Skip to main content
SpringerLink
Log in
Book cover

Essentials of Bioinformatics, Volume II pp 119–150Cite as

Dental Stem Cells in Regenerative Medicine: Emerging Trends and Prospects in the Era of Bioinformatics

  • Chapter
  • First Online:

  • 1378 Accesses

Abstract

The craniofacial skeleton comprising the teeth, gums and tongue is an excellent model of organogenesis. Mesenchymal stem cells (MSCs) present within various zones of the oro-dental tissue exhibit exceptional regeneration potential and contribute to tissue restoration and regeneration following infection/inflammation or trauma. Oro-dental disorders are multifactorial and encompass a wide array of diseases involving tooth germ formation, tooth shape, number, size and alignment. Oral microbial pathogens and their colonization as biofilm largely remain a threat to oral and dental health. Biofilms are associated with dental caries, periodontitis and peri-implantitis which often leads to oral disorders, tissue loss and dental implant failures. Scientific advancements have led to the identification of newer nanomaterials which can resist biofilms. Parallelly, isolation and differentiation of MSCs from within the dental structures and its adnexa offer great promise for dental restoration/regeneration. Robust screening systems are available today and provide an opportunity to screen pathogen susceptibility, properties of nanomaterials, stem cell plasticity, and gene, protein and cellular interactions. High-throughput technologies and availability of vast information from transcriptomics, epigenetics, genomics, proteomics and metabolomics studies will enable in-depth understanding of the oro-dental disorders as well as the regenerative/differentiation potential of the dental stem cells. Insights from HTS will pave way for successful utilization and effective clinical translation of the dental stem cells and bring about a paradigm shift in the field of tissue engineering and regenerative medicine applications in relation to dentistry.

This is a preview of subscription content, 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   169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
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

Learn about institutional subscriptions

Abbreviations

APC:

Adenomatous polyposis coli

ATP:

Adenosine triphosphate

BLAST:

Basic local alignment search tool

CCAP:

Cancer Chromosome Aberration Project

CGAP:

Cancer Genome Anatomy Project

cGMP:

Current Good Manufacturing Practice

COMS:

Complementary metal oxide semiconductor

CT:

Computed tomography

DAVID:

Database for annotation, visualization and integrated discovery

DNA:

Deoxyribonucleic acid

dNTPs:

Deoxyribonucleotide triphosphates

DPSCs:

Dental pulp stem cells

EBI:

European Bioinformatics Institute

EMBL:

European molecular biology laboratory

ESCs:

Embryonic stem cells

G-CSF:

Granulocyte colony-stimulating factor

GEO:

Gene expression omnibus

GO:

Gene ontology

HCS:

High-content screening

HGBASE:

Human genic biallelic sequences

HGP:

Human Genome Project

HTS:

High-throughput screening

IKB:

Immunome knowledge base

iPSCs:

Induced pluripotent stem cells

KEGG:

Kyoto Encyclopedia of Genes and Genomes

miRNA:

MicroRNA

MRI:

Magnetic resonance imaging

MSCs:

Mesenchymal stem cells

MSD:

Macromolecular structure database

NCBI:

National Center for Biotechnology Information

NIH:

National Institutes of Health

NM:

Nanomaterial

OMIM:

Online Mendelian inheritance in man

ORF Finder:

Open reading frame finder

PCR:

Polymerase chain reaction

PDLSCs:

Periodontal ligament stem cells

RefSeq:

Reference sequence

RNA:

Ribonucleic acid

SAGE:

Serial analysis of gene expression

SCAP:

Stem cells from apical papilla

SGSCs:

Salivary gland stem cells

SMRT:

Single-molecule real time

SMS:

Single-molecule sequencing

SNP:

Single-nucleotide polymorphisms

SOLiD:

Sequencing oligonucleotides by ligation and detection

UniProt:

Universal Protein resource

UniRef:

UniProt Reference

ZMW:

Zero-mode waveguides

References

  • Akintoye SO, Lam T, Shi S, Brahim J, Collins MT, Robey PG (2006) Skeletal site-specific characterization of orofacial and iliac crest human bone marrow stromal cells in same individuals. Bone 38:758–768

