Trio RNA sequencing in a cohort of medically complex children.

Genome sequencing (GS) is a powerful test for the diagnosis of rare genetic disorders. Although GS can enumerate most non-coding variation, determining which non-coding variants are disease-causing is challenging. RNA sequencing (RNA-seq) has emerged as an important tool to help address this issue, but its diagnostic utility remains understudied, and the added value of a trio design is unknown. We performed GS plus RNA-seq from blood using an automated clinical-grade high-throughput platform on 97 individuals from 39 families where the proband was a child with unexplained medical complexity. RNA-seq was an effective adjunct test when paired with GS. It enabled clarification of putative splice variants in three families, but it did not reveal variants not already identified by GS analysis. Trio RNA-seq decreased the number of candidates requiring manual review when filtering for de novo dominant disease-causing variants, allowing for the exclusion of 16% of gene-expression outliers and 27% of allele-specific-expression outliers. However, clear diagnostic benefit from the trio design was not observed. Blood-based RNA-seq can facilitate genome analysis in children with suspected undiagnosed genetic disease. In contrast to DNA sequencing, the clinical advantages of a trio RNA-seq design may be more limited.

Precision cut intestinal slices, a novel model of acute food allergic reactions.

BACKGROUND: Food allergy affects up to 10% of the pediatric population. Despite ongoing efforts, treatment options remain limited. Novel models of food allergy are needed to study response patterns downstream of IgE-crosslinking and evaluate drugs modifying acute events. Here, we report a novel human ex vivo model that displays acute, allergen-specific, IgE-mediated smooth muscle contractions using precision cut intestinal slices (PCIS). METHODS: PCIS were generated using gut tissue samples from children who underwent clinically indicated surgery. Viability and metabolic activity were assessed from 0 to 24 h. Distribution of relevant cell subsets was confirmed using single nucleus RNA sequencing. PCIS were passively sensitized using plasma from peanut allergic donors or peanut-sensitized non-allergic donors, and exposed to various stimuli including serotonin, histamine, FcɛRI-crosslinker, and food allergens. Smooth muscle contractions and mediator release functioned as readouts. A novel program designed to measure contractions was developed to quantify responses. The ability to demonstrate the impact of antihistamines and immunomodulation from peanut oral immunotherapy (OIT) was assessed. RESULTS: PCIS viability was maintained for 24 h. Cellular distribution confirmed the presence of key cell subsets including mast cells. The video analysis tool reliably quantified responses to different stimulatory conditions. Smooth muscle contractions were allergen-specific and reflected the clinical phenotype of the plasma donor. Tryptase measurement confirmed IgE-dependent mast cell-derived mediator release. Antihistamines suppressed histamine-induced contraction and plasma from successful peanut OIT suppressed peanut-specific PCIS contraction. CONCLUSION: PCIS represent a novel human tissue-based model to study acute, IgE-mediated food allergy and pharmaceutical impacts on allergic responses in the gut.

The Genomic Architecture of Pregnancy-Associated Plasticity in the Maternal Mouse Hippocampus.

Pregnancy is associated with extraordinary plasticity in the maternal brain. Studies in humans and other mammals suggest extensive structural and functional remodeling of the female brain during and after pregnancy. However, we understand remarkably little about the molecular underpinnings of this natural phenomenon. To gain insight into pregnancy-associated hippocampal plasticity, we performed single nucleus RNA sequencing (snRNA-seq) and snATAC-seq from the mouse hippocampus before, during, and after pregnancy. We identified cell type-specific transcriptional and epigenetic signatures associated with pregnancy and postpartum adaptation. In addition, we analyzed receptor-ligand interactions and transcription factor (TF) motifs that inform hippocampal cell type identity and provide evidence of pregnancy-associated adaption. In total, these data provide a unique resource of coupled transcriptional and epigenetic data across a dynamic time period in the mouse hippocampus and suggest opportunities for functional interrogation of hormone-mediated plasticity.

The effect of leading edge porosity on airfoil turbulence interaction noise.

