Abstract
Introduction
In recent years, the use of high-throughput transcriptomics and proteomics has expanded
rapidly in molecular biology and biomedical science. These methods, including DNA
microarray and suppression subtractive hybridization at the mRNA level and 2-dimensional
electrophoresis and antibody arrays at the protein level, enable studying the expression
levels of thousands of genes and proteins simultaneously and thus allow forming genome-wide
expression profiles and evaluation of biologic signaling networks.
Methods
This review discusses the most used high-throughput expression analysis methods and
their use in pulp biologic research.
Results
The use of these methods in pulp biology has been limited but is expanding. The methods
have been used to compare pulp and bone marrow stem cells and to study the function
of pulp tissue in vivo and in vitro.
Conclusions
Even though the adoption of the high-throughput transcriptomic and proteomic techniques
in pulp biology has been fairly slow, their use is increasing and will significantly
increase the understanding of pulp tissue physiology and pathology. The comprehensive
data of the transcriptome and proteome of the pulp tissue and the odontoblasts will
facilitate the understanding of their functions during health and disease and provide
novel target molecules for diagnosis and treatment. Identification of the genes controlling
odontoblast differentiation might lead to development of methods enabling induction
of reparative dentin formation under carious lesions. Identification of the genes
active during dentinogenesis might lead to recognition of regulatory factors, which
would cause secondary dentinogenesis to proceed at the rate of primary dentinogenesis.
Key Words
To read this article in full you will need to make a payment
Purchase one-time access:
Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online accessOne-time access price info
- For academic or personal research use, select 'Academic and Personal'
- For corporate R&D use, select 'Corporate R&D Professionals'
Subscribe:
Subscribe to Journal of EndodonticsAlready a print subscriber? Claim online access
Already an online subscriber? Sign in
Register: Create an account
Institutional Access: Sign in to ScienceDirect
References
- A comparison of selected mRNA and protein abundances in human liver.Electrophoresis. 1997; 18: 533-537
- Regeneration potential of the young permanent tooth: what does the future hold?.Pediatr Dent. 2008; 30: 253-260
- Quantitative monitoring of gene expression patterns with a complementary DNA microarray.Science. 1995; 270: 467-470
- Expression monitoring by hybridization to high-density oligonucleotide arrays.Nat Biotechnol. 1996; 14: 1675-1680
- A novel approach for high-quality microarray processing using third-dye array visualization technology.IEEE Trans Nanobioscience. 2003; 2: 193-201
- Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays.BMC Bioinformatics. 2006; 7: 378
- Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression.Proc Natl Acad Sci U S A. 2004; 101: 9309-9314
- A gene-coexpression network for global discovery of conserved genetic modules.Science. 2003; 302: 249-255
- Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues.Genome Biol. 2008; 9: R139
- Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.Nat Genet. 2001; 29: 365-371
- The MicroArray quality control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.Nat Biotechnol. 2006; 24: 1151-1161
- Evaluation of DNA microarray results with quantitative gene expression platforms.Nat Biotechnol. 2006; 24: 1115-1122
- Comparative gene expression profile analysis between native human odontoblasts and pulp tissue.Int Endod J. 2008; 41: 117-127
- Effects of pooling mRNA in microarray class comparisons.Bioinformatics. 2004; 20: 3318-3325
- On the utility of pooling biological samples in microarray experiments.Proc Natl Acad Sci U S A. 2005; 102: 4252-4257
