Skip to main content
SpringerLink
Log in

Elucidating Tooth Development and Pulp Biology by Single-Cell Sequencing Technology

  • Chapter
  • First Online:
Contemporary Endodontics for Children and Adolescents

  • 633 Accesses

Abstract

Single-cell RNA sequencing (scRNA-seq) is a powerful technique that enables scientists to interrogate the expression level of every gene in individual cells of a complex tissue. This chapter discusses recent advances in using the single-cell transcriptomic technology to study tooth development and pulp biology. We begin by introducing the main stages of tooth and pulp development, highlighting knowledge gaps that single-cell transcriptomics can fill. We then consider the basic principles of scRNA-seq technology and how it is experimentally applied in dental research. Next, we focus on recent benchmark single-cell studies that addressed key questions in tooth and pulp development. We present findings that expand our understanding of how the dental pulp forms and functions, including cell heterogeneity in the pulp, the regulatory interactions between cell populations, and inherent cell lineages, signaling interactions, and transcriptional controls of tooth development and regeneration. These recent discoveries demonstrate the potential of scRNA-seq to revolutionize dentistry by stimulating new ideas and applications that will shape the future of the field.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Gronthos S, Mankani M, Brahim J, Robey PG, Shi S. Postnatal human dental pulp stem cells (DPSCs) in vitro and in vivo. Proc Natl Acad Sci. 2000;97(25):13625–30.

    Article  PubMed  PubMed Central  Google Scholar 

  2. Seo BM, Miura M, Gronthos S, Bartold PM, Batouli S, Brahim J, et al. Investigation of multipotent postnatal stem cells from human periodontal ligament. Lancet. 2004;364(9429):149–55.

    Article  PubMed  Google Scholar 

  3. Sui B, Wu D, Xiang L, Fu Y, Kou X, Shi S. Dental pulp stem cells: from discovery to clinical application. J Endod. 2020;46(9):S46–55.

    Article  PubMed  Google Scholar 

  4. Gong T, Heng BC, Lo ECM, Zhang C. Current advance and future prospects of tissue engineering approach to dentin/pulp regenerative therapy. Stem Cells Int. 2016;2016:9204574.

    Article  PubMed  PubMed Central  Google Scholar 

  5. Yang J, Yuan G, Chen Z. Pulp regeneration: current approaches and future challenges. Front Physiol. 2016;7:58.

    Article  PubMed  PubMed Central  Google Scholar 

  6. Moussa DG, Aparicio C. Present and future of tissue engineering scaffolds for dentin-pulp complex regeneration. J Tissue Eng Regen Med. 2019;13(1):58–75.

    PubMed  Google Scholar 

  7. Frisdal A, Trainor PA. Development and evolution of the pharyngeal apparatus. Wiley Interdiscip Rev Dev Biol. 2014;3(6):403–18.

    Article  PubMed  PubMed Central  Google Scholar 

  8. García-Castro MI, Marcelle C, Bronner-Fraser M. Ectodermal Wnt function as a neural crest inducer. Science. 2002;297(5582):848–51.

    Article  PubMed  Google Scholar 

  9. Monsoro-Burq AH, Fletcher RB, Harland RM. Neural crest induction by paraxial mesoderm in Xenopus embryos requires FGF signals. Development. 2003;130(14):3111–24.

    Article  PubMed  Google Scholar 

  10. Blentic A, Tandon P, Payton S, Walshe J, Carney T, Kelsh RN, et al. The emergence of ectomesenchyme. Dev Dyn. 2008;237(3):592–601.

    Article  PubMed  PubMed Central  Google Scholar 

  11. Breau MA, Pietri T, Stemmler MP, Thiery JP, Weston JA. A nonneural epithelial domain of embryonic cranial neural folds gives rise to ectomesenchyme. Proc Natl Acad Sci U S A. 2008;105(22):7750–5.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Lee RTH, Nagai H, Nakaya Y, Sheng G, Trainor PA, Weston JA, et al. Cell delamination in the mesencephalic neural fold and its implication for the origin of ectomesenchyme. Development. 2013;140(24):4890–902.

    Article  PubMed  PubMed Central  Google Scholar 

  13. Chai Y, Jiang X, Ito Y, Bringas P, Han J, Rowitch DH, et al. Fate of the mammalian cranial neural crest during tooth and mandibular morphogenesis. Development. 2000;127(8):1671–9.

    Article  PubMed  Google Scholar 

  14. Le Douarin NM, Creuzet S, Couly G, Dupin E. Neural crest cell plasticity and its limits. Development. 2004;131(19):4637–50.

