Q1291H-CFTR molecular dynamics simulations and ex vivo theratyping in nasal epithelial models and clinical response to elexacaftor/tezacaftor/ivacaftor in a Q1291H/F508del patient

Background: Cystic fibrosis (CF) is caused by a wide spectrum of mutations in the CF transmembrane conductance regulator (CFTR) gene, with some leading to non-classical clinical presentations. We present an integrated in vivo, in silico and in vitro investigation of an individual with CF carrying the rare Q1291H-CFTR allele and the common F508del allele. At age 56 years, the participant had obstructive lung disease and bronchiectasis, qualifying for Elexacaftor/Tezacaftor/Ivacaftor (ETI) CFTR modulator treatment due to their F508del allele. Q1291H CFTR incurs a splicing defect, producing both a normally spliced but mutant mRNA isoform and a misspliced isoform with a premature termination codon, causing nonsense mediated decay. The effectiveness of ETI in restoring Q1291H-CFTR is largely unknown. Methods: We collected clinical endpoint measurements, including forced expiratory volume in 1 s percent predicted (FEV1pp) and body mass index (BMI), and examined medical history. In silico simulations of the Q1291H-CFTR were compared to Q1291R, G551D, and wild-type (WT)-CFTR. We quantified relative Q1291H CFTR mRNA isoform abundance in patient-derived nasal epithelial cells. Differentiated pseudostratified airway epithelial cell models at air liquid interface were created and ETI treatment impact on CFTR was assessed by electrophysiology assays and Western blot. Results: The participant ceased ETI treatment after 3 months due to adverse events and no improvement in FEV1pp or BMI. In silico simulations of Q1291H-CFTR identified impairment of ATP binding similar to known gating mutants Q1291R and G551D-CFTR. Q1291H and F508del mRNA transcripts composed 32.91% and 67.09% of total mRNA respectively, indicating 50.94% of Q1291H mRNA was misspliced and degraded. Mature Q1291H-CFTR protein expression was reduced (3.18% ± 0.60% of WT/WT) and remained unchanged with ETI. Baseline CFTR activity was minimal (3.45 ± 0.25 μA/cm²) and not enhanced with ETI (5.73 ± 0.48 μA/cm²), aligning with the individual's clinical evaluation as a non-responder to ETI. Conclusion: The combination of in silico simulations and in vitro theratyping in patient-derived cell models can effectively assess CFTR modulator efficacy for individuals with non-classical CF manifestations or rare CFTR mutations, guiding personalized treatment strategies and optimizing clinical outcomes.

Comparing Cytology Brushes for Optimal Human Nasal Epithelial Cell Collection: Implications for Airway Disease Diagnosis and Research

Primary nasal epithelial cells and culture models are used as important diagnostic, research and drug development tools for several airway diseases. Various instruments have been used for the collection of human nasal epithelial (HNE) cells but no global consensus yet exists regarding the optimal tool. This study compares the efficiency of two cytology brushes (Olympus (2 mm diameter) and Endoscan (8 mm diameter)) in collecting HNE cells. The study involved two phases, with phase one comparing the yield, morphology and cilia beat frequency (CBF) of cells collected from paediatric participants using each of the two brushes. Phase two compared nasal brushing under general anaesthetic and in the awake state, across a wide age range, via the retrospective audit of the use of the Endoscan brush in 145 participants. Results indicated no significant difference in CBF measurements between the two brushes, suggesting that the choice of brush does not compromise diagnostic accuracy. However, the Endoscan brush collected significantly more total and live cells than the Olympus brush, making it a more efficient option. Importantly, the Endoscan brush is more cost-effective, with a notable price difference between the two brushes.

