Rare disease research workflow using multilayer networks elucidates the molecular determinants of severity in Congenital Myasthenic Syndromes.

Exploring the molecular basis of disease severity in rare disease scenarios is a challenging task provided the limitations on data availability. Causative genes have been described for Congenital Myasthenic Syndromes (CMS), a group of diverse minority neuromuscular junction (NMJ) disorders; yet a molecular explanation for the phenotypic severity differences remains unclear. Here, we present a workflow to explore the functional relationships between CMS causal genes and altered genes from each patient, based on multilayer network community detection analysis of complementary biomedical information provided by relevant data sources, namely protein-protein interactions, pathways and metabolomics. Our results show that CMS severity can be ascribed to the personalized impairment of extracellular matrix components and postsynaptic modulators of acetylcholine receptor (AChR) clustering. This work showcases how coupling multilayer network analysis with personalized -omics information provides molecular explanations to the varying severity of rare diseases; paving the way for sorting out similar cases in other rare diseases.

Organizational factors to optimize mental health nurses' wellbeing in the workplace: An integrative literature review.

Mental health nursing is a privilege and a rewarding profession. There has been a call for transformational change in mental health services to improve outcomes for the people of New Zealand, with mental health nurses integral to this. However, with predicted nursing shortages, high levels of burnout, and increasing demands in the workplace, an organizational focus on wellbeing for mental health nurses is needed to sustain the workforce, implement change and improve outcomes for people using mental health services. An integrative review of the literature was undertaken to explore how organizations can optimize mental health nurses' wellbeing in the workplace and to identify measures for organizations to support mental health nurses' wellbeing with a focus on New Zealand. Seven articles were included in this review after a search, data extraction and evaluation. Data were synthesized and categorized using thematic analysis. The findings indicate organizations can invest in several initiatives to enhance mental health nurses' wellbeing in the workplace. These include professional development, skills to build resilience, enabling time to reflect on practice, enhancing professional supervision, having the right managerial support and focusing on individual's strengths. Organizations need to prioritize mental health nurses' wellbeing by embedding the practical strategies this review identified and by addressing organizational barriers to wellbeing. Organizations should consider implementing multileveled organizational wellbeing initiatives to nurture and grow the New Zealand mental health nursing workforce which in turn will contribute to quality care and enable mental health nurses to have long meaningful careers. Time, investment and resources are essential for these initiatives to be effective.

A systematic review of standardised tools used in perinatal death review programmes.

INTRODUCTION: Reducing preventable perinatal deaths is the focus of perinatal death surveillance and response programmes. Standardised review tools can help identify modifiable factors in perinatal deaths. AIM: This systematic review aimed to identify, compare, and appraise perinatal mortality review tools (PMRTs) in upper-middle to high-income countries. METHODS: Four major scientific databases were searched for publications relating to perinatal death reviews. There were no restrictions on date, study, or publication type. Professional websites for each country were searched for relevant material. The Appraisal of Guidelines Research and Evaluation Health Systems (AGREE-HS) checklist was used for quality appraisal of each tool. A narrative synthesis was used to describe and compare tools. FINDINGS: Ten PMRTs were included. Five PMRTs were from high-income countries, four from upper-middle income countries and one was designed for use in a global context. The structure, content, and quality of each PMRT varied. Each tool collected information about the antepartum, intrapartum, and neonatal periods and a section to classify perinatal deaths using a standardised classification system. All tools reviewed the care provided. Five tools included recommendation development for changes to clinical care. Four tools mentioned parent involvement in the review process. For quality appraisal, one review tool scored "high quality", six scored "moderate quality" and two scored "poor quality". CONCLUSION: There is little standardisation when it comes to PMRTs. Guidance on structuring PMRTs in a standardised way is needed. Recommendation development from a review is important to highlight changes to care required to reduce preventable perinatal deaths.

Understanding the evolution of immune genes in jawed vertebrates.

Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.

Clinical practice guidelines for the antenatal management of dichorionic diamniotic twin pregnancies: a systematic review.

