Transcriptome Signatures of Vismodegib-Treated Fibroblasts and Basal Cell Carcinoma Cells

Objectives: Abnormal activation of the sonic-hedgehog (SHh) pathway results in numerous basal cell carcinomas (BCC) and keratocystic odontogenic tumors in Gorlin syndrome patients. The SHh inhibitor, Vismodegib, decreases BCC cell growth, but its effect on fibroblasts within the tumor microenvironment is unclear. We used next-generation sequencing to compare whole-transcriptome profiles of human fibroblasts and BCC cells in Vismodegib-treated cultures, to delineate signaling networks that contribute to epithelial-stromal cross-talk and may be modified by this inhibitor.
Methods: cDNA libraries were generated from total RNA samples of primary fibroblasts treated with DMSO (control), 10nM or 10μM Vismodegib, and sequenced on HiSeq 2500 platform (Illumina). Cuffdiff of Tuxedo Tools were used for differential gene expression analyses of fibroblasts, as well as previously acquired whole-transcriptomes of control and Vismodegib-treated BCC cells (TE-354.T). Genes with p-value ≤0.05 were considered significant and used as input for Ingenuity Pathway Analysis (QIAGEN).
Results: Compared to controls, 10nM and 10μM Vismodegib-treated fibroblasts demonstrated altered expression of 62 and 272 genes, respectively, while Vismodegib-treated BCC cells revealed altered expression of 957 and 341 genes, respectively. The top disease and disorder bio-functions altered in both Vismodegib-treated fibroblast and BCC cells were cancer and organismal injury. In 10nM Vismodegib-treated fibroblasts, top associated network functions included genes that control cellular movement and molecular transport, while in 10uM Vismodegib-treated fibroblasts, top associated genes regulated cell morphology, survival, and cell-cell interactions. In contrast, in 10nM Vismodegib-treated BCC cells, top associated network functions included genes that control cellular function and maintenance, developmental and heredity disorder, cell cycle, cellular assembly and organization, whereas in 10uM Vismodegib-treated BCC cells, top associated genes regulated cell morphology, cell-cell signaling, connective tissue disorders and molecular transport.
Conclusions: Genome-wide transcriptomes of Vismodegib-treated fibroblasts and BCC cells highlighted biological pathways that can influence the cross-talk between these two cell types, and contribute to the pathogenesis of BCC.