Joint models for longitudinal and survival data have become a popular framework for studying the association between repeatedly measured biomarkers and clinical events. Nevertheless, addressing complex survival data structures, especially handling both recurrent and competing event times within a single model, remains a challenge. This causes important information to be disregarded. Moreover, existing frameworks rely on a Gaussian distribution for continuous markers, which may be unsuitable for bounded biomarkers, resulting in biased estimates of associations. To address these limitations, we propose a Bayesian shared-parameter joint model that simultaneously accommodates multiple (possibly bounded) longitudinal markers, a recurrent event process, and competing risks. We use the beta distribution to model responses bounded within any interval ( a , b ) $$ \left(a,b\right) $$ without sacrificing the interpretability of the association. The model offers various forms of association, discontinuous risk intervals, and both gap and calendar timescales. A simulation study shows that it outperforms simpler joint models. We utilize the US Cystic Fibrosis Foundation Patient Registry to study the associations between changes in lung function and body mass index, and the risk of recurrent pulmonary exacerbations, while accounting for the competing risks of death and lung transplantation. Our efficient implementation allows fast fitting of the model despite its complexity and the large sample size from this patient registry. Our comprehensive approach provides new insights into cystic fibrosis disease progression by quantifying the relationship between the most important clinical markers and events more precisely than has been possible before. The model implementation is available in the R package JMbayes2.

Cystic fibrosis transmembrane conductance regulator (CFTR) modulators improve the physiological defect causing cystic fibrosis, but the lungs of most people remain infected and inflamed. A leading hypothesis implicates damaged segments as the cause of persistent infection and predicts that mildly diseased segments within an individual's lungs will clear after treatment, whereas severely diseased segments will not. Our findings contradict this hypothesis. We used bronchoscopy to sample the least- and most-damaged lung segments in Pseudomonas aeruginosa (Pa)-infected individuals before modulators and returned to these same segments after 1.5 years. Surprisingly, we find an "all-or-none" infection clearance response: the most-diseased segments clear if any other lung segment in that person clears, and the least-diseased segments remain infected if others in that person do. Furthermore, neutrophilic inflammation completely resolves where Pa clears but remains elevated where Pa persists. These data indicate that post-modulator infections are not limited to severely diseased segments and that Pa infections drive persistent lung inflammation after modulators.

Cystic fibrosis (CF) is characterized by impaired mucociliary clearance and pulmonary infections. Accumulating evidence suggests that fundamentally abnormal inflammatory responses also contribute to CF pathology. Transforming growth factor β (TGF-β), a pleiotropic cytokine, is a modifier of CF lung disease; its mechanism of action in CF is unclear. Previous studies have shown that TGF-β induces interleukin-6 (IL-6) secretion from lung epithelium, which may drive worse pulmonary outcomes in CF and other lung diseases. However, the nature of the TGF-β/IL-6 relationship in CF is not fully understood. In this study, we demonstrated that TGF-β and IL-6 concentrations were positively associated in bronchoalveolar lavage fluid from children with CF. Furthermore, pulmonary TGF-β exposure in a CF mouse model induced heightened IL-6 secretion when compared with non-CF mice. CF airway epithelial cells had increased IL-6 secretion and phosphoinositide 3-kinase (PI3K) signaling after TGF-β exposure. In wild-type airway epithelium, TGF-β exposure and cystic fibrosis transmembrane conductance regulator (CFTR) inhibition synergistically provoked IL-6 secretion. Restoration of CFTR function by a CFTR modulator and inhibition of PI3K signaling both normalized IL-6 secretion from CF airway epithelial cells. These data indicate that TGF-β drives abnormal IL-6 secretion via the PI3K pathway in the CF airway, demonstrating an inherent inflammatory abnormality in CF and suggesting potential therapeutic targets.NEW & NOTEWORTHY The etiology of IL-6 oversecretion in cystic fibrosis (CF) is unclear, as is the mechanism of CF lung disease modification by TGF-β. We show that TGF-β induces IL-6 oversecretion in human and mouse models of CF. In mechanistic studies, we further demonstrate that loss of CFTR function drives increased IL-6 secretion via the PI3K pathway downstream of TGF-β. Treatment of CF airway epithelial cells with a CFTR modulator rescues this IL-6 oversecretion.

