Conserved patterns across ion channels correlate with variant pathogenicity and clinical phenotypes

Clinically identified genetic variants in ion channels can be benign or cause disease by increasing or decreasing the protein function. As a consequence, therapeutic decision-making is challenging without molecular testing of each variant. Our biophysical knowledge of ion-channel structures and function is just emerging, and it is currently not well understood which amino acid residues cause disease when mutated. We sought to systematically identify biological properties associated with variant pathogenicity across all major voltage and ligand-gated ion-channel families. We collected and curated 3049 pathogenic variants from hundreds of neurodevelopmental and other disorders and 12 546 population variants for 30 ion channel or channel subunits for which a high-quality protein structure was available. Using a wide range of bioinformatics approaches, we computed 163 structural features and tested them for pathogenic variant enrichment. We developed a novel 3D spatial distance scoring approach that enables comparisons of pathogenic and population variant distribution across protein structures. We discovered and independently replicated that several pore residue properties and proximity to the pore axis were most significantly enriched for pathogenic variants compared to population variants. Using our 3D scoring approach, we showed that the strongest pathogenic variant enrichment was observed for pore-lining residues and alpha-helix residues within 5Å distance from the pore axis centre and not involved in gating. Within the subset of residues located at the pore, the hydrophobicity of the pore was the feature most strongly associated with variant pathogenicity. We also found an association between the identified properties and both clinical phenotypes and functional in vitro assays for voltage-gated sodium channels (SCN1A, SCN2A, SCN8A) and N-methyl-D-aspartate receptor (GRIN1, GRIN2A, GRIN2B) encoding genes. In an independent expert-curated dataset of 1422 neurodevelopmental disorder pathogenic patient variants and 679 electrophysiological experiments, we show that pore axis distance is associated with seizure age of onset and cognitive performance as well as differential gain versus loss-of-channel function. In summary, we identified biological properties associated with ion-channel malfunction and show that these are correlated with in vitro functional readouts and clinical phenotypes in patients with neurodevelopmental disorders. Our results suggest that clinical decision support algorithms that predict variant pathogenicity and function are feasible in the future.

Comorbidities and predictors of health-related quality of life in Dravet syndrome: A 10-year, prospective follow-up study

OBJECTIVE

Dravet syndrome (DS) is a severe developmental and epileptic encephalopathy, leading to reduced health-related quality of life (HRQOL). Prospective outcome data on HRQOL are sparse, and this study investigated long-term predictors of HRQOL in DS.

METHODS

One hundred thirteen families of SCN1A-positive patients with DS, who were recruited as part of our 2010 study were contacted at 10-year follow-up, of which 68 (60%) responded. The mortality was 5.8%. Detailed clinical and demographic information was available for each patient. HRQOL was evaluated with two epilepsy-specific instruments, the Impact of Pediatric Epilepsy Scale (IPES) and the Epilepsy & Learning Disabilities Quality of Life Questionnaire (ELDQOL); a generic HRQOL instrument, the Pediatric Quality of Life Inventory (PedsQL); and a behavioral screening tool, the Strength and Difficulties Questionnaire (SDQ).

RESULTS

Twenty-eight patients were 10-15 years of age (0-5 years at baseline) and 40 were ≥16 years of age (≥6 years at baseline). Patients 0- to 5-years-old at baseline showed a significant decline in mean scores on the PedsQL total score (p = .004), physical score (p < .001), cognitive score (p = .011), social score (p = .003), and eating score (p = .030) at follow-up. On multivariate regression, lower baseline and follow-up HRQOL for the whole cohort were associated with worse epilepsy severity and a high SDQ total score (R²  = 33% and 18%, respectively). In the younger patient group, younger age at first seizure and increased severity of epilepsy were associated with a lower baseline HRQOL (R²  = 35%). In the older age group, worse epilepsy severity (F = 6.40, p = .016, R²  = 14%) and the use of sodium-channel blockers were independently associated with a lower HRQOL at 10-year follow-up (F = 4.13, p = .05, R²  = 8%).