    Article  PubMed  Google Scholar 

  15. Neubüser A, Peters H, Balling R, Martin GR. Antagonistic interactions between FGF and BMP signaling pathways: a mechanism for positioning the sites of tooth formation. Cell. 1997;90(2):247–55.

    Article  PubMed  Google Scholar 

  16. Tucker AS, Matthews KL, Sharpe PT. Transformation of tooth type induced by inhibition of BMP signaling. Science. 1998;282(5391):1136–8.

    Article  PubMed  Google Scholar 

  17. Liu W, Selever J, Murali D, Sun X, Brugger SM, Ma L, et al. Threshold-specific requirements for Bmp4 in mandibular development. Dev Biol. 2005;283(2):282–93.

    Article  PubMed  Google Scholar 

  18. MacKenzie A, Ferguson MW, Sharpe PT. Expression patterns of the homeobox gene, Hox-8, in the mouse embryo suggest a role in specifying tooth initiation and shape. Development. 1992;115(2):403–20.

    Article  PubMed  Google Scholar 

  19. Krivanek J, Adameyko I, Fried K. Heterogeneity and developmental connections between cell types inhabiting teeth. Front Physiol. 2017;8:376.

    Article  PubMed  PubMed Central  Google Scholar 

  20. Nakashima M, Iohara K. Mobilized dental pulp stem cells for pulp regeneration: initiation of clinical trial. J Endod. 2014;40(4 Suppl):S26–32.

    Article  PubMed  Google Scholar 

  21. Mitsiadis TA, Orsini G, Jimenez-Rojo L. Stem cell-based approaches in dentistry. Eur Cell Mater. 2015;30:248–57.

    Article  PubMed  Google Scholar 

  22. Papalexi E, Satija R. Single-cell RNA sequencing to explore immune cell heterogeneity. Nat Rev Immunol. 2018;18(1):35–45.

    Article  PubMed  Google Scholar 

  23. Hwang B, Lee JH, Bang D. Single-cell RNA sequencing technologies and bioinformatics pipelines. Exp Mol Med. 2018;50(8):1–14.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Wagner DE, Klein AM. Lineage tracing meets single-cell omics: opportunities and challenges. Nat Rev Genet. 2020;21(7):410–27.

    Article  PubMed  PubMed Central  Google Scholar 

  25. Slovin S, Carissimo A, Panariello F, Grimaldi A, Bouché V, Gambardella G, et al. Single-cell RNA sequencing analysis: a step-by-step overview. Methods Mol Biol. 2021;2284:343–65.

    Article  PubMed  Google Scholar 

  26. Ziegenhain C, Vieth B, Parekh S, Reinius B, Guillaumet-Adkins A, Smets M, et al. Comparative analysis of single-cell RNA sequencing methods. Mol Cell. 2017;65(4):631–643.e4.

    Article  PubMed  Google Scholar 

  27. Lee J, Hyeon DY, Hwang D. Single-cell multiomics: technologies and data analysis methods. Exp Mol Med. 2020;52(9):1428–42.

    Article  PubMed  PubMed Central  Google Scholar 

  28. Spitz F, Furlong EEM. Genomics and development: taking developmental biology to new heights. Dev Cell. 2006;11(4):451–7.

    Article  PubMed  Google Scholar 

  29. Potter AS, Steven PS. Dissociation of tissues for single-cell analysis. In: Vainio S, editor. Kidney organogenesis: methods and protocols [internet]. New York, NY: Springer; 2019. p. 55–62. [Accessed 10 Oct 2022] (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-9021-4_5.

    Chapter  Google Scholar 

  30. Denisenko E, Guo BB, Jones M, Hou R, de Kock L, Lassmann T, et al. Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows. Genome Biol. 2020;21(1):130.

    Article  PubMed  PubMed Central  Google Scholar 

  31. Krivanek J, Lavicky J, Bouderlique T, Adameyko I. Rapid isolation of single cells from mouse and human teeth. J Vis Exp. 2021;(176). https://doi.org/10.3791/63043.

  32. Bronner-Fraser M, Fraser SE. Cell lineage analysis reveals multipotency of some avian neural crest cells. Nature. 1988;335(6186):161–4.

    Article  PubMed  Google Scholar 

  33. Schilling TF, Kimmel CB. Segment and cell type lineage restrictions during pharyngeal arch development in the zebrafish embryo. Development. 1994;120(3):483–94.

