The Palestinian primary ciliary dyskinesia population: first results of the diagnostic and genetic spectrum.

Background: Diagnostic testing for primary ciliary dyskinesia (PCD) started in 2013 in Palestine. We aimed to describe the diagnostic, genetic and clinical spectrum of the Palestinian PCD population. Methods: Individuals with symptoms suggestive of PCD were opportunistically considered for diagnostic testing: nasal nitric oxide (nNO) measurement, transmission electron microscopy (TEM) and/or PCD genetic panel or whole-exome testing. Clinical characteristics of those with a positive diagnosis were collected close to testing including forced expiratory volume in 1 s (FEV1) Global Lung Index z-scores and body mass index z-scores. Results: 68 individuals had a definite positive PCD diagnosis, 31 confirmed by genetic and TEM results, 23 by TEM results alone, and 14 by genetic variants alone. 45 individuals from 40 families had 17 clinically actionable variants and four had variants of unknown significance in 14 PCD genes. CCDC39, DNAH11 and DNAAF11 were the most commonly mutated genes. 100% of variants were homozygous. Patients had a median age of 10.0 years at diagnosis, were highly consanguineous (93%) and 100% were of Arabic descent. Clinical features included persistent wet cough (99%), neonatal respiratory distress (84%) and situs inversus (43%). Lung function at diagnosis was already impaired (FEV1 z-score median -1.90 (-5.0-1.32)) and growth was mostly within the normal range (z-score mean -0.36 (-3.03-2.57). 19% individuals had finger clubbing. Conclusions: Despite limited local resources in Palestine, detailed geno- and phenotyping forms the basis of one of the largest national PCD populations globally. There was notable familial homozygosity within the context of significant population heterogeneity.

Biallelic variants in CEP164 cause a motile ciliopathy-like syndrome.

Ciliopathies may be classed as primary or motile depending on the underlying ciliary defect and are usually considered distinct clinical entities. Primary ciliopathies are associated with multisystem syndromes typically affecting the brain, kidney, and eye, as well as other organ systems such as the liver, skeleton, auditory system, and metabolism. Motile ciliopathies are a heterogenous group of disorders with defects in specialised motile ciliated tissues found within the lung, brain, and reproductive system, and are associated with primary ciliary dyskinesia, bronchiectasis, infertility and rarely hydrocephalus. Primary and motile cilia share defined core ultra-structures with an overlapping proteome, and human disease phenotypes can reflect both primary and motile ciliopathies. CEP164 encodes a centrosomal distal appendage protein vital for primary ciliogenesis. Human CEP164 mutations are typically described in patients with nephronophthisis-related primary ciliopathies but have also been implicated in motile ciliary dysfunction. Here we describe a patient with an atypical motile ciliopathy phenotype and biallelic CEP164 variants. This work provides further evidence that CEP164 mutations can contribute to both primary and motile ciliopathy syndromes, supporting their functional and clinical overlap, and informs the investigation and management of CEP164 ciliopathy patients.

Temporal Whole-Transcriptomic Analysis of Characterized In Vitro and Ex Vivo Primary Nasal Epithelia.

Air-liquid interface (ALI) cell culture of primary airway progenitors enables the differentiation and recapitulation of a pseudostratified epithelium in vitro, providing a highly useful tool for researching respiratory health and disease. Previous studies into gene expression in ALI-cultures compared to ex vivo nasal brushings have been limited in the number of time-points and/or the number of genes studied. In this study physiological and global transcriptomic changes were assessed in an extended in vitro 63-day human healthy nasal epithelium ALI-culture period and compared to ex vivo nasal brushing samples. Ex vivo nasal brushing samples formed distinct transcriptome clusters to in vitro ALI-cultured nasal epithelia, with from day 14 onwards ALI samples best matching the ex vivo samples. Immune response regulation genes were not expressed in the in vitro ALI-culture compared to the ex vivo nasal brushing samples, likely because the in vitro cultures lack an airway microbiome, lack airborne particles stimulation, or did not host an immune cell component. This highlights the need for more advanced co-cultures with immune cell representation to better reflect the physiological state. During the first week of ALI-culture genes related to metabolism and proliferation were increased. By the end of week 1 epithelial cell barrier function plateaued and multiciliated cell differentiation started, although widespread ciliation was not complete until day 28. These results highlight that time-points at which ALI-cultures are harvested for research studies needs to be carefully considered to suit the purpose of investigation (transcriptomic and/or functional analysis).