    Article  CAS  PubMed  Google Scholar 

  • Ali J, Sabiha B, Jan HU, Haider SA, Khan AA, Ali SS (2017) Genetic etiology of oral cancer. Oral Oncol 70:23–28

    Article  CAS  PubMed  Google Scholar 

  • Alongi DJ et al (2010) Stem/progenitor cells from inflamed human dental pulp retain tissue regeneration potential. Regen Med 5:617–631

    Article  CAS  PubMed  Google Scholar 

  • Amirkia V, Qiubao P (2012) Cell-culture database: literature-based reference tool for human and mammalian experimentallybased cell culture applications. Bioinformation 8:237

    Article  PubMed  PubMed Central  Google Scholar 

  • Apweiler R et al (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Res 32:D115–D119

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arnsdorf EJ, Jones LM, Carter DR, Jacobs CR (2009) The periosteum as a cellular source for functional tissue engineering. Tissue Eng A 15:2637–2642

    Article  CAS  Google Scholar 

  • Ashburner M et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Beikler T, Peters U, Prior K, Eisenacher M, Flemmig TF (2008) Gene expression in periodontal tissues following treatment. BMC Med Genet 1:30. https://doi.org/10.1186/1755-8794-1-30

    Article  CAS  Google Scholar 

  • Bentley DR et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59. https://doi.org/10.1038/nature07517

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ben-Yakar A (2019) High-content and high-throughput in vivo drug screening platforms using microfluidics. Assay Drug Dev Technol 17:8–13

    Article  CAS  PubMed  Google Scholar 

  • Bernimoulin JP (2003) Recent concepts in plaque formation. J Clin Periodontol 30:7–9

    Article  PubMed  Google Scholar 

  • Bongso A, Fong C-Y, Ng S-C, Ratnam S (1994) Fertilization and early embryology: isolation and culture of inner cell mass cells from human blastocysts. Hum Reprod 9:2110–2117

    Article  CAS  PubMed  Google Scholar 

  • Braslavsky I, Hebert B, Kartalov E, Quake SR (2003) Sequence information can be obtained from single DNA molecules. Proc Natl Acad Sci U S A 100:3960–3964. https://doi.org/10.1073/pnas.0230489100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brookes AJ et al (2000) HGBASE: a database of SNPs and other variations in and around human genes. Nucleic Acids Res 28:356–360

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carinci F, Palmieri A, Girardi A, Cura F, Scapoli L, Lauritano D (2015) Genetic risk assessment of periodontal disease in healthy patients. J Forensics Res 6:260

    Google Scholar 

  • Catón J, Bostanci N, Remboutsika E, De Bari C, Mitsiadis TA (2011) Future dentistry: cell therapy meets tooth and periodontal repair and regeneration. J Cell Mol Med 15:1054–1065

    Article  PubMed  PubMed Central  Google Scholar 

  • Chen F-M, Jin Y (2010) Periodontal tissue engineering and regeneration: current approaches and expanding opportunities. Tissue Eng Part B Rev 16:219–255

    Article  CAS  PubMed  Google Scholar 

  • Chen F-M et al (2016) Treatment of periodontal intrabony defects using autologous periodontal ligament stem cells: a randomized clinical trial. Stem Cell Res Ther 7:33

    Article  PubMed  PubMed Central  Google Scholar 

  • Chimenti I et al (2012) Isolation and expansion of adult cardiac stem/progenitor cells in the form of cardiospheres from human cardiac biopsies and murine hearts. In: Somatic stem cells: Methods and Protocols. Humana Press, Totowa, NJ, pp 327–338

    Chapter  Google Scholar 

  • Cho M, Cho T-J, Lim JM, Lee G, Cho J (2013) The establishment of mouse embryonic stem cell cultures on 96-well plates for high-throughput screening. Mol Cells 35:456–461

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chou C-H et al (2015) miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res 44:D239–D247

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cooper PR, Chicca IJ, Holder MJ, Milward MR (2017) Inflammation and regeneration in the dentin-pulp complex: net gain or net loss? J Endod 43:S87–S94

