Journal of Cystic Fibrosis

BackgroundPatients with cystic fibrosis (CF) are characterised by abnormalities of the intestinal tract relating to gut motility and physiological issues, with daily symptoms of disease including abdominal pain, flatulence, bloating, and constipation. With improvements in respiratory outcomes, a shift in disease manifestations has highlighted the prevalence of the gastrointestinal-related problems associated with CF, yet most therapies currently in clinical use for the gut symptoms of CF have been repurposed from other disease indications and have not been developed with a knowledge of the mechanisms underpinning gastrointestinal disease in CF. Increased attention towards the role of intestinal inflammation and microbial dysbiosis in the CF population warrants a comprehensive knowledge of these aspects alongside the increased luminal fat content, dysmotility, and small intestinal bacterial overgrowth (SIBO) resultant of the primary consequences of CFTR dysfunction (disrupted fluid secretion and pancreatic insufficiency), and how they contribute towards the intestinal complications of CF disease. Methods and Study DesignWe will conduct a systematic review to comprehensively address our current understanding of the primary consequences of CFTR dysfunction, and their subsequent secondary effects that contribute towards the disruption of gut motility, health, and associated symptoms in the CF intestine. Databases searched will include PubMed, CINAHL, MEDLINE and the Cochrane library from 1939 until a specified date of last search, alongside clinical trial databases for ongoing studies. Search strategies will include various terminology that relates to the primary mechanistic defects of CF, postulated secondary effects of such defects, and symptoms experienced in patients. A full search strategy is outlined in appendix B. One reviewer will apply an inclusion criterion to obtained abstracts. Following agreement from a second reviewer, full-text articles will be sought, and data will be extracted from relevant articles. Disagreements will be resolved with a third reviewer. The quality of data will be assessed by the GRADE criteria. Data will be used to present a narrative, and where possible, quantitative synthesis. DiscussionThis systematic review will discuss our current understanding of the underpinning mechanisms of the persisting abnormalities in gut health and motility within CF, addressing potential intricate relationships that further contribute to disease progression within the intestinal tract. Furthermore, we will identify current gaps in the literature to propose directions for future research. A comprehensive understanding of these aspects in relation to intestinal abnormalities will aid future clinical directions.

RationaleThe CFTR function-phenotype relationship remains incompletely understood, with prior work yielding heterogeneous findings suggesting linear and nonlinear associations. ObjectiveDefine the genotype-function-phenotype relationship using data from the Clinical and Functional TRanslation of CFTR (CFTR2) and human nasal epithelial (HNE) studies. MethodsClinical data (sweat chloride, lung function, pancreatic status) from 84,418 individuals in CFTR2 were linked to CFTR functional measures derived from 289 CFTR genotypes. Total genotype function was calculated as the average percent wild-type chloride conductance of both variants in heterologous cell lines. This framework was applied to an HNE cohort including people with CF, CF heterozygotes, and controls. CFTR function was derived from short circuit measurements in HNEs from 153 individuals and correlated with phenotype for 415 individuals. Weighted linear and logarithmic regressions were applied to evaluate the function-phenotype relationship. Measurements and Main ResultsSimple linear regression obscured marked heterogeneity across datasets. Piecewise linear regressions revealed marked attenuation of slope magnitude with increasing function across phenotypes. This pattern was well-described by a logarithmic function, such that modeling function on a log scale rendered the relationship approximately linear. HNE data demonstrated similar attenuation, corroborating this pattern. ConclusionsLarge-scale natural history data integrated with primary cell findings show that the function-phenotype relationship is not sufficiently described by a single linear effect but is a proportional relationship, in which equivalent changes in CFTR function yield different phenotypic outcomes depending on baseline function. This framework provides precision in predicting clinical benefits from CFTR-directed therapies and identifying meaningful thresholds of CFTR rescue. Impact StatementThis work integrates registry and primary cell data to define the relationship amongst CFTR genotype, CFTR protein function, and clinical phenotype. These findings establish reference points for evaluating the degree of phenotypic improvement anticipated from functional restoration from CFTR-targeted treatments. More broadly, this study advances the understanding of CF disease mechanisms by linking molecular function to real-world clinical outcomes across data sources. At a Glance CommentaryO_ST_ABSScientific Knowledge on the SubjectC_ST_ABSThe relationship between CFTR function and clinical phenotype remains incompletely understood. Prior studies have suggested both linear and nonlinear associations between CFTR activity and disease manifestations. Defining this relationship is increasingly important for interpreting functional data and predicting clinical benefit from CFTR-directed therapies. What This Study Adds to the FieldUsing clinical and functional data from more than 84,000 individuals in CFTR2 together with primary human nasal epithelial cell measurements spanning people with cystic fibrosis, carriers, and unaffected controls, we demonstrate that the CFTR function-phenotype relationship is not adequately described by a single linear model. Instead, the relationship is best fitted by piecewise linear regressions of varying slope conforming to a logarithmic pattern, with the greatest phenotypic gains occurring at the lowest levels of baseline CFTR function. These findings provide a quantitative framework for interpreting functional rescue and predicting therapeutic benefit across the CFTR functional spectrum.

