INTRODUCTION: In the rat cranial suture model, the posterior frontal (PF) suture fuses while all other sutures, including the sagittal (SAG), remain patent. Cranial suture fate (i.e. fusion or patency) appears to be governed by paracrine signaling from the underlying dura mater. Using a candidate gene approach, we have discovered that the dura mater is regionally differentiated and controls gene expression in the overlying cranial suture complex, by temporally and spatially supplying osteoinductive growth factors (e.g. TGF-bs or FGF-2). For the past 5 years, our laboratory has been genetically piecing together this cranial suture paracrine signaling puzzle one gene at a time. Until recently, examining the coordinate control of gene expression was time consuming and progress was slow. With the introduction of microarray technology, we can now simultaneously examine the expression of over 8,000 genes in the rat cranial suture complex. In this study, we simultaneously examined the expression profiles of genes during programmed suture fusion or patency in order to identify additional candidate genes and develop a genomic "blueprint" of cranial suture biology. By developing blueprints of gene expression in fusing and patent sutures, we can begin to understand the coordinated control of gene expression, but more importantly, we can begin to understand gene function. Ultimately, comparative expression analysis may identify signature craniosynostotic gene cascades that will lead to the intelligent design of upstream-targeted biologic therapeutic interventions.

METHODS: PF and SAG sutures with associated dura mater were harvested from rats before, during, and after the period of predicted suture fusion (postnatal days 5, 10, 15, 20, and 30). The gene expression profiles were compared using the Affymetrix Rat Genome U34A chip, containing 16-20 pairs of specific, unique 25-mer oligonucleotide probes for full length annotated genes and EST clusters. Data mining and cluster analysis was performed using Affymetrix Microarray Suite (version 4.0) and Genespring (version 4.5) software.

RESULTS: There were significant differences in the gene expression profiles for all comparison groups at each time point examined. For example, when we compared day 15 PF (fusing) sutures to day 15 SAG (patent) sutures, 68 genes were increased and 157 genes were decreased >3-fold, respectively. Importantly, many of the genes identified in these comparisons have not been previously reported in association with cranial suture biology. For example, BMP-3, a powerful osteogenic antagonist, was markedly elevated in the patent SAG suture, but completely absent in the fusing PF suture.

CONCLUSIONS: In this study, we have identified many known and unknown candidate genes that may play an important role in cranial suture fusion or patency. Ongoing studies are defining the function of these genes within the suture complex.