Variable Responses to CFTR Correctors in vitro: Estimating the Design Effect in Precision Medicine

Abstract

Interest in precision medicine has grown in recent years due to the variable clinical benefit provided by some medications, their cost, and by new opportunities to tailor therapies to individual patients. In cystic fibrosis it may soon be possible to test several corrector drugs that improve the folding and functional expression of mutant cystic fibrosis transmembrane conductance regulator (CFTR) prospectively using cells from a patient to find the one that is best for that individual. Patient-to-patient variation in cell culture responses to correctors and the reproducibility of those responses has not been studied quantitatively. We measured the functional correction provided by lumacaftor (VX-809) using bronchial epithelial cells from 20 patients homozygous for the F508del-CFTR mutation. Significant differences were observed between individuals, supporting the utility of prospective testing. However, when correction of F508del-CFTR was measured repeatedly using cell aliquots from the same individuals, a design effect was observed that would impact statistical tests of significance. The results suggest that the sample size obtained from power calculations should be increased to compensate for group sampling when CFTR corrector drugs are compared in vitro for precision medicine.

CFTR Correctors and Antioxidants Partially Normalize Lipid Imbalance but not Abnormal Basal Inflammatory Cytokine Profile in CF Bronchial Epithelial Cells

“…Primary airway cells from newborn CFTR KO and control piglets and human lungs were isolated and cultured in parallel at ALI on permeable membranes to allow differentiation to airway epithelial cells (Methods BEGM) as described in Stolarczyk et al (2016 , 2018) . Undifferentiated CF and non-CF primary epithelial cells frozen in liquid nitrogen were obtained from the CF Translational Center, McGill University, Montreal, Canada where they were prepared according to a protocol previously described in detail ( Matthes et al, 2018 ). Non-CF undifferentiated primary epithelial cells from Erasmus MC were obtained stored in liquid nitrogen and cultured using essentially the same method ( Amatngalim et al, 2018 ).…”

“…Patients vary in their responses to CFTR modulators in vitro HBE cells ( Matthes et al, 2018 ). To examine the impact of CFTR deficiency on lipid profiles and cytokines in cells with strong and weak drug responses, cells were studied from the CF patients used in lipid analysis, three of which are homozygous and two heterozygous for F508del-CFTR, after selection based on CFTR dependent responses in Ussing chamber experiments ( Table 1 ).…”

“…Well-differentiated monolayers were pretreated for 24 h at 37°C with vehicle (0.1% DMSO) or under conditions designed to mimic the clinically-prescribed combination drugs lumacaftor/ivacaftor (1 μM VX809 for 24 h, followed by acute treatment with 300 nM VX770 or 50 μM genistein) or ivacaftor/tezacaftor/elexacaftor (3 μM VX445-1 plus 3 μM VX661 with or without 10 nM VX770 for 24 h). Monolayers were mounted in modified Ussing chambers and short-circuit current ( I sc in μA·cm −2 ) was measured to assay of CFTR function as described previously ( Matthes et al, 2018 ). Transepithelial voltage was clamped at 0 mV except for 2 s bipolar pulses to ±1 mV at 100 s intervals to monitor transepithelial resistance.…”

CFTR Modulators: The Changing Face of Cystic Fibrosis in the Era of Precision Medicine

“…Noteworthy, CFTR mutations may differently respond to the same intervention (e.g., correction by low temperature or by chemical compounds), even for those classified as belonging to the same defect class (Rapino et al, 2015;Dekkers et al, 2016a;Dekkers et al, 2016b;Lopes-Pacheco et al, 2016;Lopes-Pacheco et al, 2017;Han et al, 2018;Awatade et al, 2019). Therapeutic responses may also differ between individuals carrying the same CF genotypes (Boyle et al, 2014;Donaldson et al, 2018a;Keating et al, 2018;Matthes et al, 2018). In fact, several other factors exert influence on disease severity beyond CFTR mutations, such as gene modifiers and epigenetic factors, social and economic status, patient's lifestyle, and adherence to therapies (Oates and Schechter, 2016;O'Neal and Knowles, 2018).…”

“…Furthermore, clinical trials in sicker or younger patients, and those carrying rarer CFTR mutations are more challenging due to small sample size, specific inclusion/exclusion criteria, or even for some hesitation on the part of the investigators. Strategies to adapt and optimize trial design and deliver for speed and efficacy have been discussed, including the use of patient-derived specimens, power calculations to compensate for group sampling, and N-of-1 and "basket" trials (Matthes et al, 2018;Amaral et al, 2019;Davies et al, 2019b).…”