Airfoil turbulence interaction noise and the flow field up to and over the porous leading edge is experimentally studied. The porous leading edges were of the same base triply periodic minimal surface structure with varying porosity to enable us to understand how the porosity, permeability, and pore size affect the generated turbulence interaction noise. The turbulent flow was generated by means of a passive turbulence grid that does not affect the normal background noise of the wind tunnel. Far-field noise results were obtained from a polar microphone array to assess the directivity of the sound as well as the narrowband frequency contributions. Far-field noise results demonstrate that increasing porosity reduces the turbulence interaction noise over low-to-mid frequencies, with a penalty of a high frequency noise increase. Flow measurement results indicate hydrodynamic penetration of the flow into the porous structure at the leading edge. Furthermore, the two-point correlation analysis of the velocity fluctuations approaching the leading edge shows that the turbulent structures approaching the solid leading edge appear to deform into more two-dimensional structures, whereas in the case of the porous leading edge, the turbulent structures appear to retain a strong spanwise coherence up to the point of hydrodynamic penetration.

X-linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition.

X-linked myotubular myopathy (XLMTM) is a fatal neuromuscular disorder caused by loss of function mutations in MTM1. At present, there are no directed therapies for XLMTM, and incomplete understanding of disease pathomechanisms. To address these knowledge gaps, we performed a drug screen in mtm1 mutant zebrafish and identified four positive hits, including valproic acid, which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model, and showed that valproic acid ameliorates the murine phenotype. These observations led us to interrogate the epigenome in Mtm1 knockout mice; we found increased DNA methylation, which is normalized with valproic acid, and likely mediated through aberrant 1-carbon metabolism. Finally, we made the unexpected observation that XLMTM patients share a distinct DNA methylation signature, suggesting that epigenetic alteration is a conserved disease feature amenable to therapeutic intervention.

Natural history of a mouse model of X-linked myotubular myopathy.

X-linked myotubular myopathy (XLMTM) is a severe monogenetic disorder of the skeletal muscle. It is caused by loss-of-expression/function mutations in the myotubularin (MTM1) gene. Much of what is known about the disease, as well as the treatment strategies, has been uncovered through experimentation in pre-clinical models, particularly the Mtm1 gene knockout mouse line (Mtm1 KO). Despite this understanding, and the identification of potential therapies, much remains to be understood about XLMTM disease pathomechanisms, and about the normal functions of MTM1 in muscle development. To lay the groundwork for addressing these knowledge gaps, we performed a natural history study of Mtm1 KO mice. This included longitudinal comparative analyses of motor phenotype, transcriptome and proteome profiles, muscle structure and targeted molecular pathways. We identified age-associated changes in gene expression, mitochondrial function, myofiber size and key molecular markers, including DNM2. Importantly, some molecular and histopathologic changes preceded overt phenotypic changes, while others, such as triad structural alternations, occurred coincidentally with the presence of severe weakness. In total, this study provides a comprehensive longitudinal evaluation of the murine XLMTM disease process, and thus provides a critical framework for future investigations.

Variants in ASPH cause exertional heat illness and are associated with malignant hyperthermia susceptibility.

Exertional heat illness (EHI) and malignant hyperthermia (MH) are life threatening conditions associated with muscle breakdown in the setting of triggering factors including volatile anesthetics, exercise, and high environmental temperature. To identify new genetic variants that predispose to EHI and/or MH, we performed genomic sequencing on a cohort with EHI/MH and/or abnormal caffeine-halothane contracture test. In five individuals, we identified rare, pathogenic heterozygous variants in ASPH, a gene encoding junctin, a regulator of excitation-contraction coupling. We validated the pathogenicity of these variants using orthogonal pre-clinical models, CRISPR-edited C2C12 myotubes and transgenic zebrafish. In total, we demonstrate that ASPH variants represent a new cause of EHI and MH susceptibility.

The effects of glucagon like peptide-1 (GLP-1) on cardiac remodeling: exploring the role of medication and physiological modulation after metabolic surgery.