Structured AbstractO_ST_ABSRationaleC_ST_ABSAn estimated 25 million people worldwide have one deleterious variant in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Chronic respiratory disease symptoms are at an increased prevalence in cystic fibrosis (CF) heterozygotes. ObjectivesDetermine the level of CFTR function in CF heterozygotes compared to individuals without CF-causing variants. Establish whether CFTR function differs between asymptomatic and symptomatic CF heterozygotes. MethodsIndividuals without respiratory symptoms or CF family history were recruited as controls. Heterozygotes were recruited from families with a CF individual harboring null alleles or c.1521_1523del (F508del) in CFTR. CFTR function was measured by short circuit current in primary human nasal epithelial cells (HNEs) from participants. Cell composition was assessed by single cell RNA sequencing. Measurements and Main ResultsCFTR function was variable in cells from control and heterozygous individuals. Mean CFTR function in asymptomatic null (8.8{+/-}0.5{micro}A/cm2 (SEM); n=30) and F508del (8.7{+/-}1.0{micro}A/cm2; n=22) heterozygotes was similar and significantly lower at 54.6% and 53.9% than controls (16.1{+/-}1.1{micro}A/cm2; n=24; p<0.0001). Mean CFTR function in symptomatic heterozygotes (8.4{+/-}1.0{micro}A/cm2; n =15) was 52.1% of controls and did not differ from asymptomatic heterozygotes (p=0.7803). Cell identities and proportions were equivalent between control and heterozygous cultures. HNEs from CF heterozygotes showed variable response to CFTR modulators. ConclusionsCFTR function in primary airway cells exhibits substantial interindividual variability and overlaps between controls and CF heterozygotes. CF heterozygotes exhibit approximately 50% of CFTR function in controls, regardless of symptom status. These findings suggest that respiratory symptoms in CF heterozygotes are influenced by factors beyond CFTR dysfunction. At a Glance CommentaryO_ST_ABSScientific Knowledge on the SubjectC_ST_ABSA growing body of evidence indicates that cystic fibrosis (CF) heterozygotes are at increased risk for a range of common and chronic respiratory diseases. Given that an estimated 10 million individuals in the United States are CF heterozygotes, this population may represent a substantial and underappreciated burden of CFTR-associated disease. However, CFTR function has not been well characterized in CF heterozygotes, and it remains uncertain whether observed clinical phenotypes reflect reduced CFTR activity. Resolving these issues will be essential for clarifying the pathobiology of common respiratory diseases and for evaluating the potential role of CFTR modulator therapy in symptomatic CF heterozygotes. What This Study Adds to the FieldAnalysis of 24 controls and 67 CF heterozygotes revealed substantial interindividual variability in CFTR function, as measured ex vivo in differentiated nasal airway epithelial cells. Mean CFTR function in CF heterozygotes was approximately 50% of that observed in controls. CFTR function did not differ significantly between symptomatic and asymptomatic heterozygotes. These findings suggest that reduced CFTR activity may contribute to symptom susceptibility in CF heterozygotes, but additional factors beyond CFTR dysfunction are likely required for the development of CF-like features. Ethical approval and participant consent statementAll participants provided written consent to the research study under IRB00116966 and/or IRB00235883 and consented to have their anonymized data published. All research was conducted in a fair and ethical manner.

