Table 3: Relevant clinical outcome measures for comparison with preclinical model results^*.

Clinical  outcome measure	Comments
CFTR biomarker	Genotype group changes in sweat chloride (and NPD, but more limited number of studies) during modulator clinical trials have correlated with CFTR responses from many preclinical model systems [5,18,19,60,61,62]. ICM measurements of G551D CFTR activity have correlated with benefit for patients treated with ivacaftor [63], or F508del CFTR activity in homozygous patients treated with lumacaftor/ivacaftor [64]. This biomarker is most valuable for demonstrating modulator bioactivity.
FEV1	Genotype group changes in FEV1 during modulator clinical trials have correlated with CFTR responses from many preclinical model systems, including heterologous expression systems, HBE cells, rectal organoids, and HNE cells [5–9,24,36,39,49,50]. Change in FEV1 over time (i.e.: FEV1 trajectory) compared with untreated patient registry controls has been assessed in open label studies of ivacaftor in G551D CF patients and lumacaftor/ivacaftor in F508del CF patients. Both analyses have demonstrated reductions in FEV1 decline trajectory [65,66]. This outcome measure is the gold standard for pulmonary drug development, but has limitations in young patients, and those with early and advanced lung disease.
Multiple breath washout/lung clearance index (MBW/LCI)	The use of MBW/LCI has been limited to studies in young people with CF and those with preserved lung function, including ivacaftor in CF subjects with gating and the R117H mutations, and lumacaftor/ivacaftor in F508del homozygotes. Genotype group changes in LCI during modulator treatment have aligned with CFTR responses in many preclinical model systems [67–69]. This outcome measure is most valuable in early lung disease and potentially younger CF subjects.
Nutrition/Growth	Genotype group changes in BMI during modulator clinical trials have aligned with CFTR responses from many preclinical model systems for ivacaftor and lumacaftor/ivacaftor [5,7–9,67,68]. In contrast, tezacaftor/ivacaftor produced similar F508del CFTR correction and potentiation in vitro, but did not demonstrate weight/BMI benefits in F508del homozygous adults relative to placebo [70]. Ivacaftor has been demonstrated to be associated with increased linear growth [71]. Growth is a valuable outcome measure (typically a secondary efficacy endpoint in modulator clinical trials), particularly in pediatric studies.
Risk of acute pulmonary exacerbation (APEx)	The data for this endpoint is less developed than that for other outcome measures. When included in clinical trials, genotype group changes in risk of APEx during modulator clinical trials have generally aligned with CFTR responses from many preclinical model systems [5,9,70]. The frequency of APEx is typically not included in crossover trials, which have been necessary for studies in rare CFTR variant groups (e.g. subjects with non- G551D gating mutations). Furthermore, many CFTR modulator trials in young CF patients do not have a placebo group, limiting assessment of APEx risk. Monitoring APEx can be complicated by variable definitions, and is most valuable outside of the young pediatric age group (since they are poorly defined in this population).
Microbiology	Detection of CF pathogens has only been carefully assessed in open label studies of ivacaftor in subjects with highly responsive CFTR vairants (e.g. gating mutations) [8,72]. The results of these studies have been mixed, and thus the relationship regarding the modulation of CFTR variants in preclinical model systems to CF microbiology is unknown. Changes in the detection of known CF pathogens is an important secondary outcome measure in clinical trials of CFTR modulators, but is limited in younger patients or patients with mild disease who fail to expectorate.
Patient Reported Outcomes (PROs)	PROs are typically included in CFTR modulator trials, and are an important secondary efficacy endpoint. The Cystic Fibrosis Quality of Life Questionnaire Revised (CFQ-R) has most commonly been included in modulator clinical trials, frequently demonstrating significant improvements in the respiratory domain that exceed the minimal clinically important difference (MCID). (5,9,68)

^*The experiential hierarchy for preclinical model system comparisons with clinical outcome measures includes primary HBE cell planar cultures > rectal organoids ~ stable CFTR expression in cell lines > transient CFTR expression in cell lines > primary HNE cell monolayers > primary HNE cell spheres.