Lower airway clinical outcome measures for use in primary ciliary dyskinesia research: a scoping review.

OBJECTIVES: Disease-specific, well-defined and validated clinical outcome measures are essential in designing research studies. Poorly defined outcome measures hamper pooling of data and comparisons between studies. We aimed to identify and describe pulmonary outcome measures that could be used for follow-up of patients with primary ciliary dyskinesia (PCD). METHODS: We conducted a scoping review by systematically searching MEDLINE, Embase and the Cochrane Database of Systematic Reviews online databases for studies published from 1996 to 2020 that included ≥10 PCD adult and/or paediatric patients. RESULTS: We included 102 studies (7289 patients). 83 studies reported on spirometry, 11 on body plethysmography, 15 on multiple-breath washout, 36 on high-resolution computed tomography (HRCT), 57 on microbiology and 17 on health-related quality of life. Measurement and reporting of outcomes varied considerably between studies (e.g. different scoring systems for chest HRCT scans). Additionally, definitions of outcome measures varied (e.g. definition of chronic colonisation by respiratory pathogen), impeding direct comparisons of results. CONCLUSIONS: This review highlights the need for standardisation of measurements and reporting of outcome measures to enable comparisons between studies. Defining a core set of clinical outcome measures is necessary to ensure reproducibility of results and for use in future trials and prospective cohorts.

Feasibility of an asynchronous general practitioner-to-general physician eConsultant outpatient substitution program: A Queensland pilot study.

BACKGROUND AND OBJECTIVES: The use of an 'eConsultant' to support the family physician is an established outpatient substitution model in North America. This pilot study investigates the feasibility of the eConsultant model for complex chronic disease management within the Australian setting. METHOD: This pilot study was implemented in one urban and four rural/remote general practices in one state. The general practitioner (GP) sent a request for advice (RFA), a clinical summary with a specific clinical question/s, via secure messaging to a physician working remotely. Responses were required for GP/patient follow-up within 72 hours. RESULTS: The mean (standard deviation [SD]) time for general physician reply was 2.1 (1.2) days, and mean (SD) time from initial to subsequent GP/patient review was 14.8 (16.7) days. Only 13.3% of eConsultations required a subsequent face-to-face outpatient department appointment. DISCUSSION: The eConsultant model is feasible in Australia, with potential for improving access and reducing time to non-GP specialist input.

Whole genome sequencing in the diagnosis of primary ciliary dyskinesia.

BACKGROUND: It is estimated that 1-13% of cases of bronchiectasis in adults globally are attributable to primary ciliary dyskinesia (PCD) but many adult patients with bronchiectasis have not been investigated for PCD. PCD is a disorder caused by mutations in genes required for motile cilium structure or function, resulting in impaired mucociliary clearance. Symptoms appear in infancy but diagnosis is often late or missed, often due to the lack of a "gold standard" diagnostic tool and non-specific symptoms. Mutations in > 50 genes account for around 70% of cases, with additional genes, and non-coding, synonymous, missense changes or structural variants (SVs) in known genes presumed to account for the missing heritability. METHODS: UK patients with no identified genetic confirmation for the cause of their PCD or bronchiectasis were eligible for whole genome sequencing (WGS) in the Genomics England Ltd 100,000 Genomes Project. 21 PCD probands and 52 non-cystic fibrosis (CF) bronchiectasis probands were recruited in Wessex Genome Medicine Centre (GMC). We carried out analysis of single nucleotide variants (SNVs) and SVs in all families recruited in Wessex GMC. RESULTS: 16/21 probands in the PCD cohort received confirmed (n = 9), probable (n = 4) or possible (n = 3) diagnosis from WGS, although 13/16 of these could have been picked up by current standard of care gene panel testing. In the other cases, SVs were identified which were missed by panel testing. We identified variants in novel PCD candidate genes (IFT140 and PLK4) in 2 probands in the PCD cohort. 3/52 probands in the non-CF bronchiectasis cohort received a confirmed (n = 2) or possible (n = 1) diagnosis of PCD. We identified variants in novel PCD candidate genes (CFAP53 and CEP164) in 2 further probands in the non-CF bronchiectasis cohort. CONCLUSIONS: Genetic testing is an important component of diagnosing PCD, especially in cases of atypical disease history. WGS is effective in cases where prior gene panel testing has found no variants or only heterozygous variants. In these cases it may detect SVs and is a powerful tool for novel gene discovery.

