Topological data analysis reveals genotype-phenotype relationships in primary ciliary dyskinesia

Background: Primary ciliary dyskinesia (PCD) is a heterogeneous inherited disorder caused by mutations in approximately 50 cilia-related genes. PCD genotype-phenotype relationships have mostly arisen from small case series because existing statistical approaches to investigate relationships have been unsuitable for rare diseases. / Methods: We applied a topological data analysis (TDA) approach to investigate genotype-phenotype relationships in PCD. Data from separate training and validation cohorts included 396 genetically defined individuals carrying pathogenic variants in PCD genes. To develop the TDA models, twelve clinical and diagnostic variables were included. TDA-driven hypotheses were subsequently tested using traditional statistics. / Results: Disease severity at diagnosis measured by FEV1 z-score was (i) significantly worse in individuals with CCDC39 mutations compared to other gene mutations and (ii) better in those with DNAH11 mutations; the latter also reported less neonatal respiratory distress. Patients without neonatal respiratory distress had better preserved FEV1 at diagnosis. Individuals with DNAH5 mutations were phenotypically diverse. Cilia ultrastructure and beat pattern defects correlated closely to specific causative gene groups, confirming these tests can be used to support a genetic diagnosis. / Conclusions: This large scale multi-national study presents PCD as a syndrome with overlapping symptoms and variation in phenotype, according to genotype. TDA modelling confirmed genotype-phenotype relationships reported by smaller studies (e.g. FEV1 worse with CCDC39 mutations), and identified new relationships, including FEV1 preservation with DNAH11 mutations and diversity of severity with DNAH5 mutations

Lung function from school age to adulthood in primary ciliary dyskinesia

Primary ciliary dyskinesia (PCD) presents with symptoms early in life and the disease course may be progressive, but longitudinal data on lung function are scarce. This multinational cohort study describes lung function trajectories in children, adolescents and young adults with PCD. We analysed data from 486 patients with repeated lung function measurements obtained between the age of 6 and 24 years from the International PCD Cohort and calculated z-scores for forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC ratio using the Global Lung Function Initiative 2012 references. We described baseline lung function and change of lung function over time and described their associations with possible determinants in mixed-effects linear regression models. Overall, FEV1, FVC and FEV1/FVC z-scores declined over time (average crude annual FEV1 decline was -0.07 z-scores), but not at the same rate for all patients. FEV1 z-scores improved over time in 21% of patients, remained stable in 40% and declined in 39%. Low body mass index was associated with poor baseline lung function and with further decline. Results differed by country and ultrastructural defect, but we found no evidence of differences by sex, calendar year of diagnosis, age at diagnosis, diagnostic certainty or laterality defect. Our study shows that on average lung function in PCD declines throughout the entire period of lung growth, from childhood to young adult age, even among patients treated in specialised centres. It is essential to develop strategies to reverse this tendency and improve prognosi

SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance

Renal medullary carcinoma (RMC) is an aggressive tumour driven by bi-allelic loss of SMARCB1 and tightly associated with sickle cell trait. However, the cell-of-origin and oncogenic mechanism remain poorly understood. Using single-cell sequencing of human RMC, we defined transformation of thick ascending limb (TAL) cells into an epithelial-mesenchymal gradient of RMC cells associated with loss of renal epithelial transcription factors TFCP2L1, HOXB9 and MITF and gain of MYC and NFE2L2-associated oncogenic and ferroptosis resistance programs. We describe the molecular basis for this transcriptional switch that is reversed by SMARCB1 re-expression repressing the oncogenic and ferroptosis resistance programs leading to ferroptotic cell death. Ferroptosis resistance links TAL cell survival with the high extracellular medullar iron concentrations associated with sickle cell trait, an environment propitious to the mutagenic events associated with RMC development. This unique environment may explain why RMC is the only SMARCB1-deficient tumour arising from epithelial cells, differentiating RMC from rhabdoid tumours arising from neural crest cells

Standardised clinical data from patients with primary ciliary dyskinesia:FOLLOW-PCD

