Transcriptional profiling of bone regeneration. Insight into the molecular complexity of wound repair

The healing of skeletal fractures is essentially a replay of bone development, involving the closely regulated, interdependent processes of chondrogenesis and osteogenesis. Using a rat femur model of bone healing to determine the degree of transcriptional complexity of these processes, suppressive subtractive hybridization (SSH) was performed between RNA isolated from intact bone to that of callus from post-fracture (PF) days 3, 5, 7, and 10 as a means of identifying up-regulated genes in the regenerative process. Analysis of 3,635 cDNA clones revealed 588 known genes (65.8%, 2392 clones) and 821 expressed sequence tags (ESTs) (31%, 1,127). The remaining 116 cDNAs (3.2%) yielded no homology and presumably represent novel genes. Microarrays were then constructed to confirm induction of expression and determine the temporal profile of all isolated cDNAs during fracture healing. These experiments confirmed that approximately 90 and approximately 80% of the subtracted known genes and ESTs are up-regulated (> or = 2.5-fold) during the repair process, respectively. Clustering analysis revealed subsets of genes, both known and unknown, that exhibited distinct expression patterns over 21 days (PF), indicating distinct roles in the healing process. Additionally, this transcriptional profiling of bone repair revealed a host of activated signaling molecules and even pathways (i.e. Wnt). In summary, the data demonstrate, for the fist time, that the healing process is exceedingly complex, involves thousands of activated genes, and indicates that groups of genes rather than individual molecules should be considered if the regeneration of bone is to be accelerated exogenously.