Polygenic risk heterogeneity among focal epilepsies

Focal epilepsy (FE) is clinically highly heterogeneous. It has been shown recently that not only rare but also a subset of common genetic variants confer risk for FE. The relatively modest power of genetic studies in FE suggests a high genetic heterogeneity of FE when grouped as one disorder. We hypothesize that the clinical heterogeneity of FE is correlated with genetic heterogeneity on a common risk variant level. To test the hypothesis, we used an FE polygenic risk score "FE-PRS" that combines small effect sizes of thousands of common variants from the largest FE-GWAS (genome-wide association study) into a single measure. We grouped 414 individuals with FE according to common clinical features into subgroups, either by one feature at a time or by all features combined in a cluster analysis. We examined their association with FE-PRS compared to 20 435 matched population controls and observed heterogeneous FE-PRS burden among the subgroups. The highest phenotypic variance explained by FE-PRS was identified in a cluster analysis-defined FE subgroup where all individuals had unknown etiologies and psychiatric comorbidities, and the majority had early onset seizures. Our results indicate that genetic factors associated with FE have differential burden among FE subtypes. Future studies using better-powered FE-PRS might have clinical utility.Peer reviewe

Prognosis and longitudinal changes of physical activity in idiopathic pulmonary fibrosis

Background: Physical activity (PA) is associated with disease severity in idiopathic pulmonary fibrosis (IPF), but longitudinal studies evaluating its prognostic value and changes over time are lacking. Methods: We measured PA (steps per day, SPD) in a cohort of 46 IPF-patients (mean age, 67 years; mean FVC, 76.1%pred.) by accelerometry at baseline, recorded survival status during 3 years follow-up and repeated measurements in survivors. We compared the prognostic value of PA to established mortality predictors including lung function (FVC, DLCO) and 6-min walking-distance (6MWD). Results: During follow-up (median 34 months) 20 patients (43%) died. SPD and FVC best identified non-survivors (AUROC-curve 0.79, p < 0.01). After adjustment for confounders (sex, age, therapy), a standardized increase (i.e. one SD) in SPD, FVC%pred. or DLCO%pred. was associated with a more than halved risk of death (HR < 0.50; p < 0.01). Compared to baseline, SPD, FVC, and 6MWD annually declined in survivors by 973 SPD, 130 ml and 9 m, resulting in relative declines of 48.3% (p < 0.001), 13.3% (p < 0.001) and 7.8% (p = 0.055), respectively. Conclusion: While PA predicts mortality of IPF patients similar to established functional measures, longitudinal decline of PA seems to be disproportionally large. Our data suggest that the clinical impact of disease progression could be underestimated by established functional measures

Simple ClinVar: an interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database

Clinical genetic testing has exponentially expanded in recent years, leading to an overwhelming amount of patient variants with high variability in pathogenicity and heterogeneous phenotypes. A large part of the variant level data is aggregated in public databases such as ClinVar. However, the ability to explore this rich resource and answer general questions such as 'How many genes inside ClinVar are associated with a specific disease? or 'In which part of the protein are patient variants located?' is limited and requires advanced bioinformatics processing. Here, we present Simple ClinVar (http://simpleclinvar.broadinstitute.org/) a web server application that is able to provide variant, gene and disease level summary statistics based on the entire ClinVar database in a dynamic and user-friendly web-interface. Overall, our web application is able to interactively answer basic questions regarding genetic variation and its known relationships to disease. By typing a disease term of interest, the user can identify in seconds the genes and phenotypes most frequently reported to ClinVar. Subsets of variants can then be further explored, filtered or mapped and visualized in the corresponding protein sequences. Our website will follow ClinVar monthly releases and provide easy access to ClinVar resources to a broader audience including basic and clinical scientists

Time to move beyond genetics towards biomedical data-driven translational genomic research in severe paediatric epilepsies

By accumulating ever greater amounts of genomic data, scientists have identified >100 genes associated with Mendelian forms of epilepsy and neurodevelopmental disorders with seizures. For most of the identified genes a wide range of genetic variants have been identified and affected patients are clinically heterogeneous. It is not clear to which degree the clinical heterogeneity can be attributed to the disease causing variant alone. We need to improve our current understanding of biophysical effects of variants on protein function and the role of polygenic background in modifying the clinical representation. In addition, longitudinal clinical data need to be recorded using standardized methods and shared across research centers to build large virtual cohorts for each single gene disorder. Without large, comprehensive, longitudinal datasets, studying the interplay of environmental factors and genetic factors will be challenging. As a community, we must work together to set the foundation for biorepositories and the collection and sharing of 'big data' in order to allow genetic-phenotypic characterization of the epilepsies and to fully utilize the potential for drug discovery, and patient-specific tailored management. (C) 2019 European Paediatric Neurology Society. Published by Elsevier Ltd. All rights reserved

An Altered Relationship between Soluble TREM2 and Inflammatory Markers in Young Adults with Down Syndrome: A Preliminary Report