Quantifying Intracellular Viral Pathogen: Specimen Preparation, Visualization and Quantification of Multiple Immunofluorescent Signals in Fixed Human Airway Epithelium Cultured at Air-Liquid Interface

Infection control and aggressive antibiotic therapy play an important role in the management of airway infections in individuals with cystic fibrosis (CF). The responses of airway epithelial cells to pathogens are likely to contribute to the pathobiology of CF lung disease. Primary airway epithelial cells obtained from individuals with CF, cultured and differentiated at air-liquid interface (ALI), effectively mimic the structure and function of the in vivo airway epithelium. With the recent respiratory viral pandemics, ALI cultures were extensively used to model respiratory infections in vitro to facilitate physiologically relevant respiratory research. Immunofluorescence staining and imaging were used as an effective tool to provide a fundamental understanding of host–pathogen interactions and for exploring the therapeutic potential of novel or repurposed drugs. Therefore, we described an optimized quantitative fluorescence microscopy assay for the wholemount staining and imaging of epithelial cell markers to identify distinct cell populations and pathogen-specific targets in ALI cultures of human airway epithelial cells grown on permeable support insert membranes. We present a detailed methodology using a graphical user interface (GUI) package to quantify the detected signals on a tiled whole membrane. Our method provided an imaging strategy of the entire membrane, overcoming the common issue of undersampling and enabling unbiased quantitative analysis.

Molecular Dynamics and Theratyping in Airway and Gut Organoids Reveal R352Q-CFTR Conductance Defect

A significant challenge to making targeted cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies accessible to all individuals with cystic fibrosis (CF) are many mutations in the CFTR gene that can cause CF, most of which remain uncharacterized. Here, we characterized the structural and functional defects of the rare CFTR mutation R352Q, with a potential role contributing to intrapore chloride ion permeation, in patient-derived cell models of the airway and gut. CFTR function in differentiated nasal epithelial cultures and matched intestinal organoids was assessed using an ion transport assay and forskolin-induced swelling assay, respectively. CFTR potentiators (VX-770, GLPG1837, and VX-445) and correctors (VX-809, VX-445, with or without VX-661) were tested. Data from R352Q-CFTR were compared with data of 20 participants with mutations with known impact on CFTR function. R352Q-CFTR has residual CFTR function that was restored to functional CFTR activity by CFTR potentiators but not the corrector. Molecular dynamics simulations of R352Q-CFTR were carried out, which indicated the presence of a chloride conductance defect, with little evidence supporting a gating defect. The combination approach of in vitro patient-derived cell models and in silico molecular dynamics simulations to characterize rare CFTR mutations can improve the specificity and sensitivity of modulator response predictions and aid in their translational use for CF precision medicine.

Molecular dynamics and functional characterization of I37R-CFTR lasso mutation provide insights into channel gating activity

Characterization of I37R, a mutation located in the lasso motif of the CFTR chloride channel, was conducted by theratyping several CFTR modulators from both potentiator and corrector classes. Intestinal current measurements in rectal biopsies, forskolin-induced swelling (FIS) in intestinal organoids, and short circuit current measurements in organoid-derived monolayers from an individual with I37R/F508del CFTR genotype demonstrated that the I37R-CFTR results in a residual function defect amenable to treatment with potentiators and type III, but not type I, correctors. Molecular dynamics of I37R using an extended model of the phosphorylated, ATP-bound human CFTR identified an altered lasso motif conformation which results in an unfavorable strengthening of the interactions between the lasso motif, the regulatory (R) domain, and the transmembrane domain 2 (TMD2). Structural and functional characterization of the I37R-CFTR mutation increases understanding of CFTR channel regulation and provides a potential pathway to expand drug access to CF patients with ultra-rare genotypes.

S945L-CFTR molecular dynamics, functional characterization and tezacaftor/ivacaftor efficacy in vivo and in vitro in matched pediatric patient-derived cell models