BackgroundWe recently demonstrated that the triple combination CFTR modulator therapy elexacaftor/tezacaftor/ivacaftor (ELX/TEZ/IVA) improves lung ventilation and airway mucus plugging determined by multiple-breath washout and magnetic resonance imaging in CF patients with at least one F508del allele. However, effects of ELX/TEZ/IVA on viscoelastic properties of airway mucus, chronic airway infection and inflammation have not been studied. The aim of this study was, therefore, to determine the effects of ELX/TEZ/IVA on airway mucus rheology, microbiome and inflammation in CF patients with one or two F508del alleles aged 12 years and older. MethodsIn this prospective observational study, we assessed sputum rheology, the microbiome, inflammation markers and proteome before and 8 to 16 weeks after initiation of ELX/TEZ/IVA. ResultsIn total, 59 patients with CF and at least one F508del allele and 10 healthy controls were enrolled in this study. ELX/TEZ/IVA improved the elastic modulus (G; -6.3 Pa; IQR, -17.9 to 1.2; P<0.01) and viscous modulus (G; -1.6 Pa; IQR, -3.6 to 0.5; P<0.05) of CF sputum. Further, ELX/TEZ/IVA improved the microbiome -diversity (0.6; IQR, 0.0 to 1.2; P<0.001) and decreased the relative abundance of Pseudomonas aeruginosa in CF sputum. ELX/TEZ/IVA also reduced IL-8 (-11.7 ng/ml, IQR, -36.5 to 11.2; P<0.05) and free NE activity (-27.5 {micro}g/ml, IQR, - 64.5 to -3.5; P<0.001), and shifted the CF sputum proteome towards healthy. ConclusionsOur data demonstrate that ELX/TEZ/IVA improves sputum viscoelastic properties, chronic airway infection and inflammation in CF patients with at least one F508del allele, however, without reaching levels close to healthy. Clinical trial registered with www.clinicaltrials.gov (NCT04732910)

BackgroundCystic Fibrosis (CF) is a lethal genetic condition affecting over 100,000 people worldwide, characterised by multi-organ dysfunction and a progressive lethal lung disease. The disease occurs due to faulty cystic fibrosis transmembrane conductance regulator (CFTR) ion channels effecting flow of chloride, bicarbonate and water out of cells. This causes thick mucus with repeated bacterial infections, systemic inflammation and a decrease in lung function. CFTR modulator therapies have shown variable improvements in lung function and reduction in exacerbation frequency. Basal cells within the lung act as a stem cell for repair following injury and can repopulate the epithelial layer. This process is dysfunctional in CF causing progressive damage. Spontaneous lung repair is well described but not well characterised. Nothing is known about the effects of CFTR modulator therapy on these cells, but this could be of major consequence for people with CF (pwCF). AimsTo determine the effects of CFTR modulator therapy on the activity of CF basal cells and relate this to progenitor function and to study the effects of CFTR modulators on systemic inflammation and clinical outcomes. MethodsClinical information, blood and nasal brushes were obtained from pwCF prior to commencing modulator therapy and at multiple time points up until 1 year of treatment. 10 pwCF were recruited to undertake thoracic CT scans pre-treatment and at 1 year of therapy. Nasal samples were used to isolate basal cells and serum to study systemic markers of inflammation. RNA sequencing of basal cells was undertaken by Ilumina Novoseq to a depth of 20 million read pairs and gene ontology analysis was performed. Functional assays of basal cell activity were carried out. Proteomic analysis and ELISAs were undertaken to determine changes in inflammatory cytokines within the serum across the first year of treatment. Quantitative results were generated by Lung Quantification (LungQ) analysis with qualitative reports from independent radiologists. Results were compared with clinical outcomes. Results110 pwCF were recruited in total who commenced a commercially available CFTR modulator therapy. Serum samples were collected from 77pwCF, nasal brushes obtained from 40 pwCF and 10 completed their CT scans following 1 year of highly effective CFTR modulator therapy. Systemic IL-6, CRP and calprotectin (a biomarker of CF exacerbation) were all significantly reduced with highly effective CFTR modulator treatment. Clinical results were in keeping with those seen in published CFTR modulator clinical trials with improvement in lung function, weight, and exacerbation frequency. Subjective improvements were seen in all 10 CT scans following 1 year of modulator therapy. Significant reductions were seen in airway wall thickening and reduction in thoracic lymphadenopathy were also observed. Basal cell RNA sequencing showed that the relative expression of 2570 genes were significantly different following treatment with CFTR modulators. Ontology analysis showed enrichment in multiple pathways including cilliagenesis and Notch signalling, a key pathway in lung tissue development and homeostasis. Functional assays exhibited a deficit in repair mechanisms of the CF basal cell compared to healthy controls, and reduction in progenitor function. ConclusionsAlthough CFTR modulators improve multiple clinical and radiological outcomes, they also have impacts on basal cell function. There are however, limited impacts on systemic inflammation and more work is needed in this area to understand the disease process.

