Biology subjects

Schenck, A.

Publications and source records attributed to Schenck, A..

10 recordsLinked to original sources

bioRxiv2026

SysNDD: A Systematic Database for Neurodevelopmental Disorders

Neurodevelopmental disorders (NDDs) are clinically and genetically heterogeneous, and evidence linking additional genes to disease evolves rapidly. We developed SysNDD, an open-access, expert-curated resource that represents distinct gene-inheritance-disease associations as entities with standardized confidence, phenotype, and variant annotations. Each entity retains its curation history, so its evidence category can change as evidence accumulates. Currently, SysNDD contains 4,275 entities curated from 4,932 publications. Of these, 3,758 entities involving 3,271 genes describe NDDs; the remainder record non-NDD disorders, nearly all linked to NDD-associated genes, included for completeness. Regarding NDD evidence categories, 1,838 genes are Definitive, 179 Moderate, 1,248 Limited, and 6 Refuted. The entity model captures inheritance-specific disorders, including 220 genes with both autosomal dominant and autosomal recessive NDD associations. Comparison with seven other NDD gene resources showed complementary coverage, and evidence categories largely agreed with those of ClinGen, Gene2Phenotype, and PanelApp for shared gene-disease pairs. NDD genes formed distinct molecular modules, whereas associated disorders formed broad, overlapping phenotype groups that corresponded to those modules only selectively. SysNDD provides a continuously maintained, programmatically accessible framework for gene-disease evidence assessment, inheritance-aware interpretation, and systematic NDD research.

genetics↗

bioRxiv2026

The evolutionarily conserved EHMT1/G9a histone methyltransferase family regulates sleep maintenance through ROS homeostasis in insulin-producing cells

Sleep disturbances are a common, still poorly characterized feature of Kleefstra syndrome (KLEFS1), a neurodevelopmental disorder caused by rare variants in the epigenetic regulator EHMT1. The gap in understanding the characteristics and origin of these sleep disturbances poses a major barrier for therapy development. In this cross-species study, we reveal that 70% of individuals with KLEFS1 experience severe sleep maintenance insomnia, marked by fragmented sleep due to frequent night awakenings. Furthermore, common genetic variation at the EHMT1 locus was associated with short sleep and insomnia symptoms in the general population. Drosophila mutants of the EHMT1 orthologue G9a recapitulate these phenotypes, exhibiting reduced and fragmented sleep. We show that G9a is required in insulin-producing cells (IPCs) and the fat body, in the latter during development, to ensure adult sleep integrity. Untargeted metabolomics revealed widespread metabolic dysregulation in G9a mutants, particularly affecting methionine metabolism. Mutants exhibited reduced methionine and elevated methionine sulfoxide (Met-SO), pointing to increased reactive oxygen species (ROS). Redox sensors revealed increased H2O2-dependent oxidation in the larval brain and an elevated glutathione redox potential in IPCs during development but not in adulthood. IPC-specific knockdown of MsrA, the enzyme that reduces Met-SO back to methionine, reproduced sleep fragmentation. Developmental, but not acute, antioxidant treatment fully restored adult sleep consolidation, demonstrating that G9a safeguards sleep via ROS homeostasis in early life. Finally, we show that a Drosophila sleep-restriction paradigm based on human sleep-restriction therapy can override the developmental defects and restore sleep continuity in adulthood. Our findings establish an evolutionarily conserved role for EHMT1/G9a in sleep regulation and provide a mechanistic framework to understand and treat sleep disturbances in KLEFS1.

genetics↗

bioRxiv2026

Polyamine dysregulation converges with RASopathies on RAS/MAPK and sensory processing phenotypes in Drosophila