Cystic Fibrosis (CF) results from over 400 different disease-causing mutations in the CF Transmembrane Conductance Regulator (CFTR) gene. These CFTR mutations lead to numerous defects in CFTR protein function. A novel class of targeted therapies (CFTR modulators) have been developed that can restore defects in CFTR folding and gating. This study aimed to characterize the functional and structural defects of S945L-CFTR and interrogate the efficacy of modulators with two modes of action: gating potentiator [ivacaftor (IVA)] and folding corrector [tezacaftor (TEZ)]. The response to these modulators in vitro in airway differentiated cell models created from a participant with S945L/G542X-CFTR was correlated with in vivo clinical outcomes of that participant at least 12 months pre and post modulator therapy. In this participants' airway cell models, CFTR-mediated chloride transport was assessed via ion transport electrophysiology. Monotherapy with IVA or TEZ increased CFTR activity, albeit not reaching statistical significance. Combination therapy with TEZ/IVA significantly (p = 0.02) increased CFTR activity 1.62-fold above baseline. Assessment of CFTR expression and maturation via western blot validated the presence of mature, fully glycosylated CFTR, which increased 4.1-fold in TEZ/IVA-treated cells. The in vitro S945L-CFTR response to modulator correlated with an improvement in in vivo lung function (ppFEV₁) from 77.19 in the 12 months pre TEZ/IVA to 80.79 in the 12 months post TEZ/IVA. The slope of decline in ppFEV1 significantly (p = 0.02) changed in the 24 months post TEZ/IVA, becoming positive. Furthermore, there was a significant improvement in clinical parameters and a fall in sweat chloride from 68 to 28 mmol/L. The mechanism of dysfunction of S945L-CFTR was elucidated by in silico molecular dynamics (MD) simulations. S945L-CFTR caused misfolding of transmembrane helix 8 and disruption of the R domain, a CFTR domain critical to channel gating. This study showed in vitro and in silico that S945L causes both folding and gating defects in CFTR and demonstrated in vitro and in vivo that TEZ/IVA is an efficacious modulator combination to address these defects. As such, we support the utility of patient-derived cell models and MD simulations in predicting and understanding the effect of modulators on CFTR function on an individualized basis.

Collection, Expansion, and Differentiation of Primary Human Nasal Epithelial Cell Models for Quantification of Cilia Beat Frequency

Measurements of cilia function (beat frequency, pattern) have been established as diagnostic tools for respiratory diseases such as primary ciliary dyskinesia. However, the wider application of these techniques is limited by the extreme susceptibility of ciliary function to changes in environmental factors e.g., temperature, humidity, and pH. In the airway of patients with Cystic Fibrosis (CF), mucus accumulation impedes cilia beating. Cilia function has been investigated in primary airway cell models as an indicator of CF Transmembrane conductance Regulator (CFTR) channel activity. However, considerable patient-to-patient variability in cilia beating frequency has been found in response to CFTR-modulating drugs, even for patients with the same CFTR mutations. Furthermore, the impact of dysfunctional CFTR-regulated chloride secretion on ciliary function is poorly understood. There is currently no comprehensive protocol demonstrating sample preparation of in vitro airway models, image acquisition, and analysis of Cilia Beat Frequency (CBF). Standardized culture conditions and image acquisition performed in an environmentally controlled condition would enable consistent, reproducible quantification of CBF between individuals and in response to CFTR-modulating drugs. This protocol describes the quantification of CBF in three different airway epithelial cell model systems: 1) native epithelial sheets, 2) air-liquid interface models imaged on permeable support inserts, and 3) extracellular matrix-embedded three-dimensional organoids. The latter two replicate in vivo lung physiology, with beating cilia and production of mucus. The ciliary function is captured using a high-speed video camera in an environment-controlled chamber. Custom-built scripts are used for the analysis of CBF. Translation of CBF measurements to the clinic is envisioned to be an important clinical tool for predicting response to CFTR-modulating drugs on a per-patient basis.

Treatment of Cystic Fibrosis: From Gene- to Cell-Based Therapies

Prognosis of patients with cystic fibrosis (CF) varies extensively despite recent advances in targeted therapies that improve CF transmembrane conductance regulator (CFTR) function. Despite being a multi-organ disease, extensive lung tissue destruction remains the major cause of morbidity and mortality. Progress towards a curative treatment strategy that implements a CFTR gene addition-technology to the patients’ lungs has been slow and not yet developed beyond clinical trials. Improved delivery vectors are needed to overcome the body’s defense system and ensure an efficient and consistent clinical response before gene therapy is suitable for clinical care. Cell-based therapy–which relies on functional modification of allogenic or autologous cells ex vivo, prior to transplantation into the patient–is now a therapeutic reality for various diseases. For CF, pioneering research has demonstrated proof-of-principle for allogenic transplantation of cultured human airway stem cells into mouse airways. However, applying a cell-based therapy to the human airways has distinct challenges. We review CF gene therapies using viral and non-viral delivery strategies and discuss current advances towards autologous cell-based therapies. Progress towards identification, correction, and expansion of a suitable regenerative cell, as well as refinement of pre-cell transplant lung conditioning protocols is discussed.