Obesity and associated comorbidities reach epidemic proportions nowadays. Several treatment strategies exist, but bariatric surgery has the only longstanding effects. Since a few years, there is increasing interest in the effects of gastro-intestinal hormones, in particular Glucagon-Like Peptide-1 (GLP-1) on the remission of Type 2 Diabetes (T2DM) and its effects on cardiac cardiovascular morbidity, cardiac remodeling, and mortality. In the past years several high quality multicenter randomized controlled trials were developed to assess the effects of GLP-1 receptor agonist therapy on cardiovascular morbidity and mortality. Most of the trials were designed and powered as non-inferiority trials to demonstrate cardiovascular safety. Most of these trials show a reduction in cardiovascular morbidity in patients with T2DM. Some follow-up studies indicate potential beneficial effects of GLP-1 receptor agonists on cardiovascular function in patients with heart failure, however the results are contradictory, and we need long-term studies to make firm conclusions about the pleiotropic properties of incretin-based therapies. However, it seems that GLP-1 receptor agonists have different effects than the increased GLP-1 production after bariatric surgery on cardiovascular remodeling. One of the hypotheses is that the blood concentrations of GLP-1 receptor agonists are three times higher compared to GLP-1 increase after bariatric and metabolic surgery. The purpose of this narrative review is to summarize the effects of GLP-1 on cardiovascular morbidity, mortality and remodeling due to medication but also due to bariatric and metabolic surgery. The second objective is to explain the possible differences in effects of GLP-1 agonists and bariatric and metabolic surgery.

"One size does not fit all" - lessons learned from a multiple-methods study of a resident wellness curriculum across sites and specialties.

BACKGROUND: There is growing recognition that wellness interventions should occur in context and acknowledge complex contributors to wellbeing, including individual needs, institutional and cultural barriers to wellbeing, as well as systems issues which propagate distress. The authors conducted a multiple-methods study exploring contributors to wellbeing for junior residents in diverse medical environments who participated in a brief resilience and stress-reduction curriculum, the Stress Management and Resiliency Training Program for Residents (SMART-R). METHODS: Using a waitlist-controlled design, the curriculum was implemented for post-graduate year (PGY)-1 or PGY-2 residents in seven residency programs across three sites. Every three months, residents completed surveys, including the Perceived Stress Scale-10, General Self-Efficacy Questionnaire, a mindfulness scale (CAMSR), and a depression screen (PHQ-2). Residents also answered free-text reflection questions about psychological wellbeing and health behaviors. RESULTS: The SMART-R intervention was not significantly associated with decreased perceived stress. Linear regression modeling showed that depression was positively correlated with reported stress levels, while male sex and self-efficacy were negatively correlated with stress. Qualitative analysis elucidated differences in these groups: Residents with lower self-efficacy, those with a positive depression screen, and/or female residents were more likely to describe experiencing lack of control over work. Residents with higher self-efficacy described more positive health behaviors. Residents with a positive depression screen were more self-critical, and more likely to describe negative personal life events. CONCLUSIONS: This curriculum did not significantly modify junior residents' stress. Certain subpopulations experienced greater stress than others (female residents, those with lower self-efficacy, and those with a positive depression screen). Qualitative findings from this study highlight universal stressful experiences early in residency, as well as important differences in experience of the learning environment among subgroups. Tailored wellness interventions that aim to support diverse resident sub-groups may be higher yield than a "one size fits all" approach. TRIAL REGISTRATION: NCT02621801 , Registration date: December 4, 2015 - Retrospectively registered.

Effects of Bariatric Surgery on Heart Rhythm Disorders: a Systematic Review and Meta-Analysis.

The aim of this systematic review is to provide an overview of the literature on the effects of bariatric surgery on obesity-associated electrocardiogram (ECG) abnormalities and cardiac arrhythmias. Fourteen studies were included with a methodological quality ranging from poor to good. Majority of the studies showed a significant decrease of QT interval and related measures after bariatric surgery. Seven studies were included in the meta-analysis on effects of bariatric surgery on QTc interval and a significant decrease in QTc interval of - 33.6 ms, 95%CI [- 49.8 to - 17.4] was seen. Bariatric surgery results in significant decrease in QTc interval and P-wave dispersion, i.e., a normalization of initial pathology. The effects on atrial fibrillation are conflicting and not yet fully understood.

Basophil activation test shows high accuracy in the diagnosis of peanut and tree nut allergy: The Markers of Nut Allergy Study.