OBJECTIVE: This review aimed to identify guidelines with recommendations applicable to the antenatal management of dichorionic diamniotic twin pregnancies within high-income countries, appraise their methodological quality, and discuss the similarities and variability across guidelines. METHOD: A systematic literature review of electronic databases was performed. Manual searches of guideline repositories and websites of professional organisations were performed to identify additional guidelines. The protocol for this systematic review was registered on PROSPERO (CRD42021248586, 25 June 2021). AGREE II and AGREE-REX tools were applied to assess the quality of eligible guidelines. A narrative and thematic synthesis described and compared the guidelines and their recommendations. RESULTS: Twenty-four guidelines were included, from which 483 recommendations were identified across 4 international organisations and 12 countries. Guidelines addressed eight themes and recommendations were classified accordingly: chorionicity and dating (103 recommendations), fetal growth (105 recommendations), termination of pregnancy (12 recommendations), fetal death (13 recommendations), fetal anomalies (65 recommendations), antenatal care (65 recommendations), preterm labour (56 recommendations) and birth (54 recommendations). Guidelines showed significant variability in recommendations, with conflicting recommendations regarding non-invasive preterm testing, definitions surrounding selective fetal growth restriction, screening for preterm labour and the timing of birth. Guidelines lacked a focus on standard antenatal management of DCDA twins, management of discordant fetal anomaly and single fetal demise. CONCLUSIONS: Specific guidance for dichorionic diamniotic twins is overall indistinct and access to guidance regarding the antenatal management of these pregnancies is currently difficult. Management of discordant fetal anomaly or single fetal demise needs greater consideration.

TEFM variants impair mitochondrial transcription causing childhood-onset neurological disease.

Mutations in the mitochondrial or nuclear genomes are associated with a diverse group of human disorders characterized by impaired mitochondrial respiration. Within this group, an increasing number of mutations have been identified in nuclear genes involved in mitochondrial RNA biology. The TEFM gene encodes the mitochondrial transcription elongation factor responsible for enhancing the processivity of mitochondrial RNA polymerase, POLRMT. We report for the first time that TEFM variants are associated with mitochondrial respiratory chain deficiency and a wide range of clinical presentations including mitochondrial myopathy with a treatable neuromuscular transmission defect. Mechanistically, we show muscle and primary fibroblasts from the affected individuals have reduced levels of promoter distal mitochondrial RNA transcripts. Finally, tefm knockdown in zebrafish embryos resulted in neuromuscular junction abnormalities and abnormal mitochondrial function, strengthening the genotype-phenotype correlation. Our study highlights that TEFM regulates mitochondrial transcription elongation and its defect results in variable, tissue-specific neurological and neuromuscular symptoms.

Severe congenital myasthenic syndromes caused by agrin mutations affecting secretion by motoneurons.

Congenital myasthenic syndromes (CMS) are predominantly characterized by muscle weakness and fatigability and can be caused by a variety of mutations in genes required for neuromuscular junction formation and maintenance. Among them, AGRN encodes agrin, an essential synaptic protein secreted by motoneurons. We have identified severe CMS patients with uncharacterized p.R1671Q, p.R1698P and p.L1664P mutations in the LG2 domain of agrin. Overexpression in primary motoneurons cultures in vitro and in chick spinal motoneurons in vivo revealed that the mutations modified agrin trafficking, leading to its accumulation in the soma and/or in the axon. Expression of mutant agrins in cultured cells demonstrated accumulation of agrin in the endoplasmic reticulum associated with induction of unfolded protein response (UPR) and impaired secretion in the culture medium. Interestingly, evaluation of the specific activity of individual agrins on AChR cluster formation indicated that when secreted, mutant agrins retained a normal capacity to trigger the formation of AChR clusters. To confirm agrin accumulation and secretion defect, iPS cells were derived from a patient and differentiated into motoneurons. Patient iPS-derived motoneurons accumulated mutant agrin in the soma and increased XBP1 mRNA splicing, suggesting UPR activation. Moreover, co-cultures of patient iPS-derived motoneurons with myotubes confirmed the deficit in agrin secretion and revealed a reduction in motoneuron survival. Altogether, we report the first mutations in AGRN gene that specifically affect agrin secretion by motoneurons. Interestingly, the three patients carrying these mutations were initially suspected of spinal muscular atrophy (SMA). Therefore, in the presence of patients with a clinical presentation of SMA but without mutation in the SMN1 gene, it can be worth to look for mutations in AGRN.

Retrospective national cohort study of pregnancy outcomes for women with type 1 and type 2 diabetes mellitus in Republic of Ireland.