Identifying safe and effective therapies that target the underlying cause of cystic fibrosis remains a key priority for the cystic fibrosis community. CFTR modulators are first-in-class, regulatory-approved therapies that improve the function of the protein encoded by the CFTR gene and are associated with dramatic and sustained clinical benefits. Although approximately 90% of the population with cystic fibrosis could benefit from these therapies based on genetic eligibility, a crucial unmet need remains: developing CFTR-directed therapies for the ultra-rare population with cystic fibrosis who are not candidates for CFTR modulators due to either ineligibility or intolerance. Addressing this unmet need will depend on the clinical advancement of nucleic acid-based therapies (NABTs), a term that includes variant-specific antisense oligonucleotide therapies and variant-agnostic mRNA and DNA-based gene therapies. The clinical development of NABTs for those who are not candidates for or unable to take CFTR modulators is challenged not only by the relatively small target population, which affects feasible trial sizes, but also by unique regulatory requirements for long-term safety follow-up and the potential yet unknown short-term and long-term risks with genetic therapy cross-exposure or re-exposure. This Personal View addresses the proactive planning needed to maximise trial opportunities for the population who are not candidates for CFTR modulators, including considerations for subsequent NABT trial participation following previous NABT exposure.

Background: Highly effective CFTR modulator therapy (HEMT) has improved the health of many people with cystic fibrosis (pwCF), offering opportunities to discontinue burdensome therapies. SIMPLIFY included randomized, controlled trials that confirmed non-inferiority of discontinuing versus continuing dornase alfa (DA) or hypertonic saline (HS) for 6 weeks in pwCF on HEMT. In this study of post-trial treatment use by SIMPLIFY participants, we hypothesized that randomization to discontinue DA or HS during the trial would be associated with a higher likelihood of non-use of each medication during follow-up. Methods: We electronically surveyed SIMPLIFY participants every 4 weeks for 24 weeks after trial completion but before the main trial results were publicly disclosed. We asked them how often they used medications during the previous week. We estimated covariate-adjusted odds ratios (ORs) of DA or HS non-use by logistic regression with generalized estimating equations. Results: After exclusions mostly due to lack of any surveys, 472 participants were included in the analysis population, 181 from the HS trial and 291 from the DA trial. Approximately half of the analysis population completed all six surveys. At every month of follow-up in both trials, the percentage of individuals reporting nonuse of DA or HS during the previous week was greater among those randomized to discontinue therapy. Among participants with responses at 24 weeks, 30/122 (24.6 %) in the HS trial and 79/222 (35.6 %) in the DA trial reported non-use of the respective study medication. After adjusting for covariates, participants randomized to discontinue DA were 8.7-times (95 % CI: 4.3-17.7) more likely to not use DA during follow-up than those randomized to continue DA, and participants randomized to discontinue HS were 5.2-times (95 % CI: 2.1-12.8) more likely to not use HS during follow-up compared to those randomized to continue. Conclusions: In healthy pwCF on ETI, randomization to discontinue DA or HS during SIMPLIFY was associated with greater odds of not using each medication after the trial compared to randomization to continue. These findings suggest that participation in a treatment discontinuation trial can influence participants' post-trial treatment decisions. This possibility may be relevant during discussions about research participation and clinical care.

Airway inflammation underlies cystic fibrosis (CF) pulmonary exacerbations. In a prospective multicenter study of randomly selected, clinically stable adolescents and adults, we assessed relationships between 24 inflammation-associated molecules and the future occurrence of CF pulmonary exacerbation using proportional hazards models. We explored relationships for potential confounding or mediation by clinical factors and assessed sensitivities to treatments including CF transmembrane regulator (CFTR) protein synthesis modulators. Results from 114 participants, including seven on ivacaftor or lumacaftor-ivacaftor, representative of the US CF population during the study period, identified 10 biomarkers associated with future exacerbations mediated by percent predicted forced expiratory volume in 1 s. The findings were not sensitive to anti-inflammatory, antibiotic, and CFTR modulator treatments. The analyses suggest that combination treatments addressing RAGE-axis inflammation, protease-mediated injury, and oxidative stress might prevent pulmonary exacerbations. Our work may apply to other airway inflammatory diseases such as bronchiectasis and the acute respiratory distress syndrome.

airway.These manifestations were not seen in the 2-month-old rats.Analysis of mucin content in the BALF of all animals indicated a potential correlation between high Muc5ac protein levels and high markers of lung damage as assessed using μCT.No correlation was observed for Muc5b.Bacterial burden of P. aeruginosa was equal in the lungs of 2-and 6-monthold rats, but S. aureus was only retained in the 6-month-old group.Conclusions: In adult CF rats, chronic co-infection with P. aeruginosa and S. aureus led to structural lung damage and decline, reflecting what has been reported clinically for PwCF.This decline was not observed in younger rats lacking the complete CF airway phenotype, indicating the importance of the CF environment in disease progression.In adult rats, S. aureus infection was also sustained over the course of the study, supporting clinical evidence that, despite having an antagonistic relationship in vitro, S. aureus escapes killing by P. aeruginosa in the context of CF.

