Cure for a genetic disease? Targeting the right drug to the right patient using intestinal stem cell cultures in Cystic Fibrosis.

Cystic Fibrosis (1:4,750) is a lethal disease, caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CF patients suffer from a multi-faceted pulmonary inflammatory condition associated with recurrent infections, reducing mean life expectancy to about 35 years. Thus far clinical treatment of patients with CF was merely symptomatic. Emerging knowledge on intracellular processes and upcoming drugs targeting the basic defect or key intracellular processes that affect CFTR announce new opportunities for curative treatment. Currently, several of these compounds enter the market, like Vertex 770 and Vertex 809. The recent introduction of CF in the national neonatal birth screening program might enable start of treatment before irreversible organ dysfunction has settled. However, patients exhibit a huge variety in clinical phenotype, probably resulting from interaction of the CFTR defect with numerous other genetic and non-genetic factors. These complex interactions in individual patients importantly hamper the translation of findings in basic science to clinical application in humans. Most basic findings result from studies in standard laboratory cell lines or animal models, which at best only partially reflect human cell biology in vivo. The lack of insight into intracellular processing of CFTR in individual patients renders the effects of new therapeutic compounds highly unpredictable. Recently, we have set up a highly innovative and unique functional CFTR assay using patient-derived intestinal stem cell cultures termed 'organoids' (Dekkers, Nat Med 2013). In this model, we documented that efficacy of the CFTR-targeting drugs is determined, as expected, by the nature of CFTR mutations. Importantly, we also uncovered differential responses between patients with the same mutation indicating the importance of patient-specific genetic background. The organoid cultures can be established from rectal biopsies frequently isolated from CF patients for diagnostic means. They provide a patient-specific platform for CF study and drug development. The unique characteristics of the organoids are their genetic and phenotypic stability while they can be expanded without apparent limitation. This functional assay is an ideal drug-screening platform to evaluate the mode of action and the efficacy of new compounds to restore CFTR function in the genetic background of individual patients. We showed the model to be of high potention to enable the study the mode of action of newly developed CFTR correcting and potentiating drugs (Okiyoneda, Nat Chem Biol. 2013) as well as genetic repair of the basic CFTR gene defect (Schwank, Cell Stem Cell 2013) We hypothesize that the organoid model adequately reflects both the patients' CFTR- as well as the non-CFTR genetic background and is therefore an ideal model to study the mode of action and effects of CFTR affecting drugs in single patients. Knowledge and in vitro prediction of drug effects in individual patients will be helpful to properly target drug therapy in the future. In this project we aim to: 1. Characterize the functional restoration and mode of action of CFTR correcting and potentiating drugs in development, to allow further optimization and prediction of optimal combination therapies. 2. Predict the clinical effect of newly developed drugs from effects on patient-derived intestinal organoids and to validate this predictive model in clinical care of individual patients. Numerous current and new compounds are available from high-throughput screens by pharmaceutical companies and academic groups using RNAi and chemical compound libraries. We will study the molecular mechanism by which the various compounds increase mutant CFTR activity, including identification of the direct and indirect target of each hit. We will probe CFTR, its domains, and various truncated constructs using limited proteolysis. Using different patient mutations will help identify the precise submolecular target in CFTR. Subsequently we will determine therapeutic efficacy of specific combinations of compounds targeting different pathways in restoring CFTR function. Additionally we will measure the clinical effects of new drugs in at least 80 patients with CF and compare the results with the effects measured in these patients' organoids. A predictive model with drug effect in the organoids as a determinant and clinical drug effect as the outcome will be established. In this proposal a strong collaborative consortium of basic and clinical scientists from Utrecht and Rotterdam aims to establish a breakthrough in CF treatment through further development of compounds that effectively modify basic disease mechanisms, combined with innovative ways to test drug efficacy in individual patients. This can ultimately lead to a laboratory setting in which the efficacy of (a combination of) drugs can be predicted in individual patients, which will enable personalized medicine.