BACKGROUND: Peanut and tree nut allergies are the most important causes of anaphylaxis. Co-reactivity to more than one nut is frequent, and co-sensitization in the absence of clinical data is often obtained. Confirmatory oral food challenges (OFCs) are inconsistently performed. OBJECTIVE: To investigate the utility of the basophil activation test (BAT) in diagnosing peanut and tree nut allergies. METHODS: The Markers Of Nut Allergy Study (MONAS) prospectively enrolled patients aged 0.5-17 years with confirmed peanut and/or tree nut (almond, cashew, hazelnut, pistachio, walnut) allergy or sensitization from Canadian (n = 150) and Austrian (n = 50) tertiary pediatric centers. BAT using %CD63+ basophils (SSClow/CCR3pos) as outcome was performed with whole blood samples stimulated with allergen extracts of each nut (0.001-1000 ng/mL protein). BAT results were assessed against confirmed allergic status in a blinded fashion to develop a generalizable statistical model for comparison to extract and marker allergen-specific IgE. RESULTS: A mixed effect model integrating BAT results for 10 and 100 ng/mL of peanut and individual tree nut extracts was optimal. The area under the ROC curve (AUROC) was 0.98 for peanut, 0.97 for cashew, 0.92 for hazelnut, 0.95 for pistachio, and 0.97 for walnut. The BAT outperformed sIgE testing for peanut or hazelnut and was comparable for walnut (AUROC 0.95, 0.94, 0.92) in a sub-analysis in sensitized patients undergoing OFC. CONCLUSIONS: Basophil activation test can predict allergic clinical status to peanut and tree nuts in multi-nut-sensitized children and may reduce the need for high-risk OFCs in patients.

Modeling the conversion between specific IgE test platforms for nut allergens in children and adolescents.

BACKGROUND: Multiplex tests allow for measurement of allergen-specific IgE responses to multiple extracts and molecular allergens and have several advantages for large cohort studies. Due to significant methodological differences, test systems are difficult to integrate in meta-analyses/systematic reviews since there is a lack of datasets with direct comparison. We aimed to create models for statistical integration of allergen-specific IgE to peanut/tree nut allergens from three IgE test platforms. METHODS: Plasma from Canadian and Austrian children/adolescents with peanut/tree nut sensitization and a cohort of sensitized, high-risk, pre-school asthmatics (total n = 166) were measured with three R&D multiplex IgE test platforms: Allergy Explorer version 1 (ALEX) (Macro Array Dx), MeDALL-chip (Mechanisms of Development of Allergy) (Thermo Fisher), and EUROLINE (EUROIMMUN). Skin prick test (n = 51) and ImmunoCAP (Thermo Fisher) (n = 62) results for extracts were available in a subset. Regression models (Multivariate Adaptive Regression Splines, local polynomial regression) were applied if >30% of samples were positive to the allergen. Intra-test correlations between PR-10 and nsLTP allergens were assessed. RESULTS: Using two regression methods, we demonstrated the ability to model allergen-specific relationships with acceptable measures of fit (r2  = 94%-56%) for peanut and tree nut sIgE testing at the extract and molecular-level, in order from highest to lowest: Ara h 2, Ara h 6, Jug r 1, Ana o 3, Ara h 1, Jug r 2, and Cor a 9. CONCLUSION: Our models support the notion that quantitative conversion is possible between sIgE multiplex platforms for extracts and molecular allergens and may provide options to aggregate data for future meta-analysis.

Cardiac remodeling in obesity and after bariatric and metabolic surgery; is there a role for gastro-intestinal hormones?

Introduction: Obesity is associated with various diseases such as type 2 diabetes, hypertension, obstructive sleep apnea syndrome (OSAS), metabolic syndrome, and cardiovascular diseases. It affects several organ systems, including the pulmonary and cardiac systems. Furthermore, it induces pulmonary and cardiac changes that can result in right and/or left heart failure.Areas covered: In this review, authors provide an overview of obesity and cardiovascular remodeling, the individual actions of the gut hormones (like GLP-1 and PYY), the effects after bariatric/metabolic surgery and its influence on cardiac remodeling. In this review, we focussed and searched for literature in Pubmed and The Cochrane library (from the earliest date until April 2019), regarding cardiac function changes before and after bariatric surgery and literature regarding changes in gastrointestinal hormones.Expert opinion: Regarding the surgical treatment of obesity and metabolic diseases there is recognition of the importance of both weight loss (bariatric surgery) and improvement in metabolic milieu (metabolic surgery). A growing body of evidence further suggests that bariatric surgical procedures [like the Sleeve Gastrectomy (SG), Roux-en Y Gastric Bypass (RYGB), or One Anastomosis Gastric Bypass (OAGB)] have can improve outcomes of patients suffering from a number of cardiovascular diseases, including heart failure.