BackgroundNonsense variants in CFTR account for ~10% of cystic fibrosis (CF) variants and cannot be treated with approved CFTR modulators. Translational readthrough agents such as ELX-02 offer a potential therapeutic strategy, but clinical trials evaluated mainly in G542X CFTR nonsense variant and underlined limited efficacy. This study aimed to evaluate ELX-02-mediated CFTR rescue across a broad range of nonsense variants using patient-derived intestinal organoids (PDIOs) to define variant-specific determinants of readthrough efficacy and assess its potential across a genetically diverse CF population. MethodThe ex vivo response to ELX-02 was assessed in 206 PDIOs carrying heterogeneous nonsense variants. CFTR function was quantified using forskolin-induced swelling (FIS) assay after 48-hour exposure to ELX-02. Responses were analysed by genotype and stop codon identity, with secondary validation performed in a selected subset of PDIOs (n = 60). ResultsELX-02-mediated CFTR rescue varied markedly, ranging from responses approaching those observed with approved CFTR modulators (LUM/IVA) to responses at or below detection limit. Overall, maximal responses were modest and at the lower end of the functional range for CFTR modulators. Rescue was dose-dependent and higher in PDIOs carrying two nonsense variants when compared with PDIOs carrying a single nonsense variant combined with a residual or minimal function variant. Nonsense variants in nucleotide-binding domain 1, including G542X, S466X, G550X and R553X, showed relatively higher responsiveness. ConclusionELX-02 induces limited and highly heterogeneous CFTR rescue across nonsense variants. PDIO-based functional screening provides a framework to guide patient selection and stratification for future readthrough therapy trials.

Background and aimsGastrointestinal symptoms remain common in adults with cystic fibrosis (CF) despite cystic fibrosis transmembrane conductance regulator modulator use, suggesting persistent and heterogeneous gut dysfunction. This prospective observational study tests the hypothesis that distinct gut symptom phenotypes in CF can be observed and linked to underlying mechanisms. MethodsAdults from three UK CF centres completed the Gastrointestinal Symptom Rating Scale, Patient Assessment of Constipation Symptoms and a bowel-habit questionnaire. Latent class analysis using an ordinal logistic model was applied to 36 symptom indicators. Associations between phenotypes and demographic, clinical, and treatment variables were examined using generalised linear models. ResultsThree hundred participants completed questionnaires (54% male; median 31 years). We identified four symptom phenotypes: mild; moderate-constipation predominant; moderate-diarrhoea predominant and severe. The severe phenotype was associated with gastroesophageal reflux (RRR 2.86; 95%CI: 1.30-6.31; p=0.009), distal intestinal obstruction syndrome (RRR 2.46; 95%CI: 1.04-5.81; p=0.04), proton pump inhibitor (RRR 3.29; 95%CI 1.39-7.74; p=0.007), and laxative use (RRR 6.13; 95%CI 2.54-14.84; p<0.001). CF-related liver disease was associated with both moderate-constipation and diarrhoea phenotypes, respectively (RRR 2.08; 95%CI 1.13-3.81; p=0.018; RRR 2.11; 95%CI 1.03-4.29; p=0.04). There was a lower likelihood of long-term oral antibiotic use in the moderate-constipation phenotype (RRR 0.53; 95%CI 0.3-0.92; p=0.025) and moderate-diarrhoea phenotype (RRR 0.46; 95%CI 0.24-0.91; p=0.025). ConclusionsFour distinct symptom phenotypes were identified, independent of demographics and pancreatic status, but associated with specific complications and medication profiles. These phenotypes provide a framework for mechanistic studies within the GRAMPUS-CF cohort and precision management of CF-related gut disease.

1BackgroundWhile cystic fibrosis is caused by loss-of-function variants in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR), other modifier genes have been shown to associate with disease severity. Co-expression of modifiers with CFTR in normal tissue indicates a cooperative relationship and suggests the potential for compensation in the presence of CFTR dysfunction. We examined the co-expression relationships with CFTR in the lung using single cell RNA sequencing to pinpoint cell types and their modifiers involved in the forced expiratory volume in 1 second (FEV1)-based cystic fibrosis lung phenotype and support target cell-type prioritization for therapy 1. MethodsSmartSeq2 single cell RNA sequencing data from non-cystic fibrosis lung tissue was used for evaluation of co-expression with CFTR and modifier genes. Zero-inflated negative binomial model was used to formally test the co-expression association. 10X Chromium based single cell RNA sequencing data from both cystic fibrosis and non-cystic fibrosis studies were assessed graphically to confirm conclusions from the SmartSeq2 primary analysis. ResultsDifferentiating basal, club and alveolar epithelial type 2 cells were found to have high proportions of cells expressing CFTR as well as the greatest number of significant co-expression relationships with the modifiers. In particular, among alveolar epithelial type 2 cells, we observed a strong co-expression trio relationship between CFTR, SLC6A14 and SLC26A9 (p < 0.05). ConclusionsCFTR-modifier gene co-expression suggests basal, club and alveolar epithelial type 2 cells show coordinated expression. Alveolar epithelial type 2 cells showed strong co-expression evidence with two of the most established cystic fibrosis modifier genes.