    Article  PubMed  Google Scholar 

  34. Baggiolini A, Varum S, Mateos JM, Bettosini D, John N, Bonalli M, et al. Premigratory and migratory neural crest cells are multipotent in vivo. Cell Stem Cell. 2015;16(3):314–22.

    Article  PubMed  Google Scholar 

  35. Soldatov R, Kaucka M, Kastriti ME, Petersen J, Chontorotzea T, Englmaier L, et al. Spatiotemporal structure of cell fate decisions in murine neural crest. Science. 2019;364(6444):eaas9536.

    Article  PubMed  Google Scholar 

  36. Tatarakis D, Cang Z, Wu X, Sharma PP, Karikomi M, MacLean AL, et al. Single-cell transcriptomic analysis of zebrafish cranial neural crest reveals spatiotemporal regulation of lineage decisions during development. Cell Rep. 2021;37(12):110140.

    Article  PubMed  PubMed Central  Google Scholar 

  37. Fabian P, Tseng KC, Thiruppathy M, Arata C, Chen HJ, Smeeton J, et al. Lifelong single-cell profiling of cranial neural crest diversification in zebrafish. Nat Commun. 2022;13(1):13.

    Article  PubMed  PubMed Central  Google Scholar 

  38. Williams RM, Candido-Ferreira I, Repapi E, Gavriouchkina D, Senanayake U, Ling ITC, et al. Reconstruction of the global neural crest gene regulatory network in vivo. Dev Cell. 2019;51(2):255–276.e7.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Oralová V, Rosa JT, Larionova D, Witten PE, Huysseune A. Multiple epithelia are required to develop teeth deep inside the pharynx. Proc Natl Acad Sci. 2020;117(21):11503–12.

    Article  PubMed  PubMed Central  Google Scholar 

  40. Tucker A, Sharpe P. The cutting-edge of mammalian development; how the embryo makes teeth. Nat Rev Genet. 2004;5(7):499–508.

    Article  PubMed  Google Scholar 

  41. Xu J, Liu H, Lan Y, Adam M, Clouthier DE, Potter S, et al. Hedgehog signaling patterns the oral-aboral axis of the mandibular arch. Elife. 2019;8:e40315.

    Article  PubMed  PubMed Central  Google Scholar 

  42. Yuan Y, Loh YHE, Han X, Feng J, Ho TV, He J, et al. Spatiotemporal cellular movement and fate decisions during first pharyngeal arch morphogenesis. Sci Adv. 2020;6(51):eabb0119.

    Article  PubMed  PubMed Central  Google Scholar 

  43. Yu T, Klein OD. Molecular and cellular mechanisms of tooth development, homeostasis and repair. Development. 2020;147(2):dev184754.

    Article  PubMed  PubMed Central  Google Scholar 

  44. Fraser GJ, Bloomquist RF, Streelman JT. Common developmental pathways link tooth shape to regeneration. Dev Biol. 2013;377(2):399–414.

    Article  PubMed  PubMed Central  Google Scholar 

  45. Hallikas O, Das Roy R, Christensen MM, Renvoisé E, Sulic A, Jernvall J. System-level analyses of keystone genes required for mammalian tooth development. J Exp Zool B Mol Dev Evol. 2021;336(1):7–17.

    Article  PubMed  Google Scholar 

  46. Wang Y, Zhao Y, Chen S, Chen X, Zhang Y, Chen H, et al. Single cell atlas of developing mouse dental germs reveals populations of CD24+ and Plac8+ odontogenic cells. Sci Bull. 2022;67(11):1154–69.

    Article  Google Scholar 

  47. Jing J, Feng J, Yuan Y, Guo T, Lei J, Pei F, et al. Spatiotemporal single-cell regulatory atlas reveals neural crest lineage diversification and cellular function during tooth morphogenesis. Nat Commun. 2022;13(1):4803.

    Article  PubMed  PubMed Central  Google Scholar 

  48. Ye Q, Bhojwani A, Hu JK. Understanding the development of oral epithelial organs through single cell transcriptomic analysis. Development. 2022;149(16):dev200539.

    Article  PubMed  PubMed Central  Google Scholar 

  49. Panousopoulou E, Green JBA. Invagination of ectodermal placodes is driven by cell intercalation-mediated contraction of the suprabasal tissue canopy. PLoS Biol. 2016;14(3):e1002405.

    Article  PubMed  PubMed Central  Google Scholar 

  50. Plikus MV, Zeichner-David M, Mayer JA, Reyna J, Bringas P, Thewissen JGM, et al. Morphoregulation of teeth: modulating the number, size, shape and differentiation by tuning bmp activity. Evol Dev. 2005;7(5):440–57.