SIGNIFICANCE

This 10-year, prospective follow-up study highlights the significant HRQOL-associated cognitive, social, and physical decline particularly affecting younger patients with DS. Sodium channel blocker use appears to negatively impact long-term HRQOL, highlighting the importance of early diagnosis and disease-specific management in DS.

The gain of function SCN1A disorder spectrum: novel epilepsy phenotypes and therapeutic implications

Brain voltage-gated sodium channel NaV1.1 (SCN1A) loss-of-function variants cause the severe epilepsy Dravet syndrome, as well as milder phenotypes associated with genetic epilepsy with febrile seizures plus. Gain of function SCN1A variants are associated with familial hemiplegic migraine type 3. Novel SCN1A-related phenotypes have been described including early infantile developmental and epileptic encephalopathy with movement disorder, and more recently neonatal presentations with arthrogryposis. Here we describe the clinical, genetic and functional evaluation of affected individuals. Thirty-five patients were ascertained via an international collaborative network using a structured clinical questionnaire and from the literature. We performed whole-cell voltage-clamp electrophysiological recordings comparing sodium channels containing wild-type versus variant NaV1.1 subunits. Findings were related to Dravet syndrome and familial hemiplegic migraine type 3 variants. We identified three distinct clinical presentations differing by age at onset and presence of arthrogryposis and/or movement disorder. The most severely affected infants (n = 13) presented with congenital arthrogryposis, neonatal onset epilepsy in the first 3 days of life, tonic seizures and apnoeas, accompanied by a significant movement disorder and profound intellectual disability. Twenty-one patients presented later, between 2 weeks and 3 months of age, with a severe early infantile developmental and epileptic encephalopathy and a movement disorder. One patient presented after 3 months with developmental and epileptic encephalopathy only. Associated SCN1A variants cluster in regions of channel inactivation associated with gain of function, different to Dravet syndrome variants (odds ratio = 17.8; confidence interval = 5.4-69.3; P = 1.3 × 10-7). Functional studies of both epilepsy and familial hemiplegic migraine type 3 variants reveal alterations of gating properties in keeping with neuronal hyperexcitability. While epilepsy variants result in a moderate increase in action current amplitude consistent with mild gain of function, familial hemiplegic migraine type 3 variants induce a larger effect on gating properties, in particular the increase of persistent current, resulting in a large increase of action current amplitude, consistent with stronger gain of function. Clinically, 13 out of 16 (81%) gain of function variants were associated with a reduction in seizures in response to sodium channel blocker treatment (carbamazepine, oxcarbazepine, phenytoin, lamotrigine or lacosamide) without evidence of symptom exacerbation. Our study expands the spectrum of gain of function SCN1A-related epilepsy phenotypes, defines key clinical features, provides novel insights into the underlying disease mechanisms between SCN1A-related epilepsy and familial hemiplegic migraine type 3, and identifies sodium channel blockers as potentially efficacious therapies. Gain of function disease should be considered in early onset epilepsies with a pathogenic SCN1A variant and non-Dravet syndrome phenotype.

Respiratory-associated deaths in people with intellectual disabilities: a systematic review and meta-analysis

OBJECTIVE

To review and synthesise evidence on rates of respiratory-associated deaths and associated risk factors in the intellectual disability population.

DESIGN

Systematic review and meta-analysis.

DATA SOURCES

Embase, CINAHL, ISI Web of Science (all databases including Medline) and PsychINFO were searched for studies published between 1st January 1985 and 27th April 2020 and examined study and outcome quality. Reference lists and Google Scholar were also hand searched.

RESULTS

We identified 2295 studies, 17 were included in the narrative synthesis and 10 studies (11 cohorts) in the meta-analysis. Data from 90 302 people with intellectual disabilities and 13 808 deaths from all causes in people with intellectual disabilities were extracted. Significantly higher rates of respiratory-associated deaths were found among people with intellectual disabilities (standardised mortality ratio(SMR): 10.86 (95% CI: 5.32 to 22.18, p<0.001) compared with those in the general population, lesser rates for adults with ID (SMR: 6.53 (95% CI: 4.29 to 9.96, p<0.001); and relatively high rates from pneumonia 26.65 (95% CI: 5.63 to 126.24, p<0.001). The overall statistical heterogeneity was I²=99.0%.

