GSE171689
Targeting Hedgehog pathway by Smoothened Antagonist
Aberrant activation of Hedgehog pathway is responsible for initiation and maintenance of various cancers, including medulloblastoma (MB), basal cell carcinoma (BCC), and other solid and hematological tumors. Therefore, targeting Hh pathway represents promising therapeutic prospects for Hh-driven cancers. In recent years, tremendous efforts have been dedicated to the discovery of Hh pathway inhibitor. While the majority of Hh pathway inhibitors target the upstream membrane protein Smoothened (SMO). Here, we performed Next Generation Sequencing to reveal the target genes of Hh pathway by treating mouse SHH-subtype medulloblastoma cells (SmoWT) with SMO inhibitor (GDC0449) or DMSO. Overall design: mRNA profiling:RNA was prepared from vehicle or GDC0449 (0.1µM) treated mouse SHH-subtype medulloblastoma cells (SmoWT) derived from spontaneous medulloblastoma of Ptch1+/-, Trp53-/- mice for 24 h.   Trim galore was used to automatically detect and trim adapters. Reads were mapped to mm10 reference genome using Hisat2. Read count was generated using HTSeq (version 0.11.1). Differentially expressed genes (DEGs) were calculated using DESeq2 (version 1.26.0). Absolute value of fold change (FC) >?1.5 and false discovery rate (FDR) <?0.05 was used as cut-off value to select significant target genes. FPKM (Fragments per Kilobase Million) was calculated from the number of reads that mapped to each particular gene sequence and the gene length and the sequencing depth were taken into account.