    Article  PubMed  Google Scholar 

  • Costerton JW, Stewart PS, Greenberg EP (1999) Bacterial biofilms: a common cause of persistent infections. Science 284:1318–1322

    Article  CAS  PubMed  Google Scholar 

  • Crawford PJ, Aldred M, Bloch-Zupan A (2007) Amelogenesis imperfecta. Orphanet J Rare Dis 2:17

    Article  PubMed  PubMed Central  Google Scholar 

  • Dabeva MD, Shafritz DA (2003) Hepatic stem cells and liver repopulation. In: Seminars in liver disease, 2003. Vol 04. Copyright© 2003 by Thieme Medical Publishers, Inc., 333 Seventh Avenue, New York, NY 10001, USA. Tel.:+ 1 (212) 584-4662, pp 349–362

    Google Scholar 

  • Davies MC et al (2010) High throughput surface characterization: a review of a new tool for screening prospective biomedical material arrays. J Drug Targeting 18:741–751

    Article  CAS  Google Scholar 

  • De Coppi P et al (2006) Isolation of mesenchymal stem cells from human vermiform appendix. J Surg Res 135:85–91

    Article  PubMed  CAS  Google Scholar 

  • Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA (2003) DAVID: database for annotation, visualization, and integrated discovery. Genome Biol 4:P3

    Article  PubMed  Google Scholar 

  • Dominici M et al (2006) Minimal criteria for defining multipotent mesenchymal stromal cells. The International Society for Cellular Therapy position statement. Cytotherapy 8:315–317

    Article  CAS  PubMed  Google Scholar 

  • Donaldson K, Poland CA (2013) Nanotoxicity: challenging the myth of nano-specific toxicity. Current Opinion in Biotechnology 24:724–734

    Article  CAS  PubMed  Google Scholar 

  • Dowthwaite GP et al (2004) The surface of articular cartilage contains a progenitor cell population. J Cell Sci 117:889–897

    Article  CAS  PubMed  Google Scholar 

  • Dweep H, Sticht C, Pandey P, Gretz N (2011) miRWalk–database: prediction of possible miRNA binding sites by “walking” the genes of three genomes. J Biomed Inform 44:839–847

    Article  CAS  PubMed  Google Scholar 

  • Ferreira JN, Rungarunlert S, Urkasemsin G, Adine C, Souza GR (2016) Three-dimensional bioprinting nanotechnologies towards clinical application of stem cells and their secretome in salivary gland regeneration. Stem Cells Int 2016:7564689

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Foster JS, Kolenbrander PE (2004) Development of a multispecies oral bacterial community in a saliva-conditioned flow cell. Appl Environ Microbiol 70:4340–4348. https://doi.org/10.1128/aem.70.7.4340-4348.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Friedenstein A, Piatetzky-Shapiro I, Petrakova K (1966) Osteogenesis in transplants of bone marrow cells. J Embryol Exp Morphol 16:381–390

    CAS  PubMed  Google Scholar 

  • Gallo R et al (2007) Generation and expansion of multipotent mesenchymal progenitor cells from cultured human pancreatic islets. Cell Death Differ 14:1860

    Article  CAS  PubMed  Google Scholar 

  • Gargett CE, Schwab KE, Zillwood RM, Nguyen HP, Wu D (2009) Isolation and culture of epithelial progenitors and mesenchymal stem cells from human endometrium. Biol Reprod 80:1136–1145

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gilbert P, Maira-Litran T, McBain AJ, Rickard AH, Whyte FW (2002) The physiology and collective recalcitrance of microbial biofilm communities. Adv Microbial Physiology 46:202–256

    Google Scholar 

  • Green ED, Watson JD, Collins FS (2015) Human Genome Project: twenty-five years of big biology. Nature 526:29

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34:D140–D144. https://doi.org/10.1093/nar/gkj112

    Article  CAS  PubMed  Google Scholar 

  • Gronthos S, Mankani M, Brahim J, Robey PG, Shi S (2000) Postnatal human dental pulp stem cells (DPSCs) in vitro and in vivo. Proc Natl Acad Sci 97:13625–13630