Clinical data on primary ciliary dyskinesia (PCD) are limited, heterogeneous and mostly derived from retrospective chart reviews, leading to missing data and unreliable symptoms and results of physical examinations. We need standardised prospective data collection to study phenotypes, severity and prognosis and improve standards of care.A large, international and multidisciplinary group of PCD experts developed FOLLOW-PCD, a standardised clinical PCD form and patient questionnaire. We identified existing forms for clinical data collection via the Better Experimental Approaches to Treat PCD (BEAT-PCD) COST Action network and a literature review. We selected and revised the content items with the working group and patient representatives. We then revised several drafts in an adapted Delphi process, refining the content and structure.FOLLOW-PCD has a modular structure, to allow flexible use based on local practice and research focus. It includes patient-completed versions for the modules on symptoms and lifestyle. The form allows a comprehensive standardised clinical assessment at baseline and for annual reviews and a short documentation for routine follow-up. It can either be completed using printable paper forms or using an online REDCap database.Data collected in FOLLOW-PCD version 1.0 is available in real-time for national and international monitoring and research. The form will be adapted in the future after extensive piloting in different settings and we encourage the translation of the patient questionnaires to multiple languages. FOLLOW-PCD will facilitate quality research based on prospective standardised data from routine care, which can be pooled between centres, to provide first-line and real-time evidence for clinical decision-making

Neural network-based emulation of interstellar medium models

The interpretation of observations of atomic and molecular tracers in the galactic and extragalactic interstellar medium (ISM) requires comparisons with state-of-the-art astrophysical models to infer some physical conditions. Usually, ISM models are too time-consuming for such inference procedures, as they call for numerous model evaluations. As a result, they are often replaced by an interpolation of a grid of precomputed models. We propose a new general method to derive faster, lighter, and more accurate approximations of the model from a grid of precomputed models. These emulators are defined with artificial neural networks (ANNs) designed and trained to address the specificities inherent in ISM models. Indeed, such models often predict many observables (e.g., line intensities) from just a few input physical parameters and can yield outliers due to numerical instabilities or physical bistabilities. We propose applying five strategies to address these characteristics: 1) an outlier removal procedure; 2) a clustering method that yields homogeneous subsets of lines that are simpler to predict with different ANNs; 3) a dimension reduction technique that enables to adequately size the network architecture; 4) the physical inputs are augmented with a polynomial transform to ease the learning of nonlinearities; and 5) a dense architecture to ease the learning of simple relations. We compare the proposed ANNs with standard classes of interpolation methods to emulate the Meudon PDR code, a representative ISM numerical model. Combinations of the proposed strategies outperform all interpolation methods by a factor of 2 on the average error, reaching 4.5% on the Meudon PDR code. These networks are also 1000 times faster than accurate interpolation methods and require ten to forty times less memory. This work will enable efficient inferences on wide-field multiline observations of the ISM

HCN emission from translucent gas and UV-illuminated cloud edges revealed by wide-field IRAM 30m maps of Orion B GMC: Revisiting its role as tracer of the dense gas reservoir for star formation