    Article  PubMed  PubMed Central  Google Scholar 

  51. Fujimori S, Novak H, Weissenböck M, Jussila M, Gonçalves A, Zeller R, et al. Wnt/β-catenin signaling in the dental mesenchyme regulates incisor development by regulating Bmp4. Dev Biol. 2010;348(1):97–106.

    Article  PubMed  PubMed Central  Google Scholar 

  52. Munne PM, Felszeghy S, Jussila M, Suomalainen M, Thesleff I, Jernvall J. Splitting placodes: effects of bone morphogenetic protein and activin on the patterning and identity of mouse incisors. Evol Dev. 2010;12(4):383–92.

    Article  PubMed  Google Scholar 

  53. Lee DJ, Kim HY, Lee SJ, Jung HS. Spatiotemporal changes in transcriptome of odontogenic and non-odontogenic regions in the dental arch of Mus musculus. Front Cell Dev Biol. 2021;9:723326.

    Article  PubMed  PubMed Central  Google Scholar 

  54. Krivanek J, Soldatov RA, Kastriti ME, Chontorotzea T, Herdina AN, Petersen J, et al. Dental cell type atlas reveals stem and differentiated cell types in mouse and human teeth. Nat Commun. 2020;11:4816.

    Article  PubMed  PubMed Central  Google Scholar 

  55. Pagella P, de Vargas RL, Stadlinger B, Moor AE, Mitsiadis TA. A single-cell atlas of human teeth. iScience. 2021;24(5):102405.

    Article  PubMed  PubMed Central  Google Scholar 

  56. Armingol E, Officer A, Harismendy O, Lewis NE. Deciphering cell–cell interactions and communication from gene expression. Nat Rev Genet. 2021;22(2):71–88.

    Article  PubMed  Google Scholar 

  57. Shi Y, Yu Y, Zhou Y, Zhao J, Zhang W, Zou D, et al. A single-cell interactome of human tooth germ from growing third molar elucidates signaling networks regulating dental development. Cell Biosci. 2021;11(1):178.

    Article  PubMed  PubMed Central  Google Scholar 

  58. Jontell M, Okiji T, Dahlgren U, Bergenholtz G. Immune defense mechanisms of the dental pulp. Crit Rev Oral Biol Med. 1998;9(2):179–200.

    Article  PubMed  Google Scholar 

  59. Opasawatchai A, Nguantad S, Sriwilai B, Matangkasombut P, Matangkasombut O, Srisatjaluk R, et al. Single-cell transcriptomic profiling of human dental pulp in sound and carious teeth: a pilot study. Front Dent Med. 2022;2:93. https://www.frontiersin.org/articles/10.3389/fdmed.2021.806294. Accessed 18 Oct 2022.

    Article  Google Scholar 

Download references

Acknowledgments

We apologize sincerely to those authors whose work we are unable to cite here owing to space constraints. Many of the scRNA-seq studies discussed here include excellent analyses of cells beyond the dental pulp, which were unfortunately omitted due to the focus on pulp development. The preparation of this book chapter was supported by the BSF grant 2021007 to J.K.H and A.S; NIH/NIDCR grants R03DE030205 and R01DE030471 to J.K.H; and the Israel Science Foundation grant 604/21 to A.S.

Author information

Authors and Affiliations

  1. School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA

    Jimmy K. Hu

  2. Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA

    Jimmy K. Hu

  3. Faculty of Dental Medicine, The Institute of Biomedical and Oral Research, Hebrew University of Jerusalem, Jerusalem, Israel

    Amnon Sharir

Authors
  1. Jimmy K. Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Amnon Sharir
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Jimmy K. Hu or Amnon Sharir .

Editor information

Editors and Affiliations

  1. Department of Pediatric Dentistry, Hadassah Medical Center, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel

    Anna B. Fuks

  2. Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel

    Moti Moskovitz

  3. The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel

    Nili Tickotsky

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Hu, J.K., Sharir, A. (2023). Elucidating Tooth Development and Pulp Biology by Single-Cell Sequencing Technology. In: Fuks, A.B., Moskovitz, M., Tickotsky, N. (eds) Contemporary Endodontics for Children and Adolescents. Springer, Cham. https://doi.org/10.1007/978-3-031-23980-9_19

Download citation

  • DOI: https://doi.org/10.1007/978-3-031-23980-9_19

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-031-23979-3

  • Online ISBN: 978-3-031-23980-9

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics

Search

Navigation