Background: The adaptive immune system is increasingly appreciated for its contributions to the exuberant and maladaptive immune response in CF.We hypothesized that the CFTR functions as a negative regulator of T helper 2 (Th2) cell function, CFTR deficiency in mouse Th2 cells increases Th2 cytokine production, therapeutic CFTR modulation can decrease Th2 effector function, allergic inflammation increases in CF mice when challenged with inhaled allergen, and CFTR expression is regulated by a novel GATA binding site in Th2 cells.Methods: Naïve CD4+ T-cells from Cftr +/+ , Cftr -/-, and Cftr -/-murine spleens expressing genomic human CFTR (B6-Tg(CFTR)1Lcl/Cwr [hCFTR]) were isolated and cultured in Th2 polarizing conditions using plate-bound anti-CD3e and anti-CD28 in the presence of soluble anti-IFNγ and IL-4 for 5 days.Naïve hCFTR expressing murine CD4+ T-cells was treated with elexacaftortezacaftor-ivacaftor (ETI) or vehicle control at activation.On Day 3, CD4+ Tcells were restimulated with IL-4, and cytokine measurements were taken 48 hours later (Day 5).Flow cytometry was performed on Th2-polarized Cftr +/+ and Cftr -/-CD4+ T-cells using antibodies to CD3, CD4, GATA3, IL-5, and IL-13.Cftr +/+ and Cftr -/-mice were sensitized and challenged using Alternaria alternata to elicit an adaptive immune response.Bronchoalveolar lavage (BAL), protein was quantified from whole-lung homogenate, and histopathological analysis was performed.Chromatin immunoprecipitation (ChIP) of GATA-3-bound chromatin fragments was performed.Results: In Cftr -/-CD4+ T-cells, Cftr expression is tightly associated with Tcell activation and subsequent GATA-3 expression.ChIP analysis of a putative Gata binding motif at site -607 respective to the Cftr transcription start site demonstrated that GATA-3 binds to nucleosomal-bound DNA within the Cftr promoter to induce local chromatin rearrangement.Th2polarized CD4+ T-cells from Cftr -/-mice produce higher levels of IL-4, IL-5, and IL-13 in response to activation than Cftr +/+ CD4+ T-cells.ETI-treated hCFTR murine CD4+ T-cells secrete less IL-5 and IL-13 than vehicle controltreated hCFTR murine CD4+ T-cells.In vivo, Cftr -/-mice display greater inflammation by histology and greater Th2 cytokine production in response to Alternaria challenge than Cftr -/-mice.Conclusions: These findings demonstrate a previously undefined role for GATA-3 regulation of CFTR expression in CD4+ T-cells.These data suggest a role for CFTR as a negative regulator of Th2 effector function in CD4+ T-cells and resultant allergic inflammation, an effect reversed by current CFTR modulator therapies.These studies highlight a potential role for CFTR modulator therapies in decreasing allergic inflammation in people with CF.

Cystic fibrosis is a multiorgan disease caused by impaired function of the cystic fibrosis transmembrane conductance regulator (CFTR). Since the introduction of the CFTR modulator combination elexacaftor-tezacaftor-ivacaftor (ETI), which acts directly on mutant CFTR to enhance its activity, most people with cystic fibrosis (pwCF) have seen pronounced reductions in symptoms, and studies project marked increases in life expectancy for pwCF who are eligible for ETI. However, modulator therapy has not cured cystic fibrosis and the success of CFTR modulators has resulted in immediate questions about the new state of cystic fibrosis disease and clinical challenges in the care of pwCF. In this Series paper, we summarise key questions about cystic fibrosis disease in the era of modulator therapy, highlighting state-of-the-art research and clinical practices, knowledge gaps, new challenges faced by pwCF and the potential for future health-care challenges, and the pressing need for additional therapies to treat the underlying genetic or molecular causes of cystic fibrosis.