Assessment of respiratory health surveillance for laboratory animal workers

BACKGROUND

Occupational asthma is the most common work-related respiratory disease in the UK. Individuals whose work potentially puts them at risk include those exposed to laboratory animals. Workplace health surveillance programmes aim to minimize these health risks but are recognized to be challenging to implement effectively.

AIMS

To evaluate the efficacy of the respiratory health surveillance programme provided by a National Health Service occupational health service (OHS) to individuals potentially exposed to respiratory sensitizers at work with laboratory animals.

METHODS

Case notes from the OHS respiratory health surveillance programme over a 2 year period were examined. Symptom detection by the OHS surveillance questionnaire was compared to a cross-sectional survey using items from the validated International Union Against Tuberculosis and Lung Disease (IUATLD) questionnaire. The surveillance spirometry records were audited against good standards of practice.

RESULTS

The response rate for the anonymized survey using IUATLD questions was 60% and detected similar numbers of potential work-related symptoms to the OHS surveillance questionnaire. Over 80% of spirometry records met accepted standards for technique, effort and recording. In this study of 85 individuals over 2 years, three cases of occupational asthma were identified.

CONCLUSIONS

The current surveillance appears to be effective in identifying potential cases of occupational asthma. Modification of the questionnaire content and layout might improve response rates. This study suggests that spirometry does not detect new cases other than those already identified by questionnaire.

Base rate data on the abnormality of subtest scatter for WAIS-R short-forms

Tables are presented which permit clinicians to determine the abnormality of a WAIS-R subtest profile when one of nine different short-forms has been administered. The tables record the discrepancy, between each subtest and the individual's mean subtest score, which must be exceeded to occur in less than 15 per cent or 5 per cent of the healthy population. Two tables are provided; the first uses a statistical formula developed by Silverstein (1984a) to estimate the discrepancies from the US standardization sample. The second presents empirically derived discrepancies based on a sample of 326 healthy individuals which was representative of the adult UK population in terms of age, sex and social class distributions. The UK sample was also used to generate base rate data on the cumulative number of abnormal subtest deviations exhibited by healthy individuals.

WAIS-R subtest scatter: base-rate data from a healthy UK sample

Base-rate data on subtest scatter for the WAIS-R was obtained from a sample of 200 healthy subjects recruited to match the adult UK population in terms of age, sex and social class distribution. Tables are presented which permit an assessment of the abnormality (i.e. rarity) of an individual's pattern of WAIS-R performance in terms of subtest range and subtest deviations from an individual's subtest mean. Guidance on the appropriate use of the tables is offered and the data are compared with data from the US WAIS-R standardization sample where appropriate. The distinction between reliable and abnormal differences is highlighted.

The WAIS-R(UK): basic psychometric properties in an adult UK sample

The WAIS-R is the most widely used measure of intellectual ability in the UK, despite never having been standardized in this country. The present study examined the psychometric properties of the WAIS-R in a sample of 200 subjects, which was representative of the adult UK population in terms of the distributions of age, sex and social class. The properties of the three IQ scales, i.e. the FSIQ, the VIQ and the PIQ, were found to be very similar to those reported for the US standardization sample: the scores were normally distributed, with means close to the desired value of 100; moreover, the reliabilities of the IQ scales were extremely high and closely matched the US reliabilities. There were also indications, however, that the scales have restricted standard deviations when used in the UK. The reliabilities of the 11 original subtests ranged from moderate to high and the majority were similar to the US reliabilities. However, in addition to evidence of restricted SDs, significant differences (sometimes as much as two-thirds of an SD) were found among the subtest means. These in-built subtest discrepancies could lead to erroneous conclusions about an individual's performance. A conversion table for UK test users is provided to overcome this problem.