Cystic fibrosis (CF), resulting from a dysfunction in the cystic fibrosis transmembrane conductance regulator (CFTR), affects multiple organs through mucus obstruction and differences in secretion. The CFTR modulator drug combination elexacaftor/tezacaftor/ivacaftor (ELX/TEZ/IVA, ETI) has markedly improved clinical symptoms, but its broader molecular and systemic effects remain to be fully elucidated. We employed mass spectrometry-based proteomics to compare the blood proteomes of CF patients treated with the earlier, less effective lumacaftor/ivacaftor (LUM/IVA) combination against those receiving the more potent ELX/TEZ/IVA therapy. Our analysis revealed both specific and common pharmacodynamic signatures associated with inflammation and metabolic processes under each treatment regimen. Notably, ELX/TEZ/IVA therapy exhibited more consistent alterations across patients that were directed towards profiles observed in healthy individuals. Furthermore, by comparing sputum and blood proteomes of ELX/TEZ/IVA treated patients we identified counter-directional changes in the pulmonary surfactant-associated protein B, SFTPB, a potential biomarker of lung tissue repair, which also correlated with lung function improvements. This study provides a comprehensive resource that enhances our understanding of CFTR modulator-driven proteome alterations, offering insights to both systemic and local protein regulation in CF. Our findings indicate that ELX/TEZ/IVA promotes broader systemic health improvements, providing critical insights that could shape future therapeutic strategies in CF.

Patient-derived organoids hold great potential as predictive biomarker for disease expression or therapeutic response. Here, we used intestinal organoids to estimate individual cystic fibrosis transmembrane conductance regulator (CFTR) function of people with cystic fibrosis, a monogenic life-shortening disease associated with more than 2000 CFTR mutations and highly variable disease progression. In vitro CFTR function in CF intestinal organoids of 176 individuals with diverse CFTR mutations was quantified by forskolin induced swelling and was strongly associated with longitudinal changes of lung function and development of pancreatic insufficiency, CF-related liver disease and diabetes. This association was not observed when the commonly used biomarker of CFTR function sweat chloride concentration was used. The data strongly exemplifies the value of an organoid-based biomarker in a clinical disease setting and supports the prognostic value of forskolin induced swelling of intestinal organoids, especially for people with CF who have rare CFTR genotypes with unclear clinical consequences.

Cystic fibrosis (CF) is caused by defective Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein. CFTR controls chloride (Cl-) and bicarbonate (HCO3-) transport into the Airway Surface Liquid (ASL).We investigated the impact of F508del-CFTR correction on HCO3- secretion by studying transepithelial HCO3- fluxes. HCO3- secretion was measured by pH-stat techniquein primary human respiratory epithelial cells from healthy subjects (WT) and people with CF (pwCF)carrying at least oneF508del variant.Its changes after CFTR modulation by the triple combination VX445/661/770 and in the context of TNF-+IL-17 induced inflammation were related to ASL pH and transcriptionnal levels of CFTRand other HCO3- transporters ofairway epithelia such asSLC26A4 (Pendrin), SLC26A9 and NBCe1. CFTR-mediated HCO3-secretion was not detected in F508del primary human respiratory epithelial cells. It was rescued up to [~] 80% of the WT levelby VX-445/661/770. In contrast,TNF-+IL-17 normalized transepithelial HCO3-transportand ASL acidic pH. This was related to anincrease in SLC26A4 and CFTR transcript levels.VX-445/661/770 induced an increase in pH only in the context of inflammation.Effects on HCO3- transport werenot differentbetween F508del homozygous and F508del heterozygous CF airway epithelia. Our studies show that correction of F508del-CFTRHCO3- is not sufficient to buffer acidic ASL and that inflammation is a key regulator of HCO3-secretion in CF airways. Prediction of the response to CFTR modulators by theratyping should take into account airway inflammation.

