Translating in vitro CFTR rescue into small molecule correctors for cystic fibrosis using the Library of Integrated Network-based Cellular Signatures drug discovery platform

Cystic fibrosis is a lethal autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The common delF508-CFTR mutation results in protein misfolding and proteasomal degradation. If delF508-CFTR trafficks to the cell surface, its anion channel function may be partially restored. Several in vitro strategies can partially correct delF508-CFTR trafficking and function, including low-temperature, small molecules, overexpression of miR-138, or knockdown of SIN3A. The challenge remains to translate such interventions into therapies and to understand their mechanisms. One approach for connecting such interventions to small molecule therapies that has previously succeeded for cystic fibrosis and other diseases is via mRNA expression profiling and iterative searches of small molecules with similar expression signatures. Here, we query the Library of Integrated Network-based Cellular Signatures (LINCS) using transcriptomic signatures from previously generated CF expression data, including RNAi- and low temperature-based rescue signatures. This LINCS in silico screen prioritized 135 small molecules that mimicked our rescue interventions based on their genome-wide transcriptional perturbations. Functional screens of these small molecules identified nine compounds that partially restored delF508-CFTR function, as assessed by cAMP-activated chloride conductance. Of these, XL147 rescued delF508-CFTR function in primary CF airway epithelia, while also showing cooperativity when administered with C18. Improved CF corrector therapies are greatly needed and this integrative drug prioritization approach offers a novel method to both identify small molecules that may rescue delF508-CFTR function and identify gene networks underlying such rescue.