The Mahalanobis Distance index of WAIS-R subtest scatter: psychometric properties in a healthy UK sample

Burgess (1991) has proposed a new index of subtest scatter for the WAIS-R which uses a test statistic, the Mahalanobis Distance (MD). When used with the WAIS-R, MD scores should be distributed as chi square with 11 degrees of freedom. The suitability of the MD index for UK clinical practice was assessed by examining its psychometric properties in a sample of 200 healthy subjects. The sample, which was representative of the adult UK population in terms of age, sex, and social class distribution, was administered a full-length WAIS-R. A goodness-of-fit test revealed that the sample distribution of MD scores did not deviate significantly from the chi square distribution. Furthermore, the percentage of subjects exceeding the critical value for significance at the .05 level (6.5 per cent) corresponded closely to the expected percentage (i.e. 5 per cent). It is concluded that the MD index is suitable for use in UK clinical practice. Demographic characteristics were only weakly related to MD scores which simplifies clinical interpretation.

Short-forms of the UK WAIS-R: regression equations and their predictive validity in a general population sample

A sample of 200 healthy subjects, representative of the adult UK population in terms of age, sex and social class distribution, were administered a full-length WAIS-R (UK). Regression equations were built to predict full-length IQ from a series of short-forms. The short-forms ranged from a two-subtest version proposed by Silverstein (1982) to a seven-subtest version proposed by Warrington, James & Maciejewski (1986). Regression equations, their standard errors of estimate and confidence intervals are presented as well as IQ conversion tables. The short-forms are evaluated in terms of their validity in predicting full-length IQ and in terms of their clinical utility. The advantages of regression-based estimates of full-length IQ over those derived from conventional prorating are discussed.

The Short NART: cross-validation, relationship to IQ and some practical considerations

Beardsall & Brayne (1990) have presented a method whereby the full-length National Adult Reading Test (NART) scores of subjects who are of below average reading ability can be predicted from performance on the first half of the test (termed the Short NART). The accuracy with which the Short NART predicted full-length NART scores was examined in a large cross-validation sample (N = 674). A subgroup of this sample (N = 142) was administered the WAIS. The results indicated that the Short NART was only moderately successful in predicting full-length NART scores. However, comparison of the accuracy with which the full-length NART and Short NART predicted WAIS IQs, revealed that the superiority of the former was very minimal. It is concluded that, despite some reservations regarding the Short NART's practical utility, it can be used with reasonable confidence in clinical practice to estimate premorbid IQ.

Assessing the validity of NART-estimated premorbid IQs in the individual case

The National Adult Reading Test (NART: Nelson, 1982) has become the standard means of estimating premorbid intelligence. The danger in using the NART for this purpose is that it yields an invalid estimate if a client's performance on the test has suffered impairment. In the present study a sample of 659 healthy subjects was used to build a regression equation for the prediction of NART scores from demographic variables (i.e. years of education, social class, age and sex). The multiple correlation between these demographic variables and the NART was .70 (p less than .0001). Comparing a client's obtained and predicted NART score will permit the clinician to assess objectively whether NART performance is impaired, and thus whether or not the NART will provide a valid estimate of premorbid intelligence.

A comparison of the WAIS and WAIS-R in matched UK samples

A matched samples design was employed to compare WAIS and WAIS-R IQ in UK subjects. The WAIS yielded significantly higher mean Full Scale, Verbal and Performance IQs. The mean differences were 7.5, 6.4 and 7.9 IQ points respectively. The WAIS and WAIS-R samples were broadly representative of the UK adult population in terms of age, sex and social class distribution, and therefore provide tentative estimates of population mean scores for both Wechsler scales. Mean WAIS IQ was 108.6, suggesting that the WAIS yields inflated IQ scores in the contemporary UK population. Encouragingly, mean WAIS-R Full Scale IQ was 101.1, suggesting that it neither markedly underestimates nor overestimates IQ in the UK.