- Biases induced by pooling samples in microarray experiments.Bioinformatics. 2007; 23: i313-i318
- Effects of TGF-beta1 on interleukin profile of human dental pulp and odontoblasts.Cytokine. 2007; 40: 44-51
- Serial analysis of gene expression.Science. 1995; 270: 484-487
- Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays.Nat Biotechnol. 2000; 18: 630-634
- Advances in functional protein microarray technology.FEBS J. 2005; 272: 5400-5411
- High resolution two-dimensional electrophoresis of basic as well as acidic proteins.Cell. 1977; 12: 1133-1141
- Proteomics.Annu Rev Biochem. 2003; 72: 783-812
- Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions.Genome Biol. 2001; 2 (RESEARCH0004)
- The application of protein microarrays to serum diagnostics: prostate cancer as a test case.Dis Markers. 2001; 17: 225-234
- BIA/MS: interfacing biomolecular interaction analysis with mass spectrometry.Anal Biochem. 1997; 244: 124-132
- Surface plasmon resonance: towards an understanding of the mechanisms of biological molecular recognition.Curr Opin Chem Biol. 2001; 5: 572-577
- Improved sensitivity of biomolecular interaction analysis mass spectrometry for the identification of interacting molecules.Proteomics. 2003; 3: 402-412
- Perivascular niche of postnatal mesenchymal stem cells in human bone marrow and dental pulp.J Bone Miner Res. 2003; 18: 696-704
- Stem cell properties of human dental pulp stem cells.J Dent Res. 2002; 81: 531-535
- Postnatal human dental pulp stem cells (DPSCs) in vitro and in vivo.Proc Natl Acad Sci U S A. 2000; 97: 13625-13630
- Odontoblast differentiation of human dental pulp cells in explant cultures.Calcif Tissue Int. 2000; 66: 129-138
- Human dentin production in vitro.Exp Cell Res. 2000; 258: 33-41
- In vitro differentiation and mineralization of human dental pulp cells induced by dentin extract.In Vitro Cell Dev Biol Anim. 2005; 41: 232-238
- Matrix and TGF-beta-related gene expression during human dental pulp stem cell (DPSC) mineralization.In Vitro Cell Dev Biol Anim. 2007; 43: 120-128
- Simvastatin induces the odontogenic differentiation of human dental pulp stem cells in vitro and in vivo.J Endod. 2009; 35: 367-372
- Odontoblast cells immortalized by telomerase produce mineralized dentin-like tissue both in vitro and in vivo.J Biol Chem. 2002; 277: 19976-19981
- Temperature sensitive simian virus 40 large T antigen immortalization of murine odontoblast cell cultures: establishment of clonal odontoblast cell line.Connect Tissue Res. 1995; 33: 97-103
- Dentin-specific proteins in MDPC-23 cell line.Eur J Oral Sci. 1998; 106: 260-266
- Cluster analysis and gene expression profiles: a cDNA microarray system-based comparison between human dental pulp stem cells (hDPSCs) and human mesenchymal stem cells (hMSCs) for tissue engineering cell therapy.Biomaterials. 2006; 27: 3766-3781
- Comparison of human dental pulp and bone marrow stromal stem cells by cDNA microarray analysis.Bone. 2001; 29: 532-539
- Activation of the FGF signaling pathway and subsequent induction of mesenchymal stem cell differentiation by inorganic polyphosphate.Int J Biol Sci. 2008; 4: 37-47
- STRO-1 selected rat dental pulp stem cells transfected with adenoviral-mediated human bone morphogenetic protein 2 gene show enhanced odontogenic differentiation.Tissue Eng. 2007; 13: 2803-2812
- Characterization and gene expression of high conductance calcium-activated potassium channels displaying mechanosensitivity in human odontoblasts.J Biol Chem. 2000; 275: 25556-25561
- General expression profiles of human native odontoblasts and pulp-derived cultured odontoblast-like cells are similar but reveal differential neuropeptide expression levels.Arch Oral Biol. 2009; 54: 55-62
- Odontoblast primary cilia: facts and hypotheses.Cell Biol Int. 2004; 28: 93-99
- Mesenchymal stem cell-mediated functional tooth regeneration in swine.PLoS One. 2006; 1: e79