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guzmán-Armstrong S (2005) Rampant caries. J Sch Nurs 21:272–278

    Article  PubMed  Google Scholar 

  • Hench LL, Polak JM (2002) Third-generation biomedical materials. Science 295:1014–1017

    Article  CAS  PubMed  Google Scholar 

  • Hook AL, Anderson DG, Langer R, Williams P, Davies MC, Alexander MR (2010) High throughput methods applied in biomaterial development and discovery. Biomaterials 31:187–198

    Article  CAS  PubMed  Google Scholar 

  • Huang GT-J, Sonoyama W, Liu Y, Liu H, Wang S, Shi S (2008) The hidden treasure in apical papilla: the potential role in pulp/dentin regeneration and bioroot engineering. J Endod 34:645–651

    Article  PubMed  PubMed Central  Google Scholar 

  • Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG (2012) ZINC: a free tool to discover chemistry for biology. J Chem Inf Model 52:1757–1768

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jenkinson HF (2011) Beyond the oral microbiome. Environ Microbiol 13:3077–3087

    Article  PubMed  Google Scholar 

  • Jones PA, Baylin SB (2002) The fundamental role of epigenetic events in cancer. Nat Rev Genet 3:415

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kang S-G et al (2010) Isolation and perivascular localization of mesenchymal stem cells from mouse brain. Neurosurgery 67:711–720

    Article  PubMed  Google Scholar 

  • Kim YG et al (2016) Transcriptome sequencing of gingival biopsies from chronic periodontitis patients reveals novel gene expression and splicing patterns. Hum Genomics 10:28. https://doi.org/10.1186/s40246-016-0084-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kolenbrander PE (2000) Oral microbial communities: biofilms, interactions, and genetic systems. Annu Rev Microbiol 54:413–437

    Article  CAS  PubMed  Google Scholar 

  • Kuroda K, Caputo GA (2013) Antimicrobial polymers as synthetic mimics of host‐defense peptides. Wiley Interdiscip Rev Nanomed Nanobiotechnol 5:49–66

    Article  CAS  PubMed  Google Scholar 

  • Laird PW (2003) Early detection: the power and the promise of DNA methylation markers. Nat Rev Cancer 3:253

    Article  CAS  PubMed  Google Scholar 

  • Lander ES (2011) Initial impact of the sequencing of the human genome. Nature 470:187–197. https://doi.org/10.1038/nature09792

    Article  CAS  PubMed  Google Scholar 

  • Lane L et al (2011) neXtProt: a knowledge platform for human proteins. Nucleic Acids Res 40:D76–D83

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ledder RG, Gilbert P, Pluen A, Sreenivasan PK, De Vizio W, McBain AJ (2006) Individual microflora beget unique oral microcosms. J Appl Microbiol 100:1123–1131. https://doi.org/10.1111/j.1365-2672.2006.02847.x

    Article  CAS  PubMed  Google Scholar 

  • Levene MJ, Korlach J, Turner SW, Foquet M, Craighead HG, Webb WW (2003) Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299:682–686. https://doi.org/10.1126/science.1079700

    Article  CAS  PubMed  Google Scholar 

  • Lim J-Y et al (2013) Systemic transplantation of human adipose tissue-derived mesenchymal stem cells for the regeneration of irradiation-induced salivary gland damage. PLoS One 8:e71167

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lin CH, Chang HC, Hsu CH (2016) A microfluidic platform for high-throughput single-cell isolation and culture. J Vis Exp. https://doi.org/10.3791/54105

  • Loesche WJ (1986) Role of Streptococcus mutans in human dental decay. Microbiol Rev 50:353

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lombaert IM et al (2008) Rescue of salivary gland function after stem cell transplantation in irradiated glands. PLoS One 3:e2063

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lombaert I, Movahednia MM, Adine C, Ferreira JN (2017) Concise review: salivary gland regeneration: therapeutic approaches from stem cells to tissue organoids. Stem Cells 35:97–105