Background Lung infections are among the most consequential manifestations of cystic fibrosis (CF) and are associated with reduced lung function and shortened survival. Drugs called CF transmembrane conductance regulator (CFTR) modulators improve activity of dysfunctional CFTR channels, which is the physiological defect causing CF. However, it is unclear how improved CFTR activity affects CF lung infections. Methods We performed a prospective, multicenter, observational study to measure the effect of the newest and most effective CFTR modulator, elexacaftor/tezacaftor/ivacaftor (ETI), on CF lung infections. We studied sputum from 236 people with CF during their first 6 months of ETI using bacterial cultures, PCR, and sequencing. Results Mean sputum densities of Staphylococcus aureus, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Achromobacter spp., and Burkholderia spp. decreased by 2–3 log10 CFU/mL after 1 month of ETI. However, most participants remained culture positive for the pathogens cultured from their sputum before starting ETI. In those becoming culture negative after ETI, the pathogens present before treatment were often still detectable by PCR months after sputum converted to culture negative. Sequence-based analyses confirmed large reductions in CF pathogen genera, but other bacteria detected in sputum were largely unchanged. ETI treatment increased average sputum bacterial diversity and produced consistent shifts in sputum bacterial composition. However, these changes were caused by ETI-mediated decreases in CF pathogen abundance rather than changes in other bacteria. Conclusions Treatment with the most effective CFTR modulator currently available produced large and rapid reductions in traditional CF pathogens in sputum, but most participants remain infected with the pathogens present before modulator treatment. Trial Registration ClinicalTrials.gov NCT04038047. Funding The Cystic Fibrosis Foundation and the NIH.

using the Cystic Fibrosis Respiratory Symptom Diary (CFRSD)-Chronic Respiratory Infection Symptom Scale (CRISS), on which lower scores indicate fewer symptoms, and the Cystic Fibrosis Questionnaire-Revised [respiratory] (CFQ-R), on which higher scores indicate fewer symptoms, five times: at enrollment and 6, 12, 18, and 24 months.Two repeatedmeasures, multilevel growth models were used to assess rate of change in symptoms overall and within groups using R-studio.Results: At enrollment, mean ppFEV 1 was 33.3% in the ETI cohort and 31.4% in the non-ETI cohort.PwCF on ETI had lower symptom severity over 24 months according to the CRISS and CFQ-R.Mean scores for the entire group were 36.7 for CRISS ( p < 0.001) 60.3 for CFQ-R ( p < 0.001).Mean difference between the groups at enrollment was 7.3 points for the CRISS and 14.5 points for the CFQ-R, with fewer symptoms in the ETI cohort.the ETI cohort had significantly fewer symptoms in over time according to both instruments (Figure 1).Mean CRISS improved by 11.7 points ( p < 0.001) and CFQ-R score by 19.3 points ( p < 0.01) in the ETI-treated group over time.We did not find a change in the trajectory between groups ( p = 0.58).Conclusions: Even with advanced lung disease, ETI-treated PwCF have a lower respiratory burden than those not on ETI.Symptoms improved over time, but this did not differ between groups, although this may be confounded by survivorship bias in the non-ETI group.In this cohort of PwCF with advanced lung disease, neither instrument demonstrated ceiling effects.Our results suggest that, although ETI has significantly improved the lived experience, PwCF with advanced disease continue to be plagued by respiratory symptoms.

The primary underlying defect in cystic fibrosis (CF) is disrupted ion transport in epithelia throughout the body. It is unclear if symptoms such as airway hyperreactivity (AHR) and increased airway smooth muscle (ASM) volume in people with CF are due to inherent abnormalities in smooth muscle or are secondary to epithelial dysfunction. Transforming Growth Factor beta 1 (TGFβ) is an established genetic modifier of CF lung disease and a known driver of abnormal ASM function. Prior studies have demonstrated that CF mice develop greater AHR, goblet cell hyperplasia, and ASM hypertrophy after pulmonary TGFβ exposure. However, the mechanism driving these abnormalities in CF lung disease, specifically the contribution of CFTR loss in ASM, was unknown. In this study, mice with smooth muscle-specific loss of CFTR function (Cftrfl/fl; SM-Cre mice) were exposed to pulmonary TGFβ. The impact on lung pathology and physiology was investigated through examination of lung mechanics, Western blot analysis, and pulmonary histology. Cftrfl/fl; SM-Cre mice treated with TGFβ demonstrated greater methacholine-induced AHR than control mice. However, Cftrfl/fl; SM-Cre mice did not develop increased inflammation, ASM area, or goblet cell hyperplasia relative to controls following TGFβ exposure. These results demonstrate a direct smooth muscle contribution to CF airway obstruction mediated by TGFβ. Dysfunction in non-epithelial tissues should be considered in the development of CF therapeutics, including potential genetic therapies.