CONCLUSION

Premature deaths due to respiratory disorders are potentially avoidable with improved public health initiatives and equitable access to quality healthcare. Further research should focus on developing prognostic guidance and validated tools for clinical practice to mitigate risks of respiratory-associated deaths.

PROSPERO REGISTRATION NUMBER

CRD42020180479.

A catalogue of new incidence estimates of monogenic neurodevelopmental disorders caused by de novo variants

A large fraction of rare and severe neurodevelopmental disorders are caused by sporadic de novo variants. Epidemiological disease estimates are not available for the vast majority of these de novo monogenic neurodevelopmental disorders because of phenotypic heterogeneity and the absence of large-scale genomic screens. Yet, knowledge of disease incidence is important for clinicians and researchers to guide health policy planning. Here, we adjusted a statistical method based on genetic data to predict, for the first time, the incidences of 101 known de novo variant-associated neurodevelopmental disorders as well as 3106 putative monogenic disorders. Two corroboration analyses supported the validity of the calculated estimates. First, greater predicted gene-disorder incidences positively correlated with larger numbers of pathogenic variants collected from patient variant databases (Kendall’s τ = 0.093, P-value = 6.9 × 10⁻⁶). Second, for six of seven (86%) de novo variant associated monogenic disorders for which epidemiological estimates were available (SCN1A, SLC2A1, SALL1, TBX5, KCNQ2, and CDKL5), the predicted incidence estimates matched the reported estimates. We conclude that in the absence of epidemiological data, our catalogue of 3207 incidence estimates for disorders caused by de novo variants can guide patient advocacy groups, clinicians, researchers, and policymakers in strategic decision-making.

Potential of genomic selection for improvement of resistance to ostreid herpesvirus in Pacific oyster (Crassostrea gigas)

In genomic selection (GS), genome-wide SNP markers are used to generate genomic estimated breeding values for selection candidates. The application of GS in shellfish looks promising and has the potential to help in dealing with one of the main issues currently affecting Pacific oyster production worldwide, which is the 'summer mortality syndrome'. This causes periodic mass mortality in farms worldwide and has mainly been attributed to a specific variant of the ostreid herpesvirus (OsHV-1). In the current study, we evaluated the potential of genomic selection for host resistance to OsHV-1 in Pacific oysters, and compared it with pedigree-based approaches. An OsHV-1 disease challenge was performed using an immersion-based virus exposure treatment for oysters for 7 days. A total of 768 samples were genotyped using the medium-density SNP array for oysters. A GWAS was performed for the survival trait using a GBLUP approach in blupf90 software. Heritability ranged from 0.25 ± 0.05 to 0.37 ± 0.05 (mean ± SE) based on pedigree and genomic information respectively. Genomic prediction was more accurate than pedigree prediction, and SNP density reduction had little impact on prediction accuracy until marker densities dropped below approximately 500 SNPs. This demonstrates the potential for GS in Pacific oyster breeding programmes, and importantly, demonstrates that a low number of SNPs might suffice to obtain accurate genomic estimated breeding values, thus potentially making the implementation of GS more cost effective.

Falling admissions to hospital with febrile seizures in the UK

OBJECTIVES

There was a reduction in febrile seizure admissions in Scotland after 2008. Our hypothesis was that a similar trend would be seen in other countries.

METHODS

We obtained the number of febrile and non-febrile seizure admissions in England and Scotland 2000-2013 and the incidence of all seizure admissions 2000-2013 in European countries. We compared the incidence of admission for febrile seizure (Scotland and England) and all seizures (all countries) between 2000-2008 and 2009-2013.

RESULTS

The incidence of febrile seizure admissions per 1000 children in 2009-2013 was lower than 2000-2008 in Scotland (0.79 vs 1.08, p=0.001) and England (0.92 vs 1.20, p<0.001). The incidence of all seizure admissions (but not non-febrile seizures) was lower in 2009-2013 compared with 2000-2008 in Scotland (1.84 vs 2.20, p=0.010) and England (2.71 vs 2.91, p=0.001). Across 12 European countries (including the UK), there was no difference in all seizure admissions after 2008. We explored the possibility that the fall was related to the introduction of routine pneumococcal vaccination in 2006 but there were insufficient data.