RASopathies are developmental conditions associated with cognitive and sensory processing impairments. They are caused by pathogenic variants in genes that result in overactivation of the RAS/MAPK signaling pathway. Genes linked to this pathway have been reported to be enriched among Drosophila models with habituation deficits, a behavioral phenotype reflecting sensory filtering. To identify hidden RASopathies - monogenic disorders that converge on RAS/MAPK overactivation without being classically linked to the pathway - we generated 89 and screened 41 viable habituation-deficient Drosophila RNAi models for RAS/MAPK overactivation, measured as an increased phosphorylated ERK to ERK ratio. This screen identified Sms, the ortholog of human spermine synthase (SMS), implicated in Snyder-Robinson syndrome. RAS/MAPK overactivation along with hyperreactivity and habituation impairments are confirmed in a full loss-of-function mutant. A RNAi screen targeting polyamine pathway genes identified Sat (human SAT1/2, SATL1) to reproduce these phenotypes. Knockdown of Sms or Sat in GABAergic neurons impaired habituation, implicating polyamine metabolism in inhibitory circuit function. These findings reveal previously unrecognized convergence between polyamine dysregulation and RASopathies, suggesting shared therapeutic opportunities through modulation of either pathway. SUMMARY STATEMENTUsing Drosophila, we uncovered polyamine metabolism genes, Sms and Sat, as modulators of RAS/MAPK and sensory processing, revealing a shared mechanism between polyaminopathies and RASopathies that may inform unified therapies.

genetics↗

bioRxiv2025

Excessive activation of the RAS/MAPK pathway triggers adult-onset motor axonal degeneration

Axonal and synaptic degeneration are key hallmarks of neurodegenerative diseases, but the underlying molecular mechanisms are incompletely understood. Here, we performed an unbiased forward genetic mosaic screen to identify genes required for maintenance of adult motor axons and neuromuscular junctions (NMJs) in the Drosophila leg. We identified 49 mutations in 30 genes, including mutations in 8 genes resulting in adult-onset progressive degeneration. We found that loss of pebbled (peb) function results in adult-onset motor axonal and NMJ degeneration, and age-dependent motor deficits. Peb is the Drosophila RREB1 ortholog, a C2H2 zinc-finger transcription factor that negatively regulates transcription of RAS/MAPK pathway target genes. Loss of peb function resulted in excessive RAS/MAPK pathway activation, and loss of function of other negative regulators of the RAS/MAPK pathway also induced adult-onset progressive NMJ degeneration and motor deficits. Importantly, treatment of adult flies with the MEK1/2 inhibitor mirdametinib induced a dosage-dependent rescue of peb mutant motor neurodegenerative phenotypes. Thus, RAS/MAPK pathway overactivation results in adult-onset progressive neurodegeneration, which can be prevented by RAS/MAPK pathway inhibition.

neuroscience↗

bioRxiv2025

A conserved epilepsy-associated gene co-expression module identifies increased metabolic rate as a shared pathomechanism

Epilepsy is a mechanistically complex, incompletely understood neurological disorder. To uncover novel converging mechanisms in epilepsy, we used Drosophila whole-brain single-cell RNA-sequencing to refine and characterize a previously proposed human epilepsy-associated gene co-expression network (GCN). We identified a conserved co-expressed module of 26 genes, which comprises fly orthologs of 13 epilepsy-associated genes and integrates synaptic and metabolic functions. Over one-third of the Drosophila pan-neuronal knockdown models targeting this module exhibited altered seizure-like behaviors in response to mechanical or heat stress. These recapitulated seizures associated with four epilepsy-associated genes, identified two novel epilepsy candidate genes, and three genes knockdown of which conferred seizure protection. Most knockdown models with altered seizure susceptibility showed changes in metabolic rate and levels of phosphorylated adenosine monophosphate-activated protein kinase (AMPK), a key regulator of cellular energy homeostasis. Enhancing AMPK activity increased seizure resistance in a dose-dependent manner. Our findings show that Drosophila single-cell expression data and behavior can aid functional validation of human GCNs and highlight a role for metabolism in modifying seizure susceptibility. SUMMARY STATEMENTIntegrating Drosophila single-cell RNA-sequencing data with seizure-like behavior and metabolic rate assays, we functionally characterized a human epilepsy-associated gene network, revealing metabolic regulation as a critical factor underlying seizure susceptibilities.

neuroscience↗

bioRxiv2022

Intellectual disability-associated disruption of O-GlcNAcylation impairs neuronal development and cognitive function in Drosophila

