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

Elizabeth Matthes,David Y Thomas,John W Hanrahan,Carolina Martini,Julie Goepp,Jiajie Shan,Jie Liao

doi:10.3389/fphar.2018.01490

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.

Highlights

Cystic fibrosis (CF) is a relatively common orphan disease caused by loss-of-function mutations in the gene encoding CFTR, a tightly regulated anion channel (Riordan, 2008)
CF modulators such as lumacaftor (VX-809) that partially correct the misfolding and/or potentiate the activity of mutant CFTR channels are available and more are in the pipeline, they are expensive and their clinical benefit varies between individuals
The variable clinical benefit provided by Orkambi R is well known (Boyle et al, 2014), it remains unclear if similar variability exists at the level of epithelial cells and persists in cell culture

Summary

INTRODUCTION

Cystic fibrosis (CF) is a relatively common orphan disease caused by loss-of-function mutations in the gene encoding CFTR (cystic fibrosis transmembrane conductance regulator), a tightly regulated anion channel (Riordan, 2008). CF seems ideally suited for applying the precision medicine approach (Amaral, 2015; Martiniano et al, 2016; Burgener and Moss, 2018; Cholon and Gentzsch, 2018), some practical issues remain to be addressed Foremost among these is whether differences in functional correction measured using primary cultured cells from different patients are statistically significant. Assays of CFTR function that utilize different cell types have been developed and could potentially be used to test the drug responsiveness of individual patients. For seven patients homozygous for F508del-CFTR there was a correlation between mean functional rescue in nasal cell cultures and the clinical response to Orkambi measured as % FEV1 (% predicted forced expiratory volume in 1 s) (Pranke et al, 2017). We observe a design effect caused by group sampling that needs to be considered when testing the statistical significance of differences in correction

MATERIALS AND METHODS

RESULTS

DISCUSSION