CONCLUSION

A fall in admissions for febrile (but not afebrile) seizures after 2008 in Scotland and England explains a fall in all emergency admissions for seizure. A fall in all seizure admissions has not occurred in other European countries, and more research is required to understand the different outcomes in the UK and non-UK countries.

Low activity sn-glycerol-3-phosphate dehydrogenase variants in natural populations of Drosophila melanogaster

Eleven Australian natural populations of Drosophila melanogaster were screened by electrophoresis for evidence of null and/or low activity variants at the Gdph locus. Of 5018 alleles investigated, 57 had markedly lower GDPH activity, as judged by their heterozygous phenotypes, than control alleles. GPDH assays of 13 of these variant alleles showed that whilst they were heterogeneous in their properties and included electrophoretic variants and two categories of low-activity variant, there were no true null alleles. The most common low-activity variants exhibited dominance for GPDH activity in heterozygotes with normal alleles, and were shown to share this property with an allele previously isolated from a London (UK) population (Langley et al., 1981).

The penetration of ofloxacin into bronchial secretions

Penetration of ofloxacin into bronchial secretions following a single 400 mg oral dose was studied in 52 patients. Bronchial secretions were aspirated at bronchoscopy between one and 24 h after dosing and blood was collected at the same time. Mean bronchial secretion concentrations between 2 and 2.6 mg/l were measured in 36 patients between 1 and 6 h but there was considerable individual variation in both serum and bronchial aspirate concentrations. Concentrations declined slowly between 9 and 24 h to a mean value of 0.4 mg/l at 24 h. Correlation between serum and sputum concentrations of ofloxacin was fairly good despite marked deviation in some individuals. The ratios of the concentration in bronchial secretion to serum were remarkably constant at 1 to 6 h, varying between 0.96 during the third and fourth hours and 0.81 in the sixth hour. The results suggest that ofloxacin in a 400 mg oral dose is likely to achieve therapeutic activity against respiratory pathogens including Streptococcus pneumoniae, with sustained activity against more sensitive organisms for up to 24 h.

Cephalosporins in gram-positive infections

Infections caused by Gram-positive bacteria are an important and common cause of morbidity and mortality. Staphylococci and streptococci are the most frequent infecting organisms in skin and soft tissue infections, pneumonia, bone and joint infections, and endocarditis. Anaerobic Gram-positive bacteria such as Clostridia spp. cause infections that can rapidly produce tissue necrosis and death. The cephalosporins are indicated for the treatment of infections caused by Gram-positive bacteria in certain circumstances. These include selected patients with endocarditis, osteomyelitis, septic arthritis and cellulitis. They are also used as alternatives to the penicillins in penicillin-allergic patients and for 'mixed' infections caused by Gram-positive and Gram-negative organisms. This article discusses the indications for the cephalosporin group of antibiotics in patients suffering from infections caused by Gram-positive bacteria.

Penetration of ofloxacin into bronchial secretions

The penetration of ofloxacin into bronchial secretions was evaluated in 16 patients after administration of a single oral dose of ofloxacin 400mg. Bronchial secretions were aspirated at bronchoscopy after 1 to 6 hours and serum was collected simultaneously. Ofloxacin concentrations were measured by a microbiological assay method. Considerable individual variations in serum and bronchial aspirate concentrations were recorded: bronchial aspirate concentrations varied between 1.1 mg/L and 4.5 mg/L but exceeded 1.5 mg/L in 14 of 16 patients between 1 and 6 hours. The ratio between simultaneous mean bronchial aspirate and serum concentrations ranged between 0.53 in the second hour and 0.92 in the fourth hour. It is likely that inhibitory activity will be sustained over at least 6 hours against most potential respiratory pathogens including Haemophilus influenzae, Branhamella catarrhalis, Gram-negative bacilli, Staphylococcus aureus, Legionella pneumophila and Mycoplasma pneumoniae. Streptococcus pneumoniae and Pseudomonas aeruginosa may have minimal inhibitory concentration (MIC) values lower than ofloxacin concentrations achieved in bronchial secretions, although some isolates are less sensitive. Clinical studies should establish the relevance of pharmacokinetic data to respiratory infections caused by organisms of borderline susceptibility.