We present 5 deg^2 (~250 pc^2) HCN, HNC, HCO+, and CO J=1-0 maps of the Orion B GMC, complemented with existing wide-field [CI] 492 GHz maps, as well as new pointed observations of rotationally excited HCN, HNC, H13CN, and HN13C lines. We detect anomalous HCN J=1-0 hyperfine structure line emission almost everywhere in the cloud. About 70% of the total HCN J=1-0 luminosity arises from gas at A_V < 8 mag. The HCN/CO J=1-0 line intensity ratio shows a bimodal behavior with an inflection point at A_V < 3 mag typical of translucent gas and UV-illuminated cloud edges. We find that most of the HCN J=1-0 emission arises from extended gas with n(H2) < 10^4 cm^-3, even lower density gas if the ionization fraction is > 10^-5 and electron excitation dominates. This result explains the low-A_V branch of the HCN/CO J=1-0 intensity ratio distribution. Indeed, the highest HCN/CO ratios (~0.1) at A_V < 3 mag correspond to regions of high [CI] 492 GHz/CO J=1-0 intensity ratios (>1) characteristic of low-density PDRs. Enhanced FUV radiation favors the formation and excitation of HCN on large scales, not only in dense star-forming clumps. The low surface brightness HCN and HCO+ J=1-0 emission scale with I_FIR (a proxy of the stellar FUV radiation field) in a similar way. Together with CO J=1-0, these lines respond to increasing I_FIR up to G0~20. On the other hand, the bright HCN J=1-0 emission from dense gas in star-forming clumps weakly responds to I_FIR once the FUV radiation field becomes too intense (G0>1500). The different power law scalings (produced by different chemistries, densities, and line excitation regimes) in a single but spatially resolved GMC resemble the variety of Kennicutt-Schmidt law indexes found in galaxy averages. As a corollary for extragalactic studies, we conclude that high HCN/CO J=1-0 line intensity ratios do not always imply the presence of dense gas.Comment: accepted for publication in A&A. 24 pages, 18 figures, plus Appendix. Abridged Abstract. English language not edite

Infection control, genetic assessment of drug resistance and drug susceptibility testing in the current management of multidrug/extensively-resistant tuberculosis (M/XDR-TB) in Europe: A tuberculosis network European Trialsgroup (TBNET) study

Aim Europe has the highest documented caseload and greatest increase in multidrug and extensively drug-resistant tuberculosis (M/XDR-TB) of all World Health Organization (WHO) regions. This survey examines how recommendations for M/XDR-TB management are being implemented. Methods TBNET is a pan-European clinical research collaboration for tuberculosis. An email survey of TBNET members collected data in relation to infection control, access to molecular tests and basic microbiology with drug sensitivity testing. Results 68/105 responses gave valid information and were from countries within the WHO European Region. Inpatient beds matched demand, but single rooms with negative pressure were only available in low incidence countries; ultraviolet decontamination was used in 5 sites, all with &gt;10 patients with M/XDR-TB per year. Molecular tests for mutations associated with rifampicin resistance were widely available (88%), even in lower income and especially in high incidence countries. Molecular tests for other first line and second line drugs were less accessible (76 and 52% respectively). A third of physicians considered that drug susceptibility results were delayed by &gt; 2 months. Conclusion Infection control for inpatients with M/XDR-TB remains a problem in high incidence countries. Rifampicin resistance is readily detected, but tests to plan regimens tailored to the drug susceptibilities of the strain of Mycobacterium tuberculosis are significantly delayed, allowing for further drug resistance to develop

The disease-specific clinical trial network for primary ciliary dyskinesia: PCD-CTN

Primary ciliary dyskinesia (PCD) is a rare genetic disorder characterised by impaired mucociliary clearance leading to irreversible lung damage. In contrast to other rare lung diseases like cystic fibrosis (CF), there are only few clinical trials and limited evidence-based treatments. Management is mainly based on expert opinions and treatment is challenging due to a wide range of clinical manifestations and disease severity. To improve clinical and translational research and facilitate development of new treatments, the clinical trial network for PCD (PCD-CTN) was founded in 2020 under the framework of the European Reference Network (ERN)-LUNG PCD Core. Applications from European PCD sites interested in participating in the PCD-CTN were requested. Inclusion criteria consisted of patient numbers, membership of ERN-LUNG PCD Core, use of associated standards of care, experience in PCD and/or CF clinical research, resources to run clinical trials, good clinical practice (GCP) certifications and institutional support. So far, applications from 22 trial sites in 18 European countries have been approved, including >1400 adult and >1600 paediatric individuals with PCD. The PCD-CTN is headed by a coordinating centre and consists of a steering and executive committee, a data safety monitoring board and committees for protocol review, training and standardisation. A strong association with patient organisations and industrial companies are further cornerstones. All participating trial sites agreed on a code of conduct. As CTNs from other diseases have demonstrated successfully, this newly formed PCD-CTN operates to establish evidence-based treatments for this orphan disease and to bring new personalised treatment approaches to patients