Comparative gene expression profile analysis between native human odontoblasts and pulp tissue.
OBJECTIVE
To undertake a large-scale analysis of the expression profiles of native human pulp tissue and odontoblasts, and search for genes expressed only in odontoblasts.


METHODS
Microarray was performed to pooled pulp and odontoblasts of native human third molars and to pooled +/- TGF-beta1 cultured pulps and odontoblasts (137 teeth). The repeatability of microarray analysis was estimated by comparing the experimental pulp samples with expression profiles of two pulp samples downloaded from the GEO database. The genes expressed only in the experimental pulp samples or in odontoblasts were divided into categories, and the expression of selected odontoblast-specific genes of extracellular matrix (ECM) organization and biogenesis category was confirmed with RT-PCR and Western blot.


RESULTS
A 85.3% repeatability was observed between pulp microarrays, demonstrating the high reliability of the technique. Overall 1595 probe sets were positive only in pulp and 904 only in odontoblasts. Sixteen expressed sequence tags (ESTs), which represent transcribed sequences encoding possibly unknown genes, were detected only in odontoblasts; two consistently expressed in all odontoblast samples. Matrilin 4 (MATN4) was the only ECM biogenesis and organization related gene detected in odontoblasts but not in pulp by microarray and RT-PCR. MATN4 protein expression only in odontoblasts was confirmed by Western blot.


CONCLUSIONS
Pulp tissue and odontoblast gene expression profiling provides basic data for further, more detailed protein analysis. In addition, MATN4 and the two ESTs could serve as an odontoblast differentiation marker, e.g. in odontoblast stem cell research.
Pääkkönen
V
V
Institute of Dentistry, University of Oulu, Oulu, Finland.
Vuoristo
J T
JT
Salo
T
T
Tjäderhane
L
L
D015415:Biomarkers / Q000032:analysis; D015153:Blotting, Western; D002478:Cells, Cultured; D024161:Collagen Type XI / Q000235:genetics; D003782:Dental Pulp / Q000378:metabolism*; D020224:Expressed Sequence Tags / Q000737:chemistry; D005109:Extracellular Matrix / Q000235:genetics; D016326:Extracellular Matrix Proteins / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D064235:Matrilin Proteins; D046228:Microarray Analysis; D009804:Odontoblasts / Q000378:metabolism*; D010750:Phosphoproteins / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012795:Sialoglycoproteins / Q000235:genetics; D046509:Tissue Culture Techniques; D014158:Transcription, Genetic / Q000235:genetics; D053773:Transforming Growth Factor beta1 / Q000378:metabolism; D000099311:Dentin Sialophosphoprotein
D015415:Biomarkers; D024161:Collagen Type XI; D016326:Extracellular Matrix Proteins; D064235:Matrilin Proteins; D010750:Phosphoproteins; D012795:Sialoglycoproteins; D053773:Transforming Growth Factor beta1; D000099311:Dentin Sialophosphoprotein; C577548:MATN4 protein, human