Unbiased transcriptome analysis of human cleft palate reveals evolutionally conserved molecular signatures of development: experimental study.

Background: The development of the secondary palate, an essential process for hard palate formation, involves intricate cellular processes. Here, the authors examined the expression patterns of palatal fusion-associated genes in postdevelopmental human palatal tissues.

Methods: Mucosal samples collected from the anterior fused (control; n =5) and posterior unfused regions (study; n =5) of cleft palate patients were subjected to RNA sequencing. Gene Set Enrichment Analysis (GSEA) was conducted to identify consistent changes in molecular signaling pathways using hallmark (h) gene set collections from the Molecular Signature Database v7.4. The results of RNA sequencing were validated by epithelial-mesenchymal transition (EMT) assays with suppression of target genes, including lrp6, shh, Tgfβ-3 (Bioneer), and negative control siRNA in a human fibroblast cell line (hs68).

Results: Transcriptome profiling of the cleft mucosa demonstrated that the fully fused anterior mucosa exhibited globally upregulated EMT, Wnt β-catenin, Hedgehog, and TGF-β signaling pathways in gene set enrichment. This strongly indicates the evolutionary conserved similarities in pathways implicated in palatogenesis, as previously shown in murine models. In EMT assays with suppression of Lrp6, Shh, and TGF-β3 in human fibroblast cell lines, suppression of Lrp6 exhibited consistent suppression effects on EMT markers. This indicates a closer association with EMT compared to the other two signals.

Conclusion: Our study highlights evolutionarily conserved molecular signatures and provides insights into the importance of the EMT pathway in palatal fusion in humans. Furthermore, intraindividual comparative analysis showed the spatial regulation of gene expression within the same organism. Further research and animal models are needed to explore the complexities of EMT-related palatal fusion.