Precision medicine for rare CFTR variants in people with Cystic Fibrosis

Cystic fibrosis (CF) is a rare hereditary disorder, caused by variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. These variants impair chloride and bicarbonate transport, leading to thick mucus in multiple organs, particularly the lungs, pancreas, and intestines. Over 2000 CFTR variants have been identified, resulting in a wide range of disease severity. CFTR modulators, small molecules that restore or enhance CFTR protein function, have transformed CF care, with the triple combination elexacaftor/tezacaftor/ivacaftor (ETI) achieving the greatest clinical impact to date. However, in Europe, ETI is currently approved only for people with CF (pwCF) with at least one F508del allele, excluding many with rare variants who might also benefit.
Because large clinical trials are not feasible for such small and genetically diverse groups, there is a pressing need for methods that can predict treatment response at the individual level. Patient-derived intestinal organoids (PDIOs) offer a promising solution. These miniature 3D cultures, grown from rectal biopsies, retain the donor’s genetic and functional characteristics. The forskolin-induced swelling (FIS) assay measures the swelling of these organoids when stimulated, serving as a functional readout of CFTR activity.
This thesis explores the potential of the FIS assay to guide modulator therapy in pwCF carrying rare mutations.
The work began with a review of advances in CF diagnostics and therapeutics, followed by engagement with the European Medicines Agency (EMA) to seek recognition of the FIS assay in three roles: as a biomarker for CFTR function, as an indicator of disease severity, and as a predictor of treatment response. The EMA expressed support for continued development.
Practical implementation was shown to be feasible and safe through the central generation of PDIOs from multiple European centres. A multicentre study demonstrated that the FIS assay is both highly repeatable and reproducible when performed with standardised protocols, with strong agreement between independent laboratories in classifying samples as treatment responders or non-responders.
Two studies using PDIOs from national biobanks in the Netherlands and Italy focused on pwCF who are currently ineligible for ETI under European labelling. Most organoids from these individuals showed meaningful restoration of CFTR function with ETI, sometimes matching the responses seen in organoids from individuals with approved genotypes. In some cases, this contrasted with results from other laboratory models, underscoring the added value of using patient-specific material.
A health-economic evaluation indicated that a strategy guided by the FIS assay could be cost-effective, particularly in groups with lower expected response rates, balancing potential savings with the need to avoid excluding true responders.
Overall, this thesis demonstrates that the FIS assay is a robust and clinically relevant tool with the potential to accelerate regulatory decisions and expand equitable access to CFTR modulators for pwCF with rare CFTR variants.