Properties of Non-Aminoglycoside Compounds Used to Stimulate Translational Readthrough of PTC Mutations in Primary Ciliary Dyskinesia.

Primary ciliary dyskinesia (PCD) is a rare disease with autosomal recessive inheritance, caused mostly by bi-allelic gene mutations that impair motile cilia structure and function. Currently, there are no causal treatments for PCD. In many disease models, translational readthrough of premature termination codons (PTC-readthrough) induced by aminoglycosides has been proposed as an effective way of restoring functional protein expression and reducing disease symptoms. However, variable outcomes of pre-clinical trials and toxicity associated with long-term use of aminoglycosides prompt the search for other compounds that might overcome these problems. Because a high proportion of PCD-causing variants are nonsense mutations, readthrough therapies are an attractive option. We tested a group of chemical compounds with known PTC-readthrough potential (ataluren, azithromycin, tylosin, amlexanox, and the experimental compound TC007), collectively referred to as non-aminoglycosides (NAGs). We investigated their PTC-readthrough efficiency in six PTC mutations found in Polish PCD patients, in the context of cell and cilia health, and in comparison to the previously tested aminoglycosides. The NAGs did not compromise the viability of the primary nasal respiratory epithelial cells, and the ciliary beat frequency was retained, similar to what was observed for gentamicin. In HEK293 cells transfected with six PTC-containing inserts, the tested compounds stimulated PTC-readthrough but with lower efficiency than aminoglycosides. The study allowed us to select compounds with minimal negative impact on cell viability and function but still the potential to induce PTC-readthrough.

Community-based integrated care versus hospital outpatient care for managing patients with complex type 2 diabetes: costing analysis.

Objective This study compared the cost of an integrated primary-secondary care general practitioner (GP)-based Beacon model with usual care at hospital outpatient departments (OPDs) for patients with complex type 2 diabetes. Methods A costing analysis was completed alongside a non-inferiority randomised control trial. Costs were calculated using information from accounting data and interviews with clinic managers. Two OPDs and three GP-based Beacon practices participated. In the Beacon practices, GPs with a special interest in advanced diabetes care worked with an endocrinologist and diabetes nurse educator to care for referred patients. The main outcome was incremental cost saving per patient course of treatment from a health system perspective. Uncertainty was characterised with probabilistic sensitivity analysis using Monte Carlo simulation. Results The Beacon model is cost saving: the incremental cost saving per patient was A$365 (95% confidence interval -A$901, A$55) and was cost saving in 93.7% of simulations. The key contributors to the variance in the cost saving per patient course of treatment were the mean number of patients seen per site and the number of additional presentations per course of treatment associated with the Beacon model. Conclusions Beacon clinics were less costly per patient course of treatment than usual care in hospital OPDs for equivalent clinical outcomes. Local contractual arrangements and potential variation in the operational cost structure are of significant consideration in determining the cost-efficiency of Beacon models. What is known about this topic? Despite the growing importance of achieving care quality within constrained budgets, there are few costing studies comparing clinically-equivalent hospital and community-based care models. What does this paper add? Costing analyses comparing hospital-based to GP-based health services require considerable effort and are complex. We show that GP-based Beacon clinics for patients with complex chronic disease can be less costly per patient course of treatment than usual care offered in hospital OPDs. What are the implications for practitioners? In addition to improving access and convenience for patients, transferring care from hospital to the community can reduce health system costs.

A novel ACE2 isoform is expressed in human respiratory epithelia and is upregulated in response to interferons and RNA respiratory virus infection.

Angiotensin-converting enzyme 2 (ACE2) is the main entry point in airway epithelial cells for SARS-CoV-2. ACE2 binding to the SARS-CoV-2 protein spike triggers viral fusion with the cell plasma membrane, resulting in viral RNA genome delivery into the host. Despite ACE2's critical role in SARS-CoV-2 infection, full understanding of ACE2 expression, including in response to viral infection, remains unclear. ACE2 was thought to encode five transcripts and one protein of 805 amino acids. In the present study, we identify a novel short isoform of ACE2 expressed in the airway epithelium, the main site of SARS-CoV-2 infection. Short ACE2 is substantially upregulated in response to interferon stimulation and rhinovirus infection, but not SARS-CoV-2 infection. This short isoform lacks SARS-CoV-2 spike high-affinity binding sites and, altogether, our data are consistent with a model where short ACE2 is unlikely to directly contribute to host susceptibility to SARS-CoV-2 infection.