    Article  CAS  PubMed  Google Scholar 

  • Lu H, Xie C, Zhao Y-M, Chen F-M (2013) Translational research and therapeutic applications of stem cell transplantation in periodontal regenerative medicine. Cell Transplant 22:205–229

    Article  PubMed  Google Scholar 

  • Luder HU (2015) Malformations of the tooth root in humans. Front Physiol 6:307

    Article  PubMed  PubMed Central  Google Scholar 

  • Maeda H, Wada N, Nakamuta H, Akamine A (2004) Human periapical granulation tissue contains osteogenic cells. Cell Tissue Res 315:203–208

    Article  PubMed  Google Scholar 

  • Magennis E, Hook A, Davies M, Alexander C, Williams P, Alexander MR (2016) Engineering serendipity: high-throughput discovery of materials that resist bacterial attachment. Acta Biomaterialia 34:84–92

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mah TF, O’Toole GA (2001) Mechanisms of biofilm resistance to antimicrobial agents. Trends Microbiol 9:34–39

    Article  CAS  PubMed  Google Scholar 

  • Marcus AJ, Woodbury D (2008) Fetal stem cells from extra-embryonic tissues: do not discard. J Cell Mol Med 12:730–742

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Margulies M et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380. https://doi.org/10.1038/nature03959

    Article  PubMed  PubMed Central  Google Scholar 

  • Marrelli M, Paduano F, Tatullo M (2013) Cells isolated from human periapical cysts express mesenchymal stem cell-like properties. Int J Biol Sci 9:1070

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marrelli M, Paduano F, Tatullo M (2015) Human periapical cyst–mesenchymal stem cells differentiate into neuronal cells. J Dent Res 94:843–852

    Article  CAS  PubMed  Google Scholar 

  • Marsh PD (1994) Microbial ecology of dental plaque and its significance in health and disease. Adv Dent Res 8:263–271

    Article  CAS  PubMed  Google Scholar 

  • Marsh PD (2006) Dental plaque as a biofilm and a microbial community–implications for health and disease. BMC Oral health BioMed Central 1:S14

    Article  CAS  Google Scholar 

  • Martin C, Li T, Hegarty E, Zhao P, Mondal S, Ben-Yakar A (2018) Line excitation array detection fluorescence microscopy at 0.8 million frames per second. Nat Commun 9:4499

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Marynka-Kalmani K, Treves S, Yafee M, Rachima H, Gafni Y, Cohen MA, Pitaru S (2010) The lamina propria of adult human oral mucosa harbors a novel stem cell population. Stem Cells 28:984–995

    CAS  PubMed  Google Scholar 

  • McBain AJ, Sissons C, Ledder RG, Sreenivasan PK, De Vizio W, Gilbert P (2005) Development and characterization of a simple perfused oral microcosm. J Appl Microbiol 98:624–634. https://doi.org/10.1111/j.1365-2672.2004.02483.x

    Article  CAS  PubMed  Google Scholar 

  • Miura M, Gronthos S, Zhao M, Lu B, Fisher LW, Robey PG, Shi S (2003) SHED: stem cells from human exfoliated deciduous teeth. Proc Natl Acad Sci 100:5807–5812

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mogushi K, Tanaka H (2013) PathAct: a novel method for pathway analysis using gene expression profiles. Bioinformation 9:394

    Article  PubMed  PubMed Central  Google Scholar 

  • Mondal S, Hegarty E, Martin C, Gökçe SK, Ghorashian N, Ben-Yakar A (2016) Large-scale microfluidics providing high-resolution and high-throughput screening of Caenorhabditis elegans poly-glutamine aggregation model. Nat Commun 7:13023

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Morsczeck C et al (2005) Isolation of precursor cells (PCs) from human dental follicle of wisdom teeth. Matrix Biol 24:155–165

    Article  CAS  PubMed  Google Scholar 

  • Nair P (2004) Pathogenesis of apical periodontitis and the causes of endodontic failures. Crit Rev Oral Biol Med 15:348–381