BackgroundCFTR 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. MethodsWe 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 ({Delta}Isc). ResultsClinical 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 {Delta}Isc and FEV1pp improvement in patients with baseline FEV1pp <90 (R{superscript 2} = 0.651, p = 0.001) and SC reduction (R{superscript 2} = 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 {Delta}Isc predicts FEV1pp changes, modulated by baseline lung function and CFTR modulator type. ConclusionPatient-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 topicO_LICFTR modulators significantly improve clinical outcomes in people with cystic fibrosis (CF), yet individual responses vary, even among those with identical CFTR genotypes. C_LIO_LIPatient-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. C_LIO_LIThe relationship between CFTR sequence variations, pharmacogene heterogeneity, and modulator response in paediatric patients has not been extensively explored. C_LI What this study addsO_LIThis study demonstrates a strong correlation between in vitro CFTR function ({Delta}Isc) and clinical improvements in FEV1pp and sweat chloride in children and adolescents with CF. C_LIO_LIWhole-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. C_LIO_LIWhile 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. C_LIO_LIDifferentiated-HNEC cultures consistently predicted clinical response across multiple CFTR modulator regimens, reinforcing their value for preclinical drug screening. C_LI How this study might affect research, practice, or policyO_LIOur findings support the integration of differentiated-HNEC models into clinical practice to personalise CFTR modulator selection, reducing ineffective treatments and improving patient outcomes. C_LIO_LIThe study underscores the need for additional clinical endpoints beyond FEV1pp to assess respiratory function in individuals with preserved lung function (FEV1pp > 90%). C_LI

BackgroundDespite significant clinical improvements, there is evidence of persisting airway inflammation in people with cystic fibrosis established on Elexacaftor/tezacaftor/ivacaftor (ETI) therapy. As CF is a multi-system disease, systemic immune profiles can reflect local inflammation within the lungs and other organs. Understanding systemic inflammation after ETI therapy may reveal important translational insights. This study aims to profile systemic inflammatory changes and relate these to the well-documented improvements observed with ETI therapy. MethodsWe conducted a single-centre longitudinal study with 57 CF subjects initiating ETI therapy. All participants were Phe508del homozygous or Phe508del/minimal function. Blood samples were collected pre-ETI and 3-12 months post-therapy initiation. Analyses included mass spectrometry-based proteomics, a multiplex immunoassay, and flow cytometry for peripheral immune cell counts and phenotype. Controls samples were provided by 29 age-matched healthy controls. ResultsSystemic inflammation reduced with ETI therapy; however, the immune profile remained distinct from healthy controls. ETI reduced neutrophil counts and was associated with a more mature, less inflammatory phenotype, as well as a shift toward an immune resolving state associated with increased CD206 expression. Cytokines known to influence neutrophil levels reduced with therapy. Despite ETI therapy, neutrophil and monocyte counts remained elevated compared to healthy controls. There was no obvious association between the ETI-related improvements in systemic inflammation and lung function. ConclusionsPatients with CF show evidence of persisting systemic inflammation despite ETI therapy, this may have long term potentially adverse effects on respiratory and other organ systems.

BackgroundCystic fibrosis (CF) research has increasingly focused on understanding the extra-pulmonary manifestations of CF, including on the gastrointestinal (GI) system. The effect of cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies outside the lungs is also a topic of research interest and both are key research priorities. However, significant evidence gaps persist in understanding the complex pathophysiology of CFTR dysfunction in the GI tract, and the treatment of these GI problems. Inconsistencies in outcome reporting may contribute towards these evidence gaps, and a standardised approach to outcome reporting may help to address this. This systematic rapid review aims to identify and catalogue the range of outcome measurement instruments (OMIs) and associated endpoints currently used in CF GI research. MethodsThis PROSPERO-registered review (CRD42021281961) was conducted following Cochrane Rapid Reviews Methods Group and COMET initiative guidance. Comprehensive searches were performed in MEDLINE, EMBASE, PubMed, Cochrane Library, and ongoing clinical trials databases, covering an 11-year period (August 2013 to November 2024). Screening and data extraction were carried out using Covidence online software. ResultsA total of 1,541 studies were identified, of which 193 met inclusion criteria. These studies collectively used 246 distinct OMIs, of which 172 (70%) were employed in only one study. The OMIs identified were grouped into 14 sub-domains representing key areas of GI research in CF, which were subsequently mapped to 11 of the 38 outcome domains in the taxonomy proposed by the COMET Initiative. The identified outcomes spanned a diverse range of mechanistic and patient-centred measures, reflecting the complexity of GI disease in CF. ConclusionsCurrent research into the GI tract in CF uses a heterogeneous array of OMIs, with limited standardisation. This highlights both the complexity of CFTR dysfunction within the GI tract, requiring a wide scope of OMIs to address this, as well the variability and potential inefficiency in current outcome reporting practices. To advance our understanding of CF pathophysiology in the GI tract, a standardised approach to outcome reporting is needed. Our findings support the development of a core outcome set to promote reporting consistency and improve comparability across studies in CF GI research.

