The transcriptome analysis of cleft lip/palate-related PTCH1 variants in GMSM-K cells show carcinogenic potential

Abstract

Cancer progression involves the sonic hedgehog (SHH) pathway, in which the receptor PTCH1 actives the downstream pathways. Dysfunction of PTCH1 can lead to nevoid basal cell carcinoma Syndrome (NBCCs) including neoplastic disease and congenital disorder. To evaluate the relationship between PTCH1 and cancer, we applied the CRISPR/Cas9 system to knock out PTCH1 in oral nontumorous epithelial cells (GMSM-K). Then we screened six PTCH1 variants associated with cleft lip/palate (CL/P), one of the congenital disorders in NBCCs, and generated PTCH1 variant and wild-type recombinant PTCH1 −/− GMSM-K cell lines. Transcriptome sequencing was conducted in these cell lines. The results revealed that differentially expressed genes (DEGs) in PTCH1 −/− GMSM-K were enriched in extracellular compartments, contributing epithelial diseases by pathway enrichment analysis. RT-PCR confirmed that KRT34, KRT81, KRT86, PDGFB, and WNT10B genes, associated with extracellular compartments were highly expressed in PTCH1 −/− . The Kyoto Encyclopedia of Genes and Genomes analysis also suggested that DEGs are closely related to focal adhesion, transcriptional misregulation, and proteoglycans in breast and gastric cancers. Comparative analysis of samples revealed that the CL/P-associated PTCH1 variants A443G and V908G are potentially carcinogenic. These findings provide new insights into the carcinogenic potential of PTCH1 dysfunction.