AIM: Report the outcomes of pregnant women with type 1 and type 2 diabetes and to identify modifiable and non-modifiable factors associated with poor outcomes. METHODS: Retrospective analysis of pregnancy preparedness, pregnancy care and outcomes in the Republic of Ireland from 2015 to 2020 and subsequent multivariate analysis. RESULTS: In total 1104 pregnancies were included. Less than one third attended pre-pregnancy care (PPC), mean first trimester haemoglobin A1c was 7.2 ± 3.6% (55.5 ± 15.7 mmol/mol) and 52% received pre-conceptual folic acid. Poor preparation translated into poorer pregnancy outcomes. Livebirth rates (80%) were comparable to the background population however stillbirth rates were 8.7/1000 (four times the national rate). Congenital anomalies occurred in 42.5/1000 births (1.5 times the background rate). More than half of infants were large for gestational age and 47% were admitted to critical care. Multivariate analyses showed strong associations between non-attendance at PPC, poor glycaemic control and critical care admission (adjusted odds ratio of 1.68 (1.48-1.96) and 1.61 (1.43-1.86), p < 0.05 respectively) for women with type 1 diabetes. Smoking and teratogenic medications were also associated with critical care admission and hypertensive disorders of pregnancy. CONCLUSION: Pregnancy outcomes in women with diabetes are suboptimal. Significant effort is needed to optimize the modifiable factors identified in this study.

Immunity and lifespan: answering long-standing questions with comparative genomics.

Long life requires individuals to defend themselves against pathogens over prolonged periods of time whilst minimising damage to themselves. In vertebrates, pathogen defence is provided by two integrated systems, innate and adaptive immunity. Innate immunity is relatively nonspecific, resulting in collateral damage to hosts, and does not involve canonical immunological memory. In contrast, adaptive immunity is highly specific and confers long-lasting memory, which are features that are predicted to facilitate long life. However, there is long-standing debate over the general importance of adaptive immunity for the evolution of extended lifespans, partly because this is difficult to test. We highlight how recent improvements in whole genome assemblies open the door to immunogenomic comparative analyses that enable the coevolution of longevity and specific immune traits to be disentangled.

A protocol for a systematic review of standardised tools used in perinatal death review programmes.

Introduction: Perinatal mortality encompasses stillbirths and early neonatal deaths. A perinatal death surveillance and response cycle has been recommended by the World Health Organization for use in the review of perinatal deaths. The main components of the cycle include identifying and reporting perinatal deaths, and reviewing the deaths, including potentially modifiable factors, in order to measure and improve quality of care provided to women and infants. There is no consensus on the best way to design, implement and conduct perinatal death reviews. This systematic review aims to identify standardised tools that are used to review perinatal deaths.  Objectives: The primary aim of this protocol is to describe methodology for a systematic search of the literature to identify standardised tools that are used to review perinatal deaths in upper-middle to high-income countries. Review tools may include standardised checklists, forms, frameworks or other structured documents used to review perinatal deaths. Review tools will be appraised to see if they incorporate the identification of modifiable factors in perinatal deaths and establish recommendations for improvements to quality of care provided. Methods: A systematic review of the literature will be performed to identify peer-reviewed publications and grey literature describing the use of perinatal mortality review tools without date restrictions. The eligibility of review tools for inclusion will be based on inclusion and exclusion criteria applied to the SPIDER framework. Data will be extracted based on the structure and content of included review tools, and the tools will be appraised using the Appraisal of Guidelines Research and Evaluation Health Systems (AGREE-HS) instrument. Conclusion: This systematic review protocol for identifying and appraising standardised perinatal mortality review tools may help to establish the optimal way to structure a standardised review process for perinatal mortality in middle- to high-income countries. PROSPERO registration: CRD42022326877.

Living with relatives offsets the harm caused by pathogens in natural populations.

Living with relatives can be highly beneficial, enhancing reproduction and survival. High relatedness can, however, increase susceptibility to pathogens. Here, we examine whether the benefits of living with relatives offset the harm caused by pathogens, and if this depends on whether species typically live with kin. Using comparative meta-analysis of plants, animals, and a bacterium (nspecies = 56), we show that high within-group relatedness increases mortality when pathogens are present. In contrast, mortality decreased with relatedness when pathogens were rare, particularly in species that live with kin. Furthermore, across groups variation in mortality was lower when relatedness was high, but abundances of pathogens were more variable. The effects of within-group relatedness were only evident when pathogens were experimentally manipulated, suggesting that the harm caused by pathogens is masked by the benefits of living with relatives in nature. These results highlight the importance of kin selection for understanding disease spread in natural populations.