The effect of human calcitonin on the cytoplasmic spreading of rat osteoclasts

We previously found that calcitonin (CT), which inhibits osteoclastic bone resorption, abolished the cytoplasmic motility of isolated osteoclasts. The transition from motility to immotility was accompanied by a characteristic change in cell shape which coincided with the loss of pseudopodial ruffling activity and gradual cytoplasmic retraction. In this report we used computer-assisted morphometry to quantify the reduction in cytoplasmic spreading induced by human CT (hCT). Osteoclasts, isolated from neonatal rat long bones, were allowed to spread on a plastic surface for 120 min. The outlines of six osteoclasts were recorded on a time-lapse video recorder. hCT, other hormones, or plasma samples were then added. The outlines of the same six osteoclasts were recorded after incubation, and the area covered by the cells after incubation was calculated as a percentage of the area covered by the same cells before hormone addition. Osteoclastic spreading was reduced by hCT in a dose-dependent manner and was significantly decreased by concentrations of 2 pg/ml and above. High concentrations of PTH and 1,25-dihydroxyvitamin D3 had no effect on osteoclasts. This technique is a sensitive and quantitative assay of hCT concentration which is unaffected by the presence of other calcium-regulating hormones likely to be present in plasma.

Penetration of ciclacillin into bronchial secretions

The penetration of ciclacillin into bronchial secretions was investigated in 105 patients undergoing bronchoscopy after a single oral dose of 500 mg ciclacillin. Comparison was made with 26 patients who received 500 mg ampicillin by mouth. Over a 6 to 8 hour period, ciclacillin achieved significantly higher levels in bronchial secretions but no statistically significant difference between serum ampicillin and ciclacillin levels was detected.

Failure of the hydrogen breath test to detect pulmonary sugar malabsorption

Five patients with sucrase-isomaltase deficiency, and one patient with primary glucose-galactose malabsorption had no increases in breath hydrogen excretion after oral sucrose or glucose. Anaerobic incubation with sugars of stool suspensions from 5 patients with primary sugar malabsorption produced by trace of hydrogen (17 microliter) in only one, while those from 13 or 14 controls produced a mean hydrogen volume of 640 microliter under similar conditions. Altered bacterial metabolism is a probable explanation. Breath hydrogen excretion did increase appreciably in 2 of these patients after oral lactulose showing that hydrogen excretion may vary according to the substrate. Therefore, observation of breath hydrogen excretion after lactulose is not recommended as a means of predicting false-negative breath tests with other sugars. The hydrogen breath test is not a reliable mean of diagnosing primary sugar malabsorption in children.

Sex differences in choice behaviour: the object-person dimension

When viewing two conflicting stimuli in a stereoscope, males reported seeing objects significantly more often than human figures. The opposite effect was observed in females.

Calcified pituitary concretions in the newborn

Anterior pituitary glands from 200 fetuses and infants ranging in age from 22 weeks' gestation to one year of life were examined histologically for the presence of concretions. Characteristically these are round, lamellated bodies, often strongly basophilic, containing phosphates and measuring between 10 micrometer and 70 micrometer in diameter. They decreased in incidence postnatally and were rarely seen 6 months after birth. It is suggested that these concretions are a degenerative change in cells subject to the vigorous secretory activity that is part of the normal physiology of the anterior lobe of the pituitary from mid-gestation.

Community care - the glebe approach

The short history of Community Health Centres in Australia has been a stormy one. They have been seen as a threat by sections of the health care professionals. To some there is insecurity of roles and status, which can arise from the claims of emerging professions who are trying to establish their identities within the health-care team. To others, livelihood is threatened and health centres have been seen as the Labor Government's first steps towards nationalisation of Health. In this context it is interesting to note that regionalisation, including neighbourhood health centres, was a policy of the New South Wales Liberal Government long before it became Federal policy under a Labor Government. Questions of leadership, co-ordination and responsibility within health centres have also caused conflict. This has occurred at a time of rapid change, not only in health care delivery, but in the whole of society. It is no wonder people are confused.