Assessment of Physical Fitness after Bariatric Surgery and Its Association with Protein Intake and Type of Cholecalciferol Supplementation.

: Background: Several studies showed that there is a relationship between vitamin and mineral status and muscle strength. In particular this is the case for handgrip strength (HS) and vitamin D deficiency. In bariatric surgery there is a risk of decrease in muscle strength after surgery and also vitamin and mineral deficiencies are not uncommon. The aim of this study is to assess the effect of low vitamin 25 (OH) cholecalciferol levels, high dose cholecalciferol supplementation regime and protein intake on physical fitness, measured using handgrip strength (HS) and the shuttle walk run test (SWRT). Methods: For this retrospective study, 100 patients who have had bariatric surgery were included. Group A (n = 50) used 800 IU oral cholecalciferol per day. Group B (n = 50) used 800 IU oral cholecalciferol daily and 50,000 IU liquid cholecalciferol monthly lifelong. Both groups were matched on common variables. To measure physical fitness, we used the HS manometer of Jamar and the Shuttle Walk Run Test (SWRT) to assess physical capacity. Results: No significant differences in HS and SWRT outcomes were found between patients with serum 25 (OH) cholecalciferol < 75 nmol/L or >75 nmol/L. The postoperative HS is significantly influenced by protein intake (p = 0.017) and no significant influence was seen in outcomes of the SWRT (p = 0.447). Conclusion: We have found that serum 25 (OH) cholecalciferol and different cholecalciferol supplementation regimes do not have a significant effect on HS and SWRT before, three and 6 months after surgery. It seems that protein intake plays a more important role in maintaining adequate muscle strength.

Utility of preoperative exercise therapy in reducing postoperative morbidity after surgery; a clinical overview of current evidence.

Introduction: Surgery is a major stressor especially for older patients that are prone for postoperative complications and mortality. Hospitalization due to surgery and illness can be major life events, and the age-related impairments in physiological function and the decreased ability to respond to metabolic and hormonal perturbations in response to surgery often lead to a longer convalescence. Areas covered: This article gives an overview of the effects of PET in various surgical fields and also what to account for and expect of PET after various types of surgery. A comprehensive literature search was performed in Pubmed, Embase, Medline, Cochrane Library, and PEDro database (from the earliest date of each database to March 2019) using search words 'Preoperative Exercise Therapy', 'Physical Therapy' and 'surgery'. Secondly, the literature searches were modified depending on the surgical specialty. Expert opinion: Evidence is growing that preoperative exercise therapy in various surgical specialties is well tolerated and effective, with by far the most evidence in the cardiac surgical field. Future improvements in standards of care and optimal pre-operative preparation should not only focus on the surgical team and the hospital organization but also on incorporating the active role of the patient.

Utility of the cold pressor test to predict future cardiovascular events.

INTRODUCTION: The cold pressor test (CPT) is a common and extensively validated test, which induces systemic stress involving immersion of an individual's hand in ice water (normally temperature between 0 and 5 degrees Celsius) for a period of time. CPT has been used in various fields, like examining effects of stress on memory, decision-making, pain and cardiovascular health. Areas covered: In terms of cardiovascular health, current research is mainly interested in predicting the occurrence of cardiovascular (CV) events. The objective of this review is to give an overview of the history and methodology of the CPT, and clinical utility in possibly predicting CV events in CAD and other atherosclerotic diseases. Secondly, we will discuss possible future applications of the CPT in clinical care. Expert opinion: An important issue to address is the fact that the physiology of the CPT is not fully understood at this moment. As pointed out multiple mechanisms might be responsible for contributing to either coronary vasodilatation or coronary vasoconstriction. Regarding the physiological mechanism of the CPT and its effect on the measurements of the carotid artery reactivity even less is known.

