Protein instability, haploinsufficiency, and cortical hyper-excitability underlie STXBP1 encephalopathy

Kovačević, Jovana; Maroteaux, Gregoire; Schut, Desiree; Loos, Maarten; Dubey, Mohit; Pitsch, Julika; Remmelink, Esther; Koopmans, Bastijn; Crowley, James J.; Cornelisse, L. Niels; Sullivan, Patrick F.; Schoch, Susanne; Toonen, Ruud F.; Stiedl, Oliver; Verhage, Matthijs

doi:10.1093/brain/awy046

Cited by 100 publications

(135 citation statements)

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“…Munc18-1 and Dyrk1a play an important role in brain development 6,29 . Both Munc18-1 and Dyrk1a haploinsufficiency cause seizures in human patients 8,11 and mice 12,34 . For example, mice deficient in Munc18-1 as well as Dyrk1a display seizures and cognitive deficiencies 12,34 .…”

Section: Discussionmentioning

confidence: 99%

“…Both Munc18-1 and Dyrk1a haploinsufficiency cause seizures in human patients 8,11 and mice 12,34 . For example, mice deficient in Munc18-1 as well as Dyrk1a display seizures and cognitive deficiencies 12,34 . De novo mutations in DYRK1A are found in 0.1-0.5% of people with autism 50 and about 0.5% of people with syndromic forms of ID 51 .…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, mutations in Dyrk1a are linked to other forms of ID 9 , similar to mutations in STXBP1/Munc18-1 11 . Mouse models for Dyrk1a and STXBP1 haploinsufficiency show similar autistic-like features and seizures 12,34 , and full deletion of both Dyrk1a and Munc18-1 is embryonically lethal 6,35 . Dyrk1a knockout mice are lethal because phosphorylation of Hip-1 blocks neuronal cell death in neural progenitor cells and promotes neurite outgrowth 36 .…”

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A Munc18-1 mutant mimicking phosphorylation by Down Syndrome-related kinase Dyrk1a supports normal synaptic transmission and promotes recovery after intense activity

Classen¹,

Saarloos²,

Meijer³

et al. 2020

Sci Rep

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Phosphorylation of Munc18 -1 (Stxbp1), a presynaptic organizer of synaptic vesicle fusion, is a powerful mechanism to regulate synaptic strength. Munc18-1 is a proposed substrate for the Down Syndromerelated kinase dual-specificity tyrosine phosphorylation-regulate kinase 1a (Dyrk1a) and mutations in both genes cause intellectual disability. However, the functional consequences of Dyrk1a-dependent phosphorylation of Munc18-1 for synapse function are unknown. Here, we show that the proposed Munc18-1 phosphorylation site, T479, is among the highly constrained phosphorylation sites in the coding regions of the gene and is also located within a larger constrained coding region. We confirm that Dyrk1a phosphorylates Munc18-1 at T479. Patch-clamp physiology in conditional null mutant hippocampal neurons expressing Cre and either wildtype, or mutants mimicking or preventing phosphorylation, revealed that synaptic transmission is similar among the three groups: frequency/ amplitude of mEPSCs, evoked EPSCs, paired pulse plasticity, rundown kinetics upon intense activity and the readily releasable pool. However, synapses expressing the phosphomimic mutant responded to intense activity with more pronounced facilitation. These data indicate that Dyrk1a-dependent Munc18-1 phosphorylation has a minor impact on synaptic transmission, only after intense activity, and that the role of genetic variation in both genes in intellectual disability may be through different mechanisms.Post-translational modification of synaptic proteins is a powerful way to regulate synaptic strength. Phosphorylation is probably the most well-studied mechanism of regulation of synaptic protein function. Many synaptic proteins have been identified in large-scale phospho-proteomics screens 1-4 , although the kinase and the function of the phosphorylation are often unknown. Presynaptic proteins (e.g. Synapsin, SNAP25, synaptotagmins, and Munc18) are phosphorylated by abundant (not neuro-specific) kinases like protein kinase C (PKC) and protein kinase A (PKA) and these modifications impact on synaptic transmission in a variety of ways (see review 5 ). However, many more (potential) phosphorylation sites in synaptic proteins are reported, for which the impact is unknown.Munc18-1 is a major regulator of synaptic transmission and among the best validated presynaptic phosphorylation targets. Loss of Munc18-1 in neurons leads to a loss of neurotransmitter release and cell death in vivo 6 and in vitro 7 . Munc18-1 null neurons survive for 4 days in culture but are subsequently unable to support viability 7 . The MUNC-18 gene in human is STXBP1, and exonic mutations in STXBP1 have been reported to cause STXBP1-encephalopathy, characterized by severe intellectual disability (ID), spasms, and epilepsy [8][9][10][11] . Many of these clinical symptoms are also observed in Stxbp1 mouse models of STXBP1-encephalopathy 12 .Several potential phosphorylation sites of Munc18-1 have been found 1 or predicted 13 . To date, all confirmed phosphorylation sites have major impact...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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A Munc18-1 mutant mimicking phosphorylation by Down Syndrome-related kinase Dyrk1a supports normal synaptic transmission and promotes recovery after intense activity