Background Reducing treatment burden is a priority for people with cystic fibrosis, whose health has benefited from using new modulators that substantially increase CFTR protein function. The SIMPLIFY study aimed to assess the effects of discontinuing nebulised hypertonic saline or dornase alfa in individuals using the CFTR modulator elexacaftor plus tezacaftor plus ivacaftor (ETI).Methods The SIMPLIFY study included two parallel, multicentre, open-label, randomised, controlled, non-inferiority trials at 80 participating clinics across the USA in the Cystic Fibrosis Therapeutics Development Network. We included individuals with cystic fibrosis aged 12-17 years with percent predicted FEV1 (ppFEV1) of 70% or more, or those aged 18 years or older with ppFEV1 of 60% or more, if they had been taking ETI and either (or both) mucoactive therapies (>= 3% hypertonic saline or dornase alfa) for at least 90 days before screening. Participants on both hypertonic saline and dornase alfa were randomly assigned to one of the two trials, and those on a single therapy were assigned to the applicable trial. All participants were then randomly assigned 1:1 to continue or discontinue therapy for 6 weeks using permuted blocks of varying size, stratified by baseline ppFEV1 (week 0; >= 90% or <90%), single or concurrent use of hypertonic saline and dornase alfa, previous SIMPLIFY study participation (yes or no), and age (>= 18 or <18 years). For participants randomly assigned to continue their therapy during a given trial, this therapy was instructed to be taken at least once daily according to each participant's pre-existing, clinically prescribed regimen. Hypertonic saline concentration was required to be at least 3%. The primary objective for each trial was to determine whether discontinuing was non-inferior to continuing, measured by the 6-week change in ppFEV1 in the per-protocol population. We established a non-inferiority margin of -3% for the difference between groups in the 6-week change in ppFEV1. Safety outcomes were analysed in the intention-to-treat population. This study is registered with ClinicalTrials.gov, NCT04378153.Findings From Aug 25, 2020, to May 25, 2022, a total of 672 unique participants were screened for eligibility for one or both trials, resulting in 847 total random assignments across both trials with 594 unique participants. 370 participants were randomly assigned in the hypertonic saline trial and 477 in the dornase alfa trial. Participants across both trials had an average ppFEV1 of 96 center dot 9%. Discontinuing treatment was non-inferior to continuing treatment with respect to the absolute 6-week change in ppFEV1 in both the hypertonic saline trial (-0 center dot 19% [95% CI -0 center dot 85 to 0 center dot 48] in the discontinuation group [n=133] vs 0 center dot 14% [-0 center dot 51 to 0 center dot 78] in the continuation group [n=140]; between-group difference -0 center dot 32% [-1 center dot 25 to 0 center dot 60]) and dornase alfa trial (0 center dot 18% [-0 center dot 38 to 0 center dot 74] in the discontinuation group [n=199] vs -0 center dot 16% [-0 center dot 73 to 0 center dot 41] in the continuation group [n=193]; between-group difference 0 center dot 35% [-0 center dot 45 to 1 center dot 14]), with consistent results in the intention-to-treat populations. In the hypertonic saline trial, 64 (35%) of 184 in the discontinuation group versus 44 (24%) of 186 participants in the continuation group and, in the dornase alfa trial, 89 (37%) of 240 in the discontinuation group versus 55 (23%) of 237 in the continuation group had at least one adverse event. Interpretation In individuals with cystic fibrosis on ETI with relatively well preserved pulmonary function, discontinuing daily hypertonic saline or dornase alfa for 6 weeks did not result in clinically meaningful differences in pulmonary function when compared with continuing treatment.Copyright (c) 2022 Published by Elsevier Ltd. All rights reserved.

The growing use of modulator therapies aimed at restoring cystic fibrosis transmembrane conductance regulator (CFTR) protein function in people with cystic fibrosis has fundamentally altered clinical trial strategies needed to advance new therapeutics across an orphan disease population that is now divided by CFTR modulator eligibility. The development of a robust pipeline of nucleic acid-based therapies (NABTs)—initially directed towards the estimated 10% of the cystic fibrosis population who are genetically ineligible for, or intolerant of, CFTR modulators—is dependent on the optimisation of restricted trial participant resources across multiple development programmes, a challenge that will preclude the use of gold standard placebo-controlled trials. Advancement of a full pipeline of symptomatic therapies across the entire cystic fibrosis population will be challenged by smaller effect sizes and uncertainty regarding their clinical importance in a growing modulator-treated population with more mild and stable pulmonary disease. In this Series paper, we aim to lay the foundation for clinical trial strategy and community partnership that must deviate from established and familiar precedent to advance the future pipeline of cystic fibrosis therapeutics.