provide support for a developmental connection, not advanced before, between specific epithelial compartments. Taken together, we established inclusive mouse and human tooth sc atlases as powerful tools to potentiate innovative research into tooth biology, development and disease. The maps are provided online in an accessible format for interactive exploration.
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Affiliation(s)
- Florian Hermans
- Laboratory of Tissue Plasticity in Health and Disease, Cluster of Stem Cell and Developmental Biology, Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven (University of Leuven), Leuven, Belgium
- UHasselt-Hasselt University, Biomedical Research Institute (BIOMED), Department of Cardio and Organ Systems, Diepenbeek, Belgium
- *Correspondence: Florian Hermans, ; Hugo Vankelecom,
| | - Celine Bueds
- Laboratory of Tissue Plasticity in Health and Disease, Cluster of Stem Cell and Developmental Biology, Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven (University of Leuven), Leuven, Belgium
| | - Lara Hemeryck
- Laboratory of Tissue Plasticity in Health and Disease, Cluster of Stem Cell and Developmental Biology, Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven (University of Leuven), Leuven, Belgium
| | - Ivo Lambrichts
- UHasselt-Hasselt University, Biomedical Research Institute (BIOMED), Department of Cardio and Organ Systems, Diepenbeek, Belgium
| | - Annelies Bronckaers
- UHasselt-Hasselt University, Biomedical Research Institute (BIOMED), Department of Cardio and Organ Systems, Diepenbeek, Belgium
| | - Hugo Vankelecom
- Laboratory of Tissue Plasticity in Health and Disease, Cluster of Stem Cell and Developmental Biology, Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven (University of Leuven), Leuven, Belgium
- *Correspondence: Florian Hermans, ; Hugo Vankelecom,
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Wu J, Ding Y, Wang J, Lyu F, Tang Q, Song J, Luo Z, Wan Q, Lan X, Xu Z, Chen L. Single‐cell RNA
sequencing in oral science: Current awareness and perspectives. Cell Prolif 2022; 55:e13287. [PMID: 35842899 PMCID: PMC9528768 DOI: 10.1111/cpr.13287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/10/2022] [Accepted: 05/29/2022] [Indexed: 11/30/2022] Open
Abstract
The emergence of single‐cell RNA sequencing enables simultaneous sequencing of thousands of cells, making the analysis of cell population heterogeneity more efficient. In recent years, single‐cell RNA sequencing has been used in the investigation of heterogeneous cell populations, cellular developmental trajectories, stochastic gene transcriptional kinetics, and gene regulatory networks, providing strong support in life science research. However, the application of single‐cell RNA sequencing in the field of oral science has not been reviewed comprehensively yet. Therefore, this paper reviews the development and application of single‐cell RNA sequencing in oral science, including fields of tissue development, teeth and jaws diseases, maxillofacial tumors, infections, etc., providing reference and prospects for using single‐cell RNA sequencing in studying the oral diseases, tissue development, and regeneration.
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Affiliation(s)
- Jie Wu
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology Sun Yat‐sen University Guangzhou China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yumei Ding
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
| | - Jinyu Wang
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
| | - Fengyuan Lyu
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
- Center of Stomatology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Qingming Tang
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
| | - Jiangyuan Song
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
| | - Zhiqiang Luo
- National Engineering Research Center for Nanomedicine College of Life Science and Technolog Huazhong University of Science and Technology Wuhan China
| | - Qian Wan
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy Huazhong University of Science and Technology Wuhan China
- Institute of Brain Research Huazhong University of Science and Technology Wuhan China
| | - Xiaoli Lan
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Key Laboratory of Molecular Imaging Wuhan China
| | - Zhi Xu
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
| | - Lili Chen
- Department of Stomatology, Union Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- School of Stomatology, Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration Wuhan China
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Casadio R, Martelli PL, Savojardo C. Machine learning solutions for predicting protein–protein interactions. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Rita Casadio
- Biocomputing Group University of Bologna Bologna Italy
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