Improving quality in general practice using the Primary Care Practice Improvement Tool (PC-PIT) with Primary Health Network support.

Optimal primary care sector performance is vital for ensuring the delivery of quality health services and effective clinical management of populations. The Primary Care Practice Improvement Tool (PC-PIT) incorporates subjective staff input and objective indicators to measure 13 elements of organisational performance. This study aimed to measure change in organisational performance for general practices using the PC-PIT with Primary Health Network (PHN) support. A pre-post design was used for changes in PC-PIT subjective and objective scores. Practices used results with PHN support to complete two Plan Do Study Act initiatives and were reassessed 9-months later. PC-PIT scales were dichotomised into lower and higher scores, with odds ratios used to determine effect size. Staff survey response rates were 55.4% at baseline and 50.1% at follow up. There were modest increases in the likelihood of staff rating several elements higher at follow up. When implemented with PHN support staff, the PC-PIT has the potential for effective, focussed and sustained quality improvement, with capacity to support Health Care Home model transition and implementation.

A Revised Protocol for Culture of Airway Epithelial Cells as a Diagnostic Tool for Primary Ciliary Dyskinesia.

Air-liquid interface (ALI) culture of nasal epithelial cells is a valuable tool in the diagnosis and research of primary ciliary dyskinesia (PCD). Ex vivo samples often display secondary dyskinesia from cell damage during sampling, infection or inflammation confounding PCD diagnostic results. ALI culture enables regeneration of healthy cilia facilitating differentiation of primary from secondary ciliary dyskinesia. We describe a revised ALI culture method adopted from April 2018 across three collaborating PCD diagnostic sites, including current University Hospital Southampton COVID-19 risk mitigation measures, and present results. Two hundred and forty nasal epithelial cell samples were seeded for ALI culture and 199 (82.9%) were ciliated. Fifty-four of 83 (63.9%) ex vivo samples which were originally equivocal or insufficient provided diagnostic information following in vitro culture. Surplus basal epithelial cells from 181 nasal brushing samples were frozen in liquid nitrogen; 39 samples were ALI-cultured after cryostorage and all ciliated. The ciliary beat patterns of ex vivo samples (by high-speed video microscopy) were recapitulated, scanning electron microscopy demonstrated excellent ciliation, and cilia could be immuno-fluorescently labelled (anti-alpha-tubulin and anti-RSPH4a) in representative cases that were ALI-cultured after cryostorage. In summary, our ALI culture protocol provides high ciliation rates across three centres, minimising patient recall for repeat brushing biopsies and improving diagnostic certainty. Cryostorage of surplus diagnostic samples was successful, facilitating PCD research.

The Primary Care Practice Improvement Tool (PC-PIT) process for organisational improvement in primary care: application by Australian Primary Health Networks.

The Primary Care Practice Improvement Tool (PC-PIT) is an organisational performance improvement tool recently implemented by two Primary Health Networks (PHNs). This study explored barriers and facilitators to implementing the PC-PIT process at scale, from the initial introduction of the tool to completion of Plan-Do-Study-Act cycles with general practices. Using a qualitative design, in-depth, semi-structured interviews were conducted with 10 PHN staff to seek feedback on the delivery of the PC-PIT to general practices. Interview results were analysed using a grounded theory approach. The identification of barriers such as difficulty engaging practices and lack of report sharing with the PHNs will help streamline future implementation. The PC-PIT was highly compatible with existing quality improvement programs and offers enhanced opportunity to support capacity building and implementation of the Health Care Home model.

Accuracy of High-Speed Video Analysis to Diagnose Primary Ciliary Dyskinesia.