BackgroundCystic fibrosis (CF) has profoundly changed since the introduction of CF Transmembrane Conductance Regulator modulator therapies (CFTRmt), a class of medications that improve function of the CFTR protein encoded by certain CF-causing gene mutations. Amongst these, the triple combination therapy elexacaftor-tezacaftor-ivacaftor (ETI) has been the most impactful and widely used to date. Given chronic respiratory infection and concomitant inflammation is the leading cause of morbidity and early mortality for the majority in CF, what is not certain are the long-term effects of ETI therapy on the respiratory microbiota and pathogens imbedded within. Here we assessed the long-term effects of ETI CFTRmt over 3-years on the respiratory microbiota of a multi-centre cohort of 276 adults with CF (awCF) from 6 CF centres in the UK, USA, and Canada, and compared to a non-CF healthy cohort. ResultsWe determined that respiratory microbiota characteristics (diversity, dominance, and composition) became decreasingly like those of awCF pre-ETI and remodelled to align more with the healthy cohort, where canonical CF pathogens increasingly became less ecologically important in terms of their distributions and abundances across awCF with increased duration on therapy. However, the on-ETI microbiota was impeded from becoming fully healthy due to continued antibiotic exposure and irreversible lung damage experienced by awCF. Specifically, we found that azithromycin, an antibiotic widely used principally for its immunomodulatory benefits, had adverse effects on the respiratory microbiota nullifying the observed positive effects of ETI treatment. When administered alongside ETI-therapy, the use of azithromycin maintained a pre-ETI microbiota dysbiosis and enabled enhanced persistence of emblematic CF pathogens. ConclusionsThe highly anticipated introduction of ETI CFTRmt has greatly changed the course of CF for many people living with this inherited disease. Here we find that ETI CFTRmt enabled positive remodelling of the respiratory microbiota towards a healthy-like state. However, azithromycin impeded total remodelling, making it an ideal candidate for evaluation for discontinuation in the CFTRmt era. While traditional pathogens become less ecologically important the potential evolution and emergence of virulent strains should be investigated. Additionally, the impacts and implications of ETI therapy on the understudied fungal microbiota should also be explored.

Chronic inflammation dominates disease pathogenesis in Cystic Fibrosis (CF) and there is a need to characterise CF immunity. Whole blood cultures offer a cost-effective and non-invasive approach to investigate immune responses within the host environment. Here we used whole blood cultures to investigate the differentiation potential of monocytes (CD45+CD14+ cells) in CF (N=10) and controls (N=8) in the presence and absence of exogenous macrophage-colony stimulatory factor (M-CSF) or granulocyte-macrophage (GM)-CSF with and without interleukin (IL)-4. In CF and control cultures, CD45+CD14+ cells upregulated HLA-DR expression in all instances, and increased CD206 in the presence of GM-CSF with and without IL-4, and CD209 in the presence of GM-CSF and IL-4. In CF, we consistently observed reduced upregulation of CD206 in response to GM-CSF and a positive correlation between CD206 expression and lung function (FEV1). This was unique to cultured monocytes, and not seen with any other marker. These results highlight the potential of whole blood cultures to reveal cellular characteristics in differentiating monocytes related to clinical parameters that could guide the identification of novel biomarkers in CF.

Characterisation of I37R - a novel mutation in the lasso motif of ABC-transporter CFTR, a chloride channel - was conducted by theratyping using CFTR potentiators which increase channel gating activity and correctors which repair protein trafficking defects. I37R-CFTR function was characterised using intestinal current measurements (ICM) in rectal biopsies, forskolin-induced swelling (FIS) in intestinal organoids and short circuit current measurements (Isc) in organoid-derived monolayers from an individual with I37R/F508del CFTR genotype. We demonstrated that the I37R-CFTR mutation results in a residual function defect amenable to treatment with potentiators and type III, but not to type I, correctors. Molecular dynamics of I37R-CFTR using an extended model of the phosphorylated, ATP-bound human CFTR identified an altered lasso motif conformation which results in an unfavourable strengthening of the interactions between the lasso motif, the regulatory (R) domain and the transmembrane domain two (TMD2). In conclusion, structural and functional characterisation of the I37R-CFTR mutation increases understanding of CFTR channel regulation and provides a potential pathway to access CFTR modulator treatments for individuals with CF caused by ultra-rare CFTR mutations.

