Human Stem Cell Cultures from Cleft Lip/Palate Patients Show Enrichment of Transcripts Involved in Extracellular Matrix Modeling By Comparison to Controls

Abstract

Nonsyndromic cleft lip and palate (NSCL/P) is a complex disease resulting from failure of fusion of facial primordia, a complex developmental process that includes the epithelial-mesenchymal transition (EMT). Detection of differential gene transcription between NSCL/P patients and control individuals offers an interesting alternative for investigating pathways involved in disease manifestation. Here we compared the transcriptome of 6 dental pulp stem cell (DPSC) cultures from NSCL/P patients and 6 controls. Eighty-seven differentially expressed genes (DEGs) were identified. The most significant putative gene network comprised 13 out of 87 DEGs of which 8 encode extracellular proteins: ACAN, COL4A1, COL4A2, GDF15, IGF2, MMP1, MMP3 and PDGFa. Through clustering analyses we also observed that MMP3, ACAN, COL4A1 and COL4A2 exhibit co-regulated expression. Interestingly, it is known that MMP3 cleavages a wide range of extracellular proteins, including the collagens IV, V, IX, X, proteoglycans, fibronectin and laminin. It is also capable of activating other MMPs. Moreover, MMP3 had previously been associated with NSCL/P. The same general pattern was observed in a further sample, confirming involvement of synchronized gene expression patterns which differed between NSCL/P patients and controls. These results show the robustness of our methodology for the detection of differentially expressed genes using the RankProd method. In conclusion, DPSCs from NSCL/P patients exhibit gene expression signatures involving genes associated with mechanisms of extracellular matrix modeling and palate EMT processes which differ from those observed in controls. This comparative approach should lead to a more rapid identification of gene networks predisposing to this complex malformation syndrome than conventional gene mapping technologies.Electronic supplementary materialThe online version of this article (doi:10.1007/s12015-010-9197-3) contains supplementary material, which is available to authorized users.

Association of MMP3 and TIMP2 promoter polymorphisms with nonsyndromic oral clefts

“…Taken together, these findings imply that Mmp-3 induces epithelial breakdown at the medial epithelial edge of fusing palatal shelves if present in adequate amounts, and that insufficient or null expression may lead to failures in palatal fusion. Corroborating with these observations, a recent transcriptome analysis comparing dental pulp stem cells from cleft lip/palate patients and controls revealed 87 differentially expressed genes and downregulation of MMP3 in cleft patients when compared to controls (Bueno et al, 2011). …”

Expression and mutation analyses implicate ARHGAP29 as the etiologic gene for the cleft lip with or without cleft palate locus identified by genome‐wide association on chromosome 1p22

“…Support for this mechanism is provided by recent expression profiling of dental pulp stem cell cultures obtained from individuals with NSCL/P which showed a nearly 3-fold decrease in ARHGAP29 compared to cultures from unaffected controls (Bueno et al, 2011). If this is the case, the loss of a GAP would maintain Rho in an active, GTP-bound form, effectively increasing Rho activity.…”

Evolutionary dynamism of the primate LRRC37 gene family

“…These isoforms, as well as LRRC37A4 proteins, may be directly secreted in the extracellular space bypassing proteolytic cleavage since they still retain the signal peptide. It is interesting that the LRRC37A family was among 87 genes recently identified as differentially expressed in dental pulp stem cell cultures from nonsyndromic cleft-lip and palate patients when compared to controls (Bueno et al 2011). Members of a corresponding gene network were enriched in cleaved extracellular matrix proteins thought to be important during early development.…”