    Article  CAS  PubMed  Google Scholar 

  • Nakashima M, Iohara K, Murakami M, Nakamura H, Sato Y, Ariji Y, Matsushita K (2017) Pulp regeneration by transplantation of dental pulp stem cells in pulpitis: a pilot clinical study. Stem Cell Res Ther 8:61

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nel A, Xia T, Meng H, Wang X, Lin S, Ji Z, Zhang H (2012) Nanomaterial toxicity testing in the 21st century: use of a predictive toxicological approach and high-throughput screening. Acc Chem Res 46:607–621

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nishimura D (2001) BioCarta Biotech Software & Internet Report: The Computer Software Journal for Scient 2:117–120

    Google Scholar 

  • Nyren P, Lundin A (1985) Enzymatic method for continuous monitoring of inorganic pyrophosphate synthesis. Anal Biochem 151:504–509

    Article  CAS  PubMed  Google Scholar 

  • Ono H, Obana A, Usami Y, Sakai M, Nohara K, Egusa H, Sakai T (2015) Regenerating salivary glands in the microenvironment of induced pluripotent stem cells. Biomed Res Int 2015:1

    Google Scholar 

  • Ortutay C, Vihinen M (2009) Immunome knowledge base (IKB): an integrated service for immunome research. BMC Immunol 10:3

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Owen M (1985) Lineage of osteogenic cells and their relationship to the stromal system. In: Peck WA, editor. Bone and mineral research, Vol. 3. Amsterdam: Elsevier Science Publishers; pp 1–25

    Google Scholar 

  • Pamies D et al (2018) Advanced Good Cell Culture Practice for human primary, stem cell-derived and organoid models as well as microphysiological systems. ALTEX 35:353–378. https://doi.org/10.14573/altex.1710081

    Article  PubMed  Google Scholar 

  • Park D, Lim J, Park JY, Lee S-H (2015) Concise review: stem cell microenvironment on a chip: current technologies for tissue engineering and stem cell biology. Stem Cells Transl Med 4:1352–1368

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Patel J, Gudehithlu KP, Dunea G, Arruda JA, Singh AK (2010) Foreign body-induced granulation tissue is a source of adult stem cells. Transl Res 155:191–199

    Article  CAS  PubMed  Google Scholar 

  • Pattyn F et al (2006) methBLAST and methPrimerDB: web-tools for PCR based methylation analysis. BMC Bioinformatics 7:496

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Peters BM, Jabra-Rizk MA, O’May GA, Costerton JW, Shirtliff ME (2012) Polymicrobial interactions: impact on pathogenesis and human disease. Clin Microbiol Rev 25:193–213. https://doi.org/10.1128/cmr.00013-11

    Article  PubMed  PubMed Central  Google Scholar 

  • Prasad MK et al (2016) A targeted next-generation sequencing assay for the molecular diagnosis of genetic disorders with orodental involvement. J Med Genet 53:98–110

    Article  CAS  PubMed  Google Scholar 

  • Prina-Mello A, Crosbie-Staunton K, Salas G, del Puerto Morales M, Volkov Y (2013) Multiparametric toxicity evaluation of SPIONs by high content screening technique: identification of biocompatible multifunctional nanoparticles for nanomedicine Ieee. Trans Magn 49:377–382

    Article  Google Scholar 

  • Pringle S et al (2016) Human salivary gland stem cells functionally restore radiation damaged salivary glands. Stem Cells 34:640–652

    Article  CAS  PubMed  Google Scholar 

  • Roberts AP, Mullany P (2010) Oral biofilms: a reservoir of transferable, bacterial, antimicrobial resistance. Expert Rev Anti Infect Ther 8:1441–1450. https://doi.org/10.1586/eri.10.106

    Article  CAS  PubMed  Google Scholar 

  • Rothberg JM et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–352. https://doi.org/10.1038/nature10242

    Article  CAS  PubMed  Google Scholar 

  • Sato A, Okumura K, Matsumoto S, Hattori K, Hattori S, Shinohara M, Endo F (2007) Isolation, tissue localization, and cellular characterization of progenitors derived from adult human salivary glands. Cloning Stem Cells 9:191–205