Individuals with Down syndrome (DS) develop Alzheimer's disease (AD)-related neuropathology, characterized by amyloid plaques with amyloid beta (A beta) and neurofibrillary tangles with tau accumulation. Peripheral inflammation and the innate immune response are elevated in DS. Triggering receptor expressed in myeloid cells 2 (TREM2) genetic variants are risk factors for AD and other neurodegenerative diseases. Soluble TREM2 (sTREM2), a soluble cleavage product of TREM2, is elevated in AD cerebrospinal fluid and positively correlates with cognitive decline. There is relatively little information about TREM2 in DS. Our objective was to examine the relationship between sTREM2 and inflammatory markers in young adults with DS, prior to the development of dementia symptoms. Because TREM2 plays a role in the innate immune response and has been associated with dementia, the hypothesis of this exploratory study was that young adults with DS predementia (n = 15, mean age = 29.5 y) would exhibit a different relationship between sTREM2 and inflammatory markers in plasma, compared with neurotypical, age-matched controls (n = 16, mean age = 29.6 y). Indeed, young adults with DS had significantly elevated plasma sTREM2 and inflammatory markers. Additionally, in young adults with DS, sTREM2 correlated positively with 24 of the measured cytokines, whereas there were no significant correlations in the control group. Hierarchical clustering of sTREM2 and cytokine concentrations also differed between the groups, supporting the hypothesis that its function is altered in people with DS predementia. This preliminary report of human plasma provides a basis for future studies investigating the relationship between TREM2 and the broader immune response predementia

Spectrum of neurodevelopmental disease associated with the GNAO1 guanosine triphosphate-binding region

Objective:To characterize the phenotypic spectrum associated withGNAO1vari-ants and establish genotype‐protein structure‐phenotype relationships. Methods:We evaluated the phenotypes of 14 patients withGNAO1variants, ana-lyzed their variants for potential pathogenici ty, and mapped them, along withthose in the literature, on a three‐dimensional structural protein model.Results:The 14 patients in our cohort, including one sibling pair, had 13 distinct,heterozygousGNAO1variants classified as pathogenic or likely pathogenic. Weattributed the same variant in two siblings to parental mosaicism. Patients initiallypresented with seizures beginning in the first 3 months of life (8/14), developmen-tal delay (4/14), hypotonia (1/14), or movement disorder (1/14). All patients hadhypotonia and developmental delay ranging from mild to severe. Nine had epi-lepsy, and nine had movement disorders, including dystonia, ataxia, chorea, anddyskinesia. The 13GNAO1variants in our patients are predicted to result inamino acid substitutions or deletions in the GNAO1 guanosine triphosphate(GTP)‐binding region, analogous to those in previous publications. Patients withvariants affecting amino acids 207‐221 had only movement disorder andhypotonia. Patients with variants affecting the C‐terminal region had the mildestphenotypes.Significance:GNAO1encephalopathy most frequently presents with seizuresbeginning in the first 3 months of life. Concurrent movement disorders are also aprominent feature in the spectrum ofGNAO1encephalopathy. All variantsaffected the GTP‐binding domain of GNAO1, highlighting the importance of thisregion for G‐protein signaling and neurodevelopment

yylncT Defines a Class of Divergently Transcribed lncRNAs and Safeguards the T-mediated Mesodermal Commitment of Human PSCs

Human protein-coding genes are often accompanied by divergently transcribed non-coding RNAs whose functions, especially in cell fate decisions, are poorly understood. Using an hESC-based cardiac differentiation model, we define a class of divergent lncRNAs, termed yin yang lncRNAs (yylncRNAs), that mirror the cell-type-specific expression pattern of their protein-coding counterparts. yylncRNAs are preferentially encoded from the genomic loci of key developmental cell fate regulators. Most yylncRNAs are spliced polyadenylated transcripts showing comparable expression patterns in vivo in mouse and in human embryos. Signifying their developmental function, the key mesoderm specifier BRACHYURY (T) is accompanied by yylncT, which localizes to the active T locus during mesoderm commitment. yylncT binds the de novo DNA methyltransferase DNMT3B, and its transcript is required for activation of the T locus, with yylncT depletion specifically abolishing mesodermal commitment. Collectively, we report a lncRNA-mediated regulatory layer safeguarding embryonic cell fate transitions

Neurodevelopmental copy-number variants: A roadmap to improving outcomes by uniting patient advocates, researchers, and clinicians for collective impact

Copy-number variants and structural variants (CNVs/SVs) drive many neurodevelopmental-related disorders. While many neurodevelopmental-related CNVs/SVs give rise to complex phenotypes, the overlap in phenotypic presentation between independent CNVs can be extensive and provides a motivation for shared approaches. This confluence at the level of clinical phenotype implies convergence in at least some aspects of the underlying genomic mechanisms. With this perspective, our Commission on Novel Technologies for Neurodevelopmental CNVs asserts that the time has arrived to approach neurodevelopmental-related CNVs/SVs as a class of disorders that can be identified, investigated, and treated on the basis of shared mechanisms and/or pathways (e.g., molecular, neurological, or developmental). To identify common etiologic mechanisms among uncommon neurodevelopmental-related disorders and to potentially identify common therapies, it is paramount for teams of scientists, clinicians, and patients to unite their efforts. We bring forward novel, collaborative, and integrative strategies to translational CNV/SV research that engages diverse stakeholders to help expedite therapeutic outcomes. We articulate a clear vision for piloted roadmap strategies to reduce patient/caregiver burden and redundancies, increase efficiency, avoid siloed data, and accelerate translational discovery across CNV/SV-based syndromes