Interaction of obesity and atrial fibrillation: an overview of pathophysiology and clinical management.

INTRODUCTION: Obesity, defined as a Body Mass Index (BMI) of ≥30 kg/m2, is the most common chronic metabolic disease worldwide and its prevalence has been strongly increasing. Obesity is associated with various diseases such as cardiovascular disease, type 2 diabetes, and hypertension. Regarding heart rhythm disorders, obesity is associated with an increase in atrial fibrillation (AF), the most common arrhythmia in clinical practice. AF is associated with increased cardiovascular morbidity and mortality. Obesity, a novel risk factor, is responsible for a 50%-increased incidence of AF. Areas covered: We will briefly discuss the obesity paradox and its mechanisms regarding cardiac and hemodynamic function changes. In the first main part of this review, we will be discussing risk assessment studies, pathophysiology, genetic predisposition, epicardial adipose tissue, and ventricular adaptation in relation to obesity and development of AF. In the second part, we will discuss treatment strategies like conservative management and the effect of bariatric and metabolic surgery. Expert opinion: Cardiac arrhythmias, in particular, AF, in patients with obesity comprise complex pathophysiological mechanisms that remain poorly understood. In recent literature, there has been increased interest in the role of epicardial adipose tissue and structural remodeling in obese hearts.

Bariatric/Metabolic Surgery in the Asia-Pacific Region: APMBSS 2018 Survey.

INTRODUCTION: The Asia-Pacific Metabolic and Bariatric Surgery Society (APMBSS) held its congress in Tokyo at the end of March, 2018, and representatives from Asia-Pacific countries presented the current status of bariatric/metabolic surgery in the "National Reports" session. The data are summarized here to show the current status and problems in the Asia-Pacific region in 2017. METHODS: A questionnaire including data of 2016 and 2017 and consisting of eight general questions was prepared and sent to representatives in 18 Asia-Pacific countries by e-mail before the congress. After the congress, the data were analyzed and summarized. RESULTS: Seventeen of 18 countries responded to the survey. The frequency of obesity (BMI ≥ 30) in the 4 Gulf countries was > 30%, much higher than that in the other countries. In total, 1640 surgeons and 869 institutions were engaging in bariatric/metabolic surgery. In many East and Southeast Asian countries, the indication for bariatric surgery was BMI ≥ 35 or ≥ 37, whereas in many Gulf countries and Australia, it was BMI ≥ 40 or ≥ 35 with obesity-related disease. Ten of the 17 countries (58.8%) but only one of the 5 Southeast Asian countries (20.0%) had public health insurance coverage for bariatric surgery. In 2017, 95,125 patients underwent bariatric/metabolic surgery, with sleeve gastrectomy accounting for 68.0%, bypass surgery for 19.5%, and others for 12.5%. Current problems included public insurance coverage, training system, national registry, and lack of awareness and comprehension. CONCLUSION: This summary showed that bariatric/metabolic surgery is rapidly developing along with various problems in Asia-Pacific countries.

General decapping activators target different subsets of inefficiently translated mRNAs.

The Dcp1-Dcp2 decapping enzyme and the decapping activators Pat1, Dhh1, and Lsm1 regulate mRNA decapping, but their mechanistic integration is unknown. We analyzed the gene expression consequences of deleting PAT1, LSM1, or DHH1, or the DCP2 C-terminal domain, and found that: i) the Dcp2 C-terminal domain is an effector of both negative and positive regulation; ii) rather than being global activators of decapping, Pat1, Lsm1, and Dhh1 directly target specific subsets of yeast mRNAs and loss of the functions of each of these factors has substantial indirect consequences for genome-wide mRNA expression; and iii) transcripts targeted by Pat1, Lsm1, and Dhh1 exhibit only partial overlap, are generally translated inefficiently, and, as expected, are targeted to decapping-dependent decay. Our results define the roles of Pat1, Lsm1, and Dhh1 in decapping of general mRNAs and suggest that these factors may monitor mRNA translation and target unique features of individual mRNAs.