    Article  CAS  PubMed  Google Scholar 

  • Selwitz RH, Ismail AI, Pitts NB (2007) Dental caries. Lancet 369:51–59

    Article  CAS  PubMed  Google Scholar 

  • Seo B-M et al (2004) Investigation of multipotent postnatal stem cells from human periodontal ligament. Lancet 364:149–155

    Article  CAS  PubMed  Google Scholar 

  • Shendure J et al (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728–1732. https://doi.org/10.1126/science.1117389

    Article  CAS  PubMed  Google Scholar 

  • Short HB, Clark VL, Kellogg DS Jr, Young FE (1982) Anaerobic survival of clinical isolates and laboratory strains of Neisseria gonorrhoea: use in transfer and storage. J Clin Microbiol 15:915–919

    CAS  PubMed  PubMed Central  Google Scholar 

  • Smith AW (2005) Biofilms and antibiotic therapy: is there a role for combating bacterial resistance by the use of novel drug delivery systems? Adv Drug Deliv Rev 57:1539–1550

    Article  CAS  PubMed  Google Scholar 

  • Smith LM et al (1986) Fluorescence detection in automated DNA sequence analysis. Nature 321:674–679. https://doi.org/10.1038/321674a0

    Article  CAS  PubMed  Google Scholar 

  • Stewart PS (1996) Theoretical aspects of antibiotic diffusion into microbial biofilms. Antimicrob Agents Chemother 40:2517–2522

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stoesser G et al (2002) The EMBL nucleotide sequence database. Nucleic Acids Res 30:21–26

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stookey GK (2008) The effect of saliva on dental caries. J Am Dent Assoc 139(Suppl):11s–17s

    Article  PubMed  Google Scholar 

  • Sud M et al (2015) Metabolomics Workbench: an international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. Nucleic Acids Res 44:D463–D470

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sumiyama K, Matsumoto N, Garcon-Yoshida J, Ukai H, Ueda HR, Tanaka Y (2018) Easy and efficient production of completely embryonic-stem-cell-derived mice using a micro-aggregation device. PLoS One 13:e0203056. https://doi.org/10.1371/journal.pone.0203056

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH (2007) UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23:1282–1288

    Article  CAS  PubMed  Google Scholar 

  • Takahashi K, Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126:663–676

    Article  CAS  PubMed  Google Scholar 

  • Tatullo M, Codispoti B, Pacifici A, Palmieri F, Marrelli M, Pacifici L, Paduano F (2017) Potential use of human periapical cyst-mesenchymal stem cells (hPCy-MSCs) as a novel stem cell source for regenerative medicine applications. Front Cell Dev Biol 5:103

    Article  PubMed  PubMed Central  Google Scholar 

  • Thomson JA, Itskovitz-Eldor J, Shapiro SS, Waknitz MA, Swiergiel JJ, Marshall VS, Jones JM (1998) Embryonic stem cell lines derived from human blastocysts science, vol 282, pp 1145–1147

    Google Scholar 

  • Toma JG, Akhavan M, Fernandes KJ, Barnabé-Heider F, Sadikot A, Kaplan DR, Miller FD (2001) Isolation of multipotent adult stem cells from the dermis of mammalian skin. Nat Cell Biol 3:778

    Article  CAS  PubMed  Google Scholar 

  • Tran SD et al (2013) Paracrine effects of bone marrow soup restore organ function, regeneration, and repair in salivary glands damaged by irradiation. PLoS One 8:e61632

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tseng SC (1989) Concept and application of limbal stem cells. Eye 3:141

    Article  PubMed  Google Scholar 

  • van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C (2014) Ten years of next-generation sequencing technology. Trends Genet 30:418–426. https://doi.org/10.1016/j.tig.2014.07.001

    Article  CAS  PubMed  Google Scholar 

  • van Vliet E (2011) Current standing and future prospects for the technologies proposed to transform toxicity testing in the 21st century. ALTEX 28:17–44

    Article  PubMed  Google Scholar 

  • Van Vliet E et al (2014) Current approaches and future role of high content imaging in safety sciences and drug discovery Alternatives to Animal Experimentation. ALTEX 31:479–493