O-GlcNAcylation is a reversible co-/post-translational modification involved in a multitude of cellular processes. The addition and removal of O-GlcNAc modification is controlled by two conserved enzymes, O-GlcNAc transferase (OGT) and O-GlcNAc hydrolase (OGA). Mutations in OGT have recently been discovered to cause a novel Congenital Disorder of Glycosylation (OGT-CDG) that is characterized by intellectual disability. The mechanisms by which OGT-CDG mutations affect cognition remain unclear. We manipulated O-GlcNAc transferase and O-GlcNAc hydrolase activity in Drosophila and demonstrate an important role of O-GlcNAcylation in habituation learning and synaptic development at the larval neuromuscular junction. Introduction of patient-specific missense mutations into Drosophila O-GlcNAc transferase using CRISPR/Cas9 gene editing, leads to deficits in locomotor function and habituation learning. The habituation deficit can be corrected by blocking O-GlcNAc hydrolysis, indicating that OGT-CDG mutations affect cognitive function via reduced protein O-GlcNAcylation. This study establishes a critical role for O-GlcNAc cycling and disrupted O-GlcNAc transferase activity in cognitive dysfunction. These findings suggest that blocking O-GlcNAc hydrolysis is a potential treatment strategy for OGT-CDG. Author summaryAttachment of single N-acetylglucosamine (GlcNAc) sugars to intracellular proteins has recently been linked to neurodevelopment and cognition. This link has been strengthened by discovery of O-GlcNAc transferase (OGT) missense mutations in intellectual disability. Most of these mutations lie outside the catalytic O-GlcNAc transferase domain and it is unclear how they affect cognitive function. Using the fruit fly Drosophila melanogaster as a model organism, we found that a balance in O-GlcNAc cycling is required for learning and neuronal development. Habituation, a fundamental form of learning, is affected in flies that carry patient-specific OGT mutations, and increasing O-GlcNAcylation genetically corrects the habituation deficit. Our work establishes a critical role for O-GlcNAc cycling in a cognition-relevant process, identifies defective O-GlcNAc transferase activity as a cause of intellectual disability, and proposes underlying mechanisms that can be further explored as treatment targets.

genetics↗

bioRxiv2019

From rare Copy Number Variations to biological processes in ADHD

AimAttention-deficit/hyperactivity disorder (ADHD) is a highly heritable psychiatric disorder. The objective of this study was to define ADHD-associated candidate genes, and their associated molecular modules and biological themes, based on the analysis of rare genetic variants.\n\nMethodsWe combined data from 11 published copy number variation (CNV) studies in 6176 individuals with ADHD and 25026 controls and prioritized genes by applying an integrative strategy based on criteria including recurrence in ADHD individuals, absence in controls, complete coverage in copy number gains, and presence in the minimal region common to overlapping CNVs, as well as on protein-protein interactions and information from cross-species genotype-phenotype annotation.\n\nResultsWe localized 2241 eligible genes in the 1532 reported CNVs, of which we classified 432 as high-priority ADHD candidate genes. The high-priority ADHD candidate genes were significantly co-expressed in the brain. A network of 66 genes was supported by ADHD-relevant phenotypes in the cross-species database. In addition, four significantly interconnected protein modules were found among the high-priority ADHD genes. A total of 26 genes were observed across all applied bioinformatic methods. Look-up in the latest genome-wide association study for ADHD showed that among those 26, POLR3C and RBFOX1 were also supported by common genetic variants.\n\nConclusionsIntegration of a stringent filtering procedure in CNV studies with suitable bioinformatics approaches can identify ADHD candidate genes at increased levels of credibility. Our pipeline provides additional insight in the molecular mechanisms underlying ADHD and allows prioritization of genes for functional validation in validated model organisms.

genetics↗

bioRxiv2019

Intellectual Disability-related genes increase ADHD risk and locomotor activity in Drosophila