Living in a group with relatives has many advantages, such as helping with child rearing and gathering food. This has led many species to evolve a range of group behaviours; for example, in honey bee populations, worker bees sacrifice themselves to save the colony from incoming enemies. But there are also downsides to living with family. For example, bacteria, viruses and other disease-causing pathogens will find it easier to spread between relatives. This is because individuals with the same genes have similar immune defences. So, is it better to live with relatives who can help with life's struggles or live with unrelated individuals where there is a lower chance of getting sick? To help answer this question, Bensch et al. analysed data from 75 studies which encompassed 56 different species of plants, animals, and one type of bacteria. This showed that creatures living in family groups experienced more disease and had a higher risk of death. However, if groups had a low chance of encountering pathogens, individuals living with relatives were more likely to survive. This cancels out the disadvantages family groups face when pathogens are more common. The analysis by Bensch et al. provides new insights into how pathogens spread in species with different social systems. This information can be used to predict how diseases occur in nature which will benefit ecologists, epidemiologists, and conservation biologists.

Valsartan exposure in pregnancy with resultant anhydramnios and chronic kidney disease in a late preterm infant.

In utero exposure to angiotensin II receptor blockers (ARBs) has fetotoxic effects including renal failure, oligohydramnios and lung hypoplasia. We present the case of a 24-year-old woman who presented to the maternity services in the 34th week of her first pregnancy. She was taking valsartan for hypertension. Ultrasound showed a structurally normal fetus with anhydramnios. The patient was admitted and valsartan was discontinued. She had spontaneous preterm delivery at 35 weeks' gestation of a baby girl. The baby's urine output was minimal in the first week of life and she was transferred to a paediatric hospital for specialist nephrology input. At 6 months of age, she requires ongoing nephrology follow-up and she remains on treatment for hypertension and anaemia. This case demonstrates the serious adverse effects resulting from ARB exposure in utero, and highlights the importance of avoiding fetotoxic medications in women of childbearing age.

INPP5K and SIL1 associated pathologies with overlapping clinical phenotypes converge through dysregulation of PHGDH.

Marinesco-Sjögren syndrome is a rare human disorder caused by biallelic mutations in SIL1 characterized by cataracts in infancy, myopathy and ataxia, symptoms which are also associated with a novel disorder caused by mutations in INPP5K. While these phenotypic similarities may suggest commonalties at a molecular level, an overlapping pathomechanism has not been established yet. In this study, we present six new INPP5K patients and expand the current mutational and phenotypical spectrum of the disease showing the clinical overlap between Marinesco-Sjögren syndrome and the INPP5K phenotype. We applied unbiased proteomic profiling on cells derived from Marinesco-Sjögren syndrome and INPP5K patients and identified alterations in d-3-PHGDH as a common molecular feature. d-3-PHGDH modulates the production of l-serine and mutations in this enzyme were previously associated with a neurological phenotype, which clinically overlaps with Marinesco-Sjögren syndrome and INPP5K disease. As l-serine administration represents a promising therapeutic strategy for d-3-PHGDH patients, we tested the effect of l-serine in generated sil1, phgdh and inpp5k a+b zebrafish models, which showed an improvement in their neuronal phenotype. Thus, our study defines a core phenotypical feature underpinning a key common molecular mechanism in three rare diseases and reveals a common and novel therapeutic target for these patients.

Dysregulation of GSK3ß-Target Proteins in Skin Fibroblasts of Myotonic Dystrophy Type 1 (DM1) Patients.

Myotonic dystrophy type 1 (DM1) is the most common monogenetic muscular disorder of adulthood. This multisystemic disease is caused by CTG repeat expansion in the 3'-untranslated region of the DM1 protein kinase gene called DMPK. DMPK encodes a myosin kinase expressed in skeletal muscle cells and other cellular populations such as smooth muscle cells, neurons and fibroblasts. The resultant expanded (CUG)n RNA transcripts sequester RNA binding factors leading to ubiquitous and persistent splicing deregulation. The accumulation of mutant CUG repeats is linked to increased activity of glycogen synthase kinase 3 beta (GSK3ß), a highly conserved and ubiquitous serine/threonine kinase with functions in pathways regulating inflammation, metabolism, oncogenesis, neurogenesis and myogenesis. As GSK3ß-inhibition ameliorates defects in myogenesis, muscle strength and myotonia in a DM1 mouse model, this kinase represents a key player of DM1 pathobiochemistry and constitutes a promising therapeutic target. To better characterise DM1 patients, and monitor treatment responses, we aimed to define a set of robust disease and severity markers linked to GSK3ßby unbiased proteomic profiling utilizing fibroblasts derived from DM1 patients with low (80- 150) and high (2600- 3600) CTG-repeats. Apart from GSK3ß increase, we identified dysregulation of nine proteins (CAPN1, CTNNB1, CTPS1, DNMT1, HDAC2, HNRNPH3, MAP2K2, NR3C1, VDAC2) modulated by GSK3ß. In silico-based expression studies confirmed expression in neuronal and skeletal muscle cells and revealed a relatively elevated abundance in fibroblasts. The potential impact of each marker in the myopathology of DM1 is discussed based on respective function to inform potential uses as severity markers or for monitoring GSK3ß inhibitor treatment responses.