AimCystic fibrosis (CF) care has been transformed by CFTR modulator therapies, yet most efficacy data arise from clinical trials with restrictive eligibility criteria. Real-world registry data can capture treatment outcomes in broader, more diverse patient populations. We used the Cystic Fibrosis Foundation Patient Registry (CFFPR) data to evaluate longitudinal clinical outcomes, and care benchmarking at a single Adult CF Program Center over a decade. MethodsA retrospective, descriptive analysis of CFFPR data (2011-2022) was performed to assess trends in modulator use, lung function (ppFEV1), body mass index (BMI), respiratory microbiology, and pulmonary exacerbations (PEx). Comparative Effectiveness Research (CER) methods were applied to compare outcomes across peak modulator eras: pre-modulator (2011), ivacaftor (2015), mixed-modulator (2019), and elexacaftor/tezacaftor/ivacaftor (ELE/TEZ/IVA) (2021). Program-level outcomes were benchmarked against national network metrics to assess adherence to guideline-based care. ResultsOver ten years, median ppFEV1 improved from 63.4% (2011) to 78.8% (2021), and BMI increased from 22.3 to 24.8 kg/m2. The proportion of adults experiencing more than one PEx annually declined from 39.7% to 19.5%, while Pseudomonas aeruginosa (P.a.) culture positivity decreased from 79% to 47%. ELE/TEZ/IVA therapy was associated with greatest clinical improvements. Program-level performance remained comparable to national network benchmarks, reflecting high adherence to standard care metrics. ConclusionRegistry-based CER provides valuable real-world insights into CF care effectiveness and quality improvement. This decade-long analysis demonstrates significant clinical gains associated with modulator therapies and highlights the importance of patient registries in monitoring outcomes, benchmarking care, and informing global CF care models and standards for rare disease management. Key Messages{square} Real-world registry data enables decade-long evaluation of CFTR modulator effectiveness. {square}Elexacaftor/tezacaftor/ivacaftor demonstrates the greatest clinical benefit among modulator therapies. {square}Benchmarking Adult CF Program performance against the Network of Adult CF Programs facilitates quality improvement and standard care guideline adherence. {square}Patient registries provide insights for personalized care, program-level decision-making, and international standards for rare disease management.

CFTR modulator therapies have transformed CF care, yet chronic airway inflammation persists in many people with cystic fibrosis (pwCF) even after long-term highly effective modulator therapy (HEMT). Because of the adverse side effects or the incompatibility with CFTR modulators, the use of traditional anti-inflammatory therapies is very limited in CF. Hence, new therapeutic strategies that rebalance inflammation without worsening infection with immunosuppression are needed. We evaluated the selective phosphodiesterase 4 (PDE4) inhibitor apremilast (Apr) for its ability to modulate dysregulated inflammation in humanized CF (G551D) rats acutely challenged with Pseudomonas aeruginosa. Apr is an approved anti-inflammatory therapeutic strategy for several chronic inflammatory conditions, but it has not been well studied in CF. In the humanized CF (G551D) rats, a short prophylactic Apr regimen significantly preserved lung function and reduced lung injury, accompanied by broad modulation of inflammatory responses, notably within Th1 and Th17 axes. Importantly, Apr did not cause a significant increase in bacterial burden. Just as importantly, Apr did not reduce CFTR mRNA or protein in vivo, and it increased G551D-CFTR phosphorylation critical for channel gating in vitro, supporting mechanistic compatibility with HEMT. These findings suggest Apr as a potential adjunct to CFTR modulators to rebalance airway inflammation while preserving host defense.

RationaleLung function (FEV1) and quality of life (QoL) are key outcomes in most interventional clinical trials conducted in people living with cystic fibrosis. However, no robust pre-clinical surrogates for FEV1 and QoL exist. The precise physiological mechanisms leading to treatment-related improvements in these outcomes are incompletely understood. In this post-hoc analysis we explored the relationship between changes in the sputum proteome and these outcomes with the aim of identifying translational biomarkers. MethodsPaired sputum samples collected during the AZTEC-CF study (NCT02894684) pre and post 14 days of antibiotic treatment for an acute pulmonary exacerbation were included. Samples were analysed using in vitro Mesoscale Discovery (MSD) assays and by nano LC-MS/MS. Peptide identification and quantification was performed and the log-fold change for individual proteins and relationships between protein change and changes in FEV1 and QoL were evaluated. ResultsDistinct patterns were found between proteins that correlated with FEV1 and those that correlated with QoL improvements. FEV1 improvement was characterised by increases in bacterially-derived proteins accompanied by decreases in proteins relating to neutrophil degranulation. Conversely, changes in QoL were associated with increases in antiprotease and antioxidant proteins. MSD analysis revealed changes in some neutrophil-associated markers significantly correlated with FEV1 improvements, but no markers significantly correlated with QoL improvements. ConclusionsThese results suggest changes in two key CF clinical trial outcomes (FEV1 and QoL) may be underpinned by different physiological mechanisms. Understanding these divergent mechanisms is vital to fortify optimal clinical trial design in CF and panels of biomarkers may be needed to improve translational confidence.