ObjectiveAttention-Deficit/Hyperactivity Disorder (ADHD) is a common, highly heritable neuropsychiatric disorder. ADHD often co-occurs with Intellectual Disability (ID), and shared overlapping genetics have been suggested. This study aimed to identify novel ADHD genes by investigating whether genes carrying rare mutations linked to ID contribute to ADHD risk through common genetic variants. Validation and characterization of candidates were performed using Drosophila melanogaster.\n\nMethodCommon genetic variants in a diagnostic gene panel of 396 autosomal ID genes were tested for association with ADHD risk, through gene-set and gene-wide analyses, using ADHD meta-analytic data of the Psychiatric Genomics Consortium (n=19,210) for discovery and iPSYCH ADHD data for replication (n=37,076). The significant genes were functionally validated and characterized in Drosophila by assessing locomotor activity and sleep upon knockdown of those genes in brain circuits.\n\nResultsThe ID gene-set was significantly associated with ADHD risk in the discovery and replication data-sets. The three genes most consistently associated were MEF2C, ST3GAL3, and TRAPPC9. Performing functional characterization of the two evolutionary conserved genes in Drosophila melanogaster, we found their knockdown in dopaminergic (dMEF2) and circadian neurons (dTRAPPC9) to result in increased locomotor activity and reduced sleep, concordant with the human phenotype.\n\nConclusionsThis study reveals that a large set of ID-related genes contributes to ADHD risk through effects of common alleles. Utilizing this continuity, we identified TRAPPC9, MEF2C, and ST3GAL3 as novel ADHD candidate genes. Characterization in Drosophila suggests that TRAPPC9 and MEF2C contribute to ADHD-related behavior through distinct neural substrates.

genetics↗

bioRxiv2018

Integrative Network and Brain Expression Analysis reveals Mechanistic Modules in Ataxia

Background: Genetic forms of ataxia are a heterogenous group of degenerative diseases of the cerebellum. Many causative genes have been identified, but a systematic investigation of these genes to understand ataxia pathophysiology has not been performed. Methods: A manually curated catalogue of 71 genes involved in disorders with progressive ataxias as a major clinical feature was subjected to an integrated gene ontology (GO), protein network, and brain gene expression profiling analysis. Results: We found that ataxia genes operate in networks with significantly enriched protein connectivity, demonstrating coherence on a global level, independent of inheritance mode. Moreover, elevated expression specifically in the cerebellum predisposes to ataxia. Genes expressed in this pattern are significantly overrepresented among ataxia genes and are enriched for ion homeostasis/synaptic functions. The majority of ataxia genes, however, does not show elevated cerebellar expression that could account for region-specific degeneration. For these, we identified defective cellular stress responses as a major common biological theme, suggesting that the defense pathways against stress are more critical to maintain cerebellar integrity than integrity of other brain regions. Approximately half of the ataxia genes, mostly part of the stress module, show higher expression at embryonic stages, which argues for a developmental predisposition. Conclusion: Genetic defects in ataxia predominantly affect neuronal homeostasis, to which the cerebellum appears to be excessively susceptible. Based on the identified modules, it is conceivable to propose common therapeutic interventions that target deregulated calcium and ROS levels, or mechanisms that can decrease the harmful downstream effects of these deleterious insults.

neuroscience↗

bioRxiv2018

Integrative cross-species analyses identify deficits in habituation learning as a widely affected mechanism in Autism

BackgroundAlthough habituation is one of the most ancient and fundamental forms of learning, its regulators and relevance for human disease are poorly understood.\n\nMethodsWe manipulated the orthologs of 286 genes implicated in intellectual disability (ID) with or without comorbid autism spectrum disorder (ASD) specifically in Drosophila neurons, and tested these models in light-off jump habituation. We dissected neuronal substrates underlying the identified habituation deficits and integrated genotype-phenotype annotations, gene ontologies and interaction networks to determine the clinical features and molecular processes that are associated with habituation deficits.\n\nResultsWe identified more than 100 genes required for habituation learning. For the vast majority of these, 93 genes, a role in habituation learning was previously unknown. These genes characterize ID disorders with overgrowth/macrocephaly and comorbid ASD. Moreover, ASD individuals from the Simons Simplex Collection carrying disruptive de novo mutations in these genes exhibit increased rates of specific aberrant behaviors including stereotypic speech, hyperactivity and irritability. At the molecular level, ID genes required for normal habituation are enriched in synaptic function and converge on Ras-MAPK signaling. Both increased Ras-MAPK signaling in GABAergic and decreased Ras-MAPK signaling in cholinergic neurons specifically inhibit the adaptive habituation response.\n\nConclusionsOur work demonstrates the relevance of habituation learning to autism, identifies an unprecedented number of novel habituation players, supports an emerging role for inhibitory neurons in habituation and reveals an opposing, circuit-level-based mechanism for Ras-MAPK signaling. This establishes habituation as a possible, widely applicable target for pharmacologic intervention in ID/ASD.

neuroscience↗