BACKGROUND: Diagnosis of primary ciliary dyskinesia (PCD) relies on a combination of tests. High-speed video microscopy analysis (HSVA) is widely used to contribute to the diagnosis. It can be analyzed on the day of diagnostic consultation, but the qualitative analyses are subjective. Diagnostic accuracy and reliability of assessing ciliary function have not been robustly evaluated. We aimed to establish the accuracy of HSVA to diagnose PCD compared with a combination of tests, and to assess the interobserver reliability of HSVA analysis. METHODS: We randomly selected and anonymized archived videos from 120 patients seen at three UK PCD centers. Three experienced scientists independently reviewed six videos per patient, using a standardized proforma, blinded to diagnostic and clinical data. We compared study outcomes with two references: (1) a combination of diagnostic tests in accordance with the European Respiratory Society PCD diagnostic guidelines and (2) original clinical outcome determined by all available diagnostic tests. RESULTS: HSVA had excellent sensitivity and specificity to diagnose PCD: (1) 100% and 96%, respectively, compared with ERS guidelines, and (2) 96% and 91% compared with diagnostic outcomes. There was high interobserver agreement for "PCD-positive" outcomes (κ = 0.7). CONCLUSIONS: Specialist scientists accurately diagnosed PCD using HSVA, with high interobserver agreement. HSVA can be reliably used to counsel patients and commence treatment on the day of testing while awaiting confirmatory investigations.

Risk factors for situs defects and congenital heart disease in primary ciliary dyskinesia.

Primary ciliary dyskinesia (PCD) is associated with abnormal organ positioning (situs) and congenital heart disease (CHD). This study investigated genotype-phenotype associations in PCD to facilitate risk predictions for cardiac and laterality defects. This retrospective cohort study of 389 UK patients with PCD found 51% had abnormal situs and 25% had CHD and/or laterality defects other than situs inversus totalis. Patients with biallelic mutations in a subset of nine PCD genes had normal situs. Patients with consanguineous parents had higher odds of situs abnormalities than patients with non-consanguineous parents. Patients with abnormal situs had higher odds of CHD and/or laterality defects.

Clinical outcomes of an integrated primary-secondary model of care for individuals with complex type 2 diabetes: a non-inferiority randomised controlled trial.

AIMS/HYPOTHESIS: The aim of the study was to determine if a Beacon model of integrated care utilising general practitioners (GPs) with special interests could achieve similar clinical outcomes to a hospital-based specialist diabetes outpatient clinic. METHODS: This pragmatic non-inferiority multisite randomised controlled trial assigned individuals with complex type 2 diabetes to care delivered by a Beacon clinic or to usual care delivered by a hospital outpatient department, in a 3:1 ratio. Owing to the nature of the study, researchers were only blinded during the allocation process. Eligible participants were aged 18 or over, had been referred by their usual GP to the hospital central referral hub with type 2 diabetes and had been triaged to be seen within 30 or 90 days. The intervention consisted of diabetes management in primary care by GPs with a special interest who had been upskilled in complex diabetes under the supervision of an endocrinologist. The primary outcome was HbA1c at 12 months post-recruitment. The non-inferiority margin was 4.4 mmol/mol (0.4%). Both per-protocol and intention-to-treat analyses are reported. RESULTS: Between 27 November 2012 and 14 July 2015, 352 individuals were recruited and 305 comprised the intention-to-treat sample (71 in usual care group and 234 in the Beacon model group). The Beacon model was non-inferior to usual care for both the per-protocol (difference -0.38 mmol/mol [95% CI -4.72, 3.96]; -0.03% [95% CI -0.43, 0.36]) and the intention-to-treat (difference -1.28 mmol/mol [95% CI -5.96, 3.40]; -0.12% [95% CI -0.55, 0.31]) analyses. Non-inferiority was sustained in a sensitivity analysis at 12 months. There were no statistically or clinically significant differences in the secondary outcomes of BP, lipids or quality of life as measured by the 12 item short-form health survey (SF-12v2) and the diabetes-related quality of life (DQoL-Brief) survey. Safety indicators did not differ between groups. Participant satisfaction on the eight-item client satisfaction questionnaire (CSQ-8) was good in both groups, but scores were significantly higher in the Beacon model group than the usual care group (mean [SD] 28.4 [4.9] vs 25.6 [4.9], respectively, p < 0.001). CONCLUSIONS/INTERPRETATION: In individuals with type 2 diabetes, a model of integrated care delivered in the community by GPs with a special interest can safely achieve clinical outcomes that are not inferior to those achieved with gold-standard hospital-based specialist outpatient clinics. Individuals receiving care in the community had greater satisfaction. Further studies will determine the cost of delivering this model of care. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry ACTRN12612000380897 FUNDING: The study was funded by the Australian National Health and Medical Research Council (GNT1001157).