- The hidden treasure in apical papilla: the potential role in pulp/dentin regeneration and bioroot engineering.J Endod. 2008; 34: 645-651
- Gene expression profiling of pulpal tissue reveals the molecular complexity of dental caries.Biochim Biophys Acta. 2005; 1741: 271-281
- Analysis of gene and protein expression in healthy and carious tooth pulp with cDNA microarray and two-dimensional gel electrophoresis.Eur J Oral Sci. 2005; 113: 369-379
- Notch signaling: cell fate control and signal integration in development.Science. 1999; 284: 770-776
- JAGGED2: a putative notch ligand expressed in the apical ectodermal ridge and in sites of epithelial-mesenchymal interactions.Mech Dev. 1997; 69: 203-207
- Delta-notch signaling in odontogenesis: correlation with cytodifferentiation and evidence for feedback regulation.Dev Biol. 1998; 204: 420-431
- Reactivation of delta-notch signaling after injury: complementary expression patterns of ligand and receptor in dental pulp.Exp Cell Res. 1999; 246: 312-318
- Notch2 protein distribution in human teeth under normal and pathological conditions.Exp Cell Res. 2003; 282: 101-109
- Molecular characterization of young and mature odontoblasts.Bone. 2009; 45: 693-703
- Microarray evaluation of age-related changes in human dental pulp.J Endod. 2009; 35: 1211-1217
- Gene expression in a pure population of odontoblasts isolated by laser-capture microdissection.J Dent Res. 2001; 80: 1963-1967
- Analysis of odontoblast gene expression using a novel approach, laser capture microdissection.Connect Tissue Res. 2002; 43: 376-380
- Microarray expression profiling of human dental pulp from single subject.Clin Invest Med. 2008; 31: E55-E61
- Altered gene expression in human cleidocranial dysplasia dental pulp cells.Arch Oral Biol. 2005; 50: 227-236
- Lipoteichoic acid increases TLR and functional chemokine expression while reducing dentin formation in in vitro differentiated human odontoblasts.J Immunol. 2006; 176: 2880-2887
- Different roles of odontoblasts and fibroblasts in immunity.J Dent Res. 2008; 87: 256-261
- Detection of dentin sialoprotein in rat periodontium.Eur J Oral Sci. 2004; 112: 163-170
- The expression of dentin sialophosphoprotein gene in bone.J Dent Res. 2002; 81: 392-394
- Dentinogenesis imperfecta 1 with or without progressive hearing loss is associated with distinct mutations in DSPP.Nat Genet. 2001; 27: 201-204
- HUGO (FNDC3A): a new gene overexpressed in human odontoblasts.J Dent Res. 2008; 87: 131-136
- Immortalization and characterization of human dental pulp cells with odontoblastic differentiation.Arch Oral Biol. 2007; 52: 727-731
- A substractive PCR-based cDNA library from human odontoblast cells: identification of novel genes expressed in tooth forming cells.Matrix Biol. 2000; 19: 421-430
- Isolation and partial sequencing of potentially odontoblast-specific/enriched rat cDNA clones obtained by suppression subtractive hybridization.Arch Oral Biol. 2001; 46: 249-260
- Identification of differentially expressed cDNA transcripts from a rat odontoblast cell line.Bone. 2005; 37: 578-588
- Differentially expressed protein profile of human dental pulp cells in the early process of odontoblast-like differentiation in vitro.J Endod. 2008; 34: 1077-1084
- Chitosan monomer promotes tissue regeneration on dental pulp wounds.J Biomed Mater Res A. 2006; 76: 711-720
- Characterization of dental pulp stem cells of human tooth germs.J Dent Res. 2008; 87: 676-681
Pääkkönen V. Expression profiling of human pulp tissue and odontoblasts in vivo and in vitro. University of Oulu, Oulu, Finland: Acta Universitatis Ouluensis, 2009. Available at: http://herkules.oulu.fi/isbn9789514290053/isbn9789514290053.pdf. Accessed October 2009.
- Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries.Proc Natl Acad Sci U S A. 1996; 93: 6025-6030
Article info
Publication history
Published online: December 07, 2009
Identification
Copyright
© 2010 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.
