INTEGRATING GENOMIC AND FUNCTIONAL TESTING TO IMPROVE CFTR MODULATOR RESPONSE PREDICTION IN CHILDREN WITH CYSTIC FIBROSIS

Background

CFTR modulators have transformed cystic fibrosis (CF) treatment, but individual responses vary even among patients with identical CFTR genotypes. This underscores the need for predictive biomarkers to optimize therapeutic selection.

Methods

We evaluated 24 paediatric patients homozygous for F508del-CFTR, assessing lung function (FEV1pp) and sweat chloride (SC) before and after CFTR modulator therapy. Whole-gene sequencing was utilised to identify CFTR and pharmacogene variants. Patient-derived human nasal epithelial cells (HNECs) were expanded and differentiated at the air-liquid interface to assess CFTR function via ion transport (ΔIsc).

Results

Clinical responses varied widely. Twelve participants changed modulators during the study. Sequencing identified 231 additional CFTR variants and pharmacogene polymorphisms, but none correlated with response variability. However, a significant linear relationship emerged between ΔIsc and FEV1pp improvement in patients with baseline FEV1pp <90 (R² = 0.651, p = 0.001) and SC reduction (R² = 0.535, p = 0.004). Receiver operating characteristic (ROC) analysis demonstrated high predictive accuracy for SC reduction (AUC = 0.88) and combined FEV1pp/SC response in patients with baseline FEV1pp <90 (AUC = 1.00). Exploratory analysis confirmed that ΔIsc predicts FEV1pp changes, modulated by baseline lung function and CFTR modulator type.

Conclusion

Patient-derived differentiated HNEC cultures serve as a robust predictive tool for CFTR modulator response in paediatric CF patients. Their integration into clinical practice can enhance personalised treatment strategies, minimising ineffective therapy use and improving CF patient outcomes with precision medicine.

What is already known on this topic

• CFTR modulators significantly improve clinical outcomes in people with cystic fibrosis (CF), yet individual responses vary, even among those with identical CFTR genotypes.

• Patient-derived human nasal epithelial cell (HNEC) models have emerged as promising tools to predict CFTR modulator response. However, existing studies have primarily focused on adult and adolescent populations, leaving a gap in personalised treatment strategies for younger children with CF.

• The relationship between CFTR sequence variations, pharmacogene heterogeneity, and modulator response in paediatric patients has not been extensively explored.

What this study adds

• This study demonstrates a strong correlation between in vitro CFTR function (ΔIsc) and clinical improvements in FEV1pp and sweat chloride in children and adolescents with CF.

• Whole-gene sequencing identified 231 additional CFTR variants , yet none were associated with CFTR modulator response, suggesting that genotype alone does not fully explain treatment variability.

• While some trends between pharmacogene activity and treatment response were observed, no strong evidence supports pharmacogene profiling as a standalone predictor of CFTR modulator efficacy in paediatric patients.

• Differentiated-HNEC cultures consistently predicted clinical response across multiple CFTR modulator regimens , reinforcing their value for preclinical drug screening.

How this study might affect research, practice, or policy

• Our findings support the integration of differentiated-HNEC models into clinical practice to personalise CFTR modulator selection, reducing ineffective treatments and improving patient outcomes.

• The study underscores the need for additional clinical endpoints beyond FEV1pp to assess respiratory function in individuals with preserved lung function (FEV1pp > 90%).