Classen¹,

Saarloos²,

Meijer³

et al. 2020

Sci Rep

Self Cite

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“…Many candidate gene sets may also be imperfect. For example, STXBP1 is a well known presynaptic gene 65,66 , but occurs in the significantly enriched PSD_Bayes2011 67 gene set. However, gTADA is a model-based analysis of DN and CC variant data; therefore, the top prioritized genes are generally supported by the DN and CC data, not solely from reference data sets ( Figure S8).…”

Section: Discussionmentioning

confidence: 99%

Integrative analysis of rare variants and pathway information shows convergent results between immune pathways, drug targets and epilepsy genes

Dobbyn

et al. 2018

Preprint

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Trio family and case-control studies of next-generation sequencing data have proven integral to understanding the contribution of rare inherited and de novo single-nucleotide variants to the genetic architecture of complex disease. Ideally, such studies should identify individual risk genes of moderate to large effect size to generate novel treatment hypotheses for further follow-up. However, due to insufficient power, gene set enrichment analyses have come to be relied upon for detecting differences between cases and controls, implicating sets of hundreds of genes rather than specific targets for further investigation. Here, we present a Bayesian statistical framework, termed gTADA, that integrates gene-set membership information with gene-level de novo and rare inherited case-control counts, to prioritize risk genes with excess rare variant burden within enriched gene sets. Applying gTADA to available whole-exome sequencing datasets for several neuropsychiatric conditions, we replicated previously reported gene set enrichments and identified novel risk genes. For epilepsy, gTADA prioritized 40 risk genes (posterior probabilities > 0.95), 6 of which replicate in an independent whole-genome sequencing study. In addition, 30/40 genes are novel genes. We found that epilepsy genes had high protein-protein interaction (PPI) network connectivity, and show specific expression during human brain development. Some of the top prioritized EPI genes were connected to a PPI subnetwork of immune genes and show specific expression in prenatal microglia. We also identified multiple enriched drug-target gene sets for EPI which included immunostimulants as well as known antiepileptics. Immune biology was supported specifically by case-control variants from familial epilepsies rather than do novo mutations in generalized encephalitic epilepsy. meta-analyzing DNMs and rare case-control (CC) variants, an approach that has been particularly successful for autism spectrum disorders (ASD) 9,10 . For epilepsy (EPI), multiple associated genes have been identified through DN based studies 4,5,11 , and in recent years, a number of EPI significant genes have also been identified through CC studies 12,13 . We hypothesized that, as for ASD, additional significant EPI genes could be discovered through the integration of DN and CC data. EPI is a serious brain disorder which includes multiple subtypes. Studies of cases/controls and twins have shown that genetic components have played important roles in EPI [14][15][16] . Some of EPI's subtypes can be explained by single genes, but multiple subtypes might be caused by multiple genes 15 . It is still challenging to develop specific drugs for this disorder. There have been multiple antiepileptic drugs used for EPI treatments; however, 20-30% of EPI patients have not been successful in controlling their seizures by using current medications 17 . Identifying additional genes or gene sets might help better understand its etiology as well as better design drug targets for the disorder.Due to the high p...

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“…In STXBP1 null mutant mice, NT release is completely blocked 51 . Recently, heterozygous Stxbp1+/-mice models were developed that recapitulate the seizure/spasm phenotype observed in humans 52 .…”

Section: Main Textmentioning

confidence: 99%

Structural analysis ofde novoSTXBP1 mutation in complex with syntaxin 1A reveals a major alteration in the interaction interface in a child with developmental delay and spasticity

Banne

Falik‐Zaccai

Brielle

et al. 2019

Preprint

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STXBP1, also known as Munc-18, is a master regulator of neurotransmitter release and synaptic function in the human brain through its direct interaction with syntaxin 1A. STXBP1 related disorders are well characterized and cover a diverse range of neurological and neurodevelopmental conditions. Through exome sequencing of a child with developmental delay, hypotonia and spasticity, we found a novel de novo insertion mutation of three nucleotides in the STXBP1 coding region, resulting in an additional arginine after position 39 (R39dup).Inconclusive results from state-of-the-art variant prediction tools mandated a structure-based approach using molecular dynamics (MD) simulations of the STXBP1-syntaxin 1A complex.Comparison of the interaction interfaces of the wild type and the R39dup complexes revealed a reduced interaction surface area in the mutant, leading to destabilization of the interaction. We applied the same MD methodology to 7 additional previously reported STXBP1 mutations. We find that the stability of the STXBP1-syntaxin 1A interface correlates with the reported clinical phenotypes. We illustrate a direct link between a patient's genetic variations and the observed clinical phenotype through protein structure, dynamics, and function.

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Protein instability, haploinsufficiency, and cortical hyper-excitability underlie STXBP1 encephalopathy

Cited by 100 publications

References 82 publications

A Munc18-1 mutant mimicking phosphorylation by Down Syndrome-related kinase Dyrk1a supports normal synaptic transmission and promotes recovery after intense activity

A Munc18-1 mutant mimicking phosphorylation by Down Syndrome-related kinase Dyrk1a supports normal synaptic transmission and promotes recovery after intense activity

Integrative analysis of rare variants and pathway information shows convergent results between immune pathways, drug targets and epilepsy genes

Structural analysis ofde novoSTXBP1 mutation in complex with syntaxin 1A reveals a major alteration in the interaction interface in a child with developmental delay and spasticity

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