Transcriptional responses of zebrafish embryos exposed to potential sonic hedgehog pathway interfering compounds deviate from expression profiles of cyclopamine

The molecular responses of two small molecules, SANT-2 and GANT-61, potentially interfering with the sonic hedgehog pathway (Shh) have been studied in zebrafish embryos by microarray analysis. For both compounds and the positive reference cyclopamine previous reporter gene assays for the transcription factor Gli1 have indicated an inhibition of the hedgehog signaling pathway. In zebrafish embryos a typical phenotype (cyclopia) associated with Shh interference was only observed for cyclopamine. Furthermore, only cyclopamine led to the repression of genes specifically associated with hedgehog signaling and confirmed published microarray data. In contrast to these data hspb11 was additionally identified as the most pronounced down-regulated genes for exposure to cyclopamine. No or different effects on gene expression patterns were provoked by SANT-2 or GANT-61, respectively. Reasons for the discrepancies between cellular reporter and the zebrafish embryo assay and potential implications for the identification of compounds interfering with specific developmental pathways are discussed.

► We compared the effects on gene expression pattern in zebrafish embryos provoked by exposure to cyclopamine, SANT-2 and GANT-61.
► In the previous reported cell-based reporter gene assay, the three small molecules interfered with hedgehog signaling.
► Only cyclopamine caused repression of hedgehog signaling associated genes in zebrafish embryos.
► Hspb11 was identified as the most pronounced down-regulated gene for exposure to cyclopamine.
► A robust gene set for hedgehog pathway inhibiting compounds in zebrafish embryos was established.