Trade-offs in expressed major histocompatibility complex diversity seen on a macroevolutionary scale among songbirds.

To survive organisms must defend themselves against pathogens. Classical Major Histocompatibility Complex (MHC) genes play a key role in pathogen defense by encoding molecules involved in pathogen recognition. MHC gene diversity influences the variety of pathogens individuals can recognize and respond to and has consequently been a popular genetic marker for disease resistance in ecology and evolution. However, MHC diversity is predominantly estimated using genomic DNA (gDNA) with little knowledge of expressed diversity. This limits our ability to interpret the adaptive significance of variation in MHC diversity, especially in species with very many MHC genes such as songbirds. Here, we address this issue using phylogenetic comparative analyses of the number of MHC class I alleles (MHC-I diversity) in gDNA and complementary DNA (cDNA), that is, expressed alleles, across 13 songbird species. We propose three theoretical relationships that could be expected between genomic and expressed MHC-I diversity on a macroevolutionary scale and test which of these are best supported. In doing so, we show that significantly fewer MHC-I alleles than the number available are expressed, suggesting that optimal MHC-I diversity could be achieved by modulating gene expression. Understanding the relationship between genomic and expressed MHC diversity is essential for interpreting variation in MHC diversity in an evolutionary context.

Wetter climates select for higher immune gene diversity in resident, but not migratory, songbirds.

Pathogen communities can vary substantially between geographical regions due to different environmental conditions. However, little is known about how host immune systems respond to environmental variation across macro-ecological and evolutionary scales. Here, we select 37 species of songbird that inhabit diverse environments, including African and Palaearctic residents and Afro-Palaearctic migrants, to address how climate and habitat have influenced the evolution of key immune genes, the major histocompatibility complex class I (MHC-I). Resident species living in wetter regions, especially in Africa, had higher MHC-I diversity than species living in drier regions, irrespective of the habitats they occupy. By contrast, no relationship was found between MHC-I diversity and precipitation in migrants. Our results suggest that the immune system of birds has evolved greater pathogen recognition in wetter tropical regions. Furthermore, evolving transcontinental migration appears to have enabled species to escape wet, pathogen-rich areas at key periods of the year, relaxing selection for diversity in immune genes and potentially reducing immune system costs.

Modulation of the Acetylcholine Receptor Clustering Pathway Improves Neuromuscular Junction Structure and Muscle Strength in a Mouse Model of Congenital Myasthenic Syndrome.

Introduction: Congenital myasthenic syndromes (CMS) are a diverse group of inherited neuromuscular disorders characterized by a failure of synaptic transmission at the neuromuscular junction (NMJ). CMS often present early with fatigable weakness and can be fatal through respiratory complications. The AGRN gene is one of over 30 genes known to harbor mutations causative for CMS. In this study, we aimed to determine if a compound (NT1654), developed to stimulate the acetylcholine receptor (AChR) clustering pathway, would benefit a mouse model of CMS caused by a loss-of-function mutation in Agrn (Agrn nmf380 mouse). Methods: Agrn nmf380 mice received an injection of either NT1654 or vehicle compound daily, with wild-type litter mates used for comparison. Animals were weighed daily and underwent grip strength assessments. After 30 days of treatment animals were sacrificed, and muscles collected. Investigations into NMJ and muscle morphology were performed on collected tissue. Results: While minimal improvements in NMJ ultrastructure were observed with electron microscopy, gross NMJ structure analysis using fluorescent labelling and confocal microscopy revealed extensive postsynaptic improvements in Agrn nmf380 mice with NT1654 administration, with variables frequently returning to wild type levels. An improvement in muscle weight and myofiber characteristics helped increase forelimb grip strength and body weight. Conclusions: We conclude that NT1654 restores NMJ postsynaptic structure and improves muscle strength through normalization of muscle fiber composition and the prevention of atrophy. We hypothesize this occurs through the AChR clustering pathway in Agrn nmf380 mice. Future studies should investigate if this may represent a viable treatment option for patients with CMS, especially those with mutations in proteins of the AChR clustering pathway.

Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales.

Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.