    Article  PubMed  Google Scholar 

  • Velugula-Yellela SR et al (2018) Use of high-throughput automated microbioreactor system for production of model IgG1 in CHO Cells. J Vis Exp JoVE. https://doi.org/10.3791/58231

  • von Bültzingslöwen I et al (2007) Salivary dysfunction associated with systemic diseases: systematic review and clinical management recommendations. Oral Surg Oral Med Oral Pathol Oral Radiol Endod 103:S57. e51–S57. e15

    Article  Google Scholar 

  • Wang F et al (2017) Transcriptome analysis of coding and long non-coding RNAs highlights the regulatory network of cascade initiation of permanent molars in miniature pigs. BMC Genomics 18:148. https://doi.org/10.1186/s12864-017-3546-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wendell S et al (2010) Taste genes associated with dental caries. J Dent Res 89:1198–1202

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Werneck R et al (2011) A major gene effect controls resistance to caries. J Dent Res 90:735–739

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wheeler DL et al (2006) Database resources of the national center for biotechnology information. Nucleic Acids Res 35:D5–D12

    Article  PubMed  PubMed Central  Google Scholar 

  • Wishart DS, Mandal R, Stanislaus A, Ramirez-Gaona M (2016) Cancer metabolomics and the human metabolome database. Meta 6:10

    Google Scholar 

  • Yang ZH et al (2009) Apical tooth germ cell-conditioned medium enhances the differentiation of periodontal ligament stem cells into cementum/periodontal ligament-like tissues. J Periodontal Res 44:199–210

    Article  PubMed  Google Scholar 

  • Yu J et al (2007) Induced pluripotent stem cell lines derived from human somatic cells. Science 318:1917–1920

    Article  CAS  PubMed  Google Scholar 

  • Zhang Q, Shi S, Liu Y, Uyanne J, Shi Y, Shi S, Le AD (2009) Mesenchymal stem cells derived from human gingiva are capable of immunomodulatory functions and ameliorate inflammation-related tissue destruction in experimental colitis. J Immunol 183:7787–7798

    Article  CAS  PubMed  Google Scholar 

  • Zuk PA et al (2001) Multilineage cells from human adipose tissue: implications for cell-based therapies. Tissue Eng 7:211–228

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors acknowledge the grant (13-MED2437-03) funding provided by the National Plan for Science, Technology and Innovation (MAARIFAH), King Abdulaziz City for Science and Technology, The Kingdom of Saudi Arabia. They also acknowledge with thanks the Science and Technology Unit (STU), King Abdulaziz University for their excellent technical support.

Statement of Conflicts of Interest 

All authors have no conflicts of interests.

Author information

Authors and Affiliations

  1. Faculty of Dentistry, Ibn Sina National College for Medical Sciences, Al Mahjar, Jeddah, Saudi Arabia

    Saravanan Ramaswamy & Kavitha Odathurai Marusamy

  2. Stem Cell Research Unit, Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia

    Gauthaman Kalamegam

  3. Faculty of Medicine, AIMST University, Semeling, Bedong, Kedah, Malaysia

    Gauthaman Kalamegam

Authors
  1. Saravanan Ramaswamy
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kavitha Odathurai Marusamy
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gauthaman Kalamegam
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gauthaman Kalamegam .

Editor information

Editors and Affiliations

  1. Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia

    Noor Ahmad Shaik

  2. Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia

    Khalid Rehman Hakeem

  3. Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia

    Babajan Banaganapalli

  4. Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia

    Ramu Elango

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Ramaswamy, S., Marusamy, K.O., Kalamegam, G. (2019). Dental Stem Cells in Regenerative Medicine: Emerging Trends and Prospects in the Era of Bioinformatics. In: Shaik, N., Hakeem, K., Banaganapalli, B., Elango, R. (eds) Essentials of Bioinformatics, Volume II. Springer, Cham. https://doi.org/10.1007/978-3-030-18375-2_8

Download citation

Publish with us

Policies and ethics

Search

Navigation