Reduced MUNC18-1 Levels, Synaptic Proteome Changes, and Altered Network Activity in STXBP1-Related Disorder Patient Neurons

Background: STXBP1-related disorder (STXBP1-RD) is a neurodevelopmental disorder caused by pathogenic variants in the STXBP1 gene. Its gene product MUNC18-1 organizes synaptic vesicle exocytosis and is essential for synaptic transmission. Patients present with developmental delay, intellectual disability, and/or epileptic seizures, with high clinical heterogeneity. To date, the cellular deficits of neurons of patients with STXBP1-RD are unknown. Methods: We combined live-cell imaging, electrophysiology, confocal microscopy, and mass spectrometry proteomics to characterize cellular phenotypes of induced pluripotent stem cell–derived neurons from 6 patients with STXBP1-RD, capturing shared features as well as phenotypic diversity among patients. Results: Neurons from all patients showed normal in vitro development, morphology, and synapse formation, but reduced MUNC18-1 RNA and protein levels. In addition, a proteome-wide screen identified dysregulation of proteins related to synapse function and RNA processes. Neuronal networks showed shared as well as patient-specific phenotypes in activity frequency, network irregularity, and synchronicity, especially when networks were challenged by increasing excitability. No shared effects were observed in synapse physiology of single neurons except for a few patient-specific phenotypes. Similarities between functional and proteome phenotypes suggested 2 patient clusters, not explained by gene variant type. Conclusions: Together, these data show that decreased MUNC18-1 levels, dysregulation of synaptic proteins, and altered network activity are shared cellular phenotypes of STXBP1-RD. The 2 patient clusters suggest distinctive pathobiology among subgroups of patients, providing a plausible explanation for the clinical heterogeneity. This phenotypic spectrum provides a framework for future validation studies and therapy design for STXBP1-RD

The adult human subventricular zone: partial ependymal coverage and proliferative capacity of cerebrospinal fluid

Neurogenesis continues throughout adulthood in specialized regions of the brain. One of these regions is the subventricular zone. During brain development, neurogenesis is regulated by a complex interplay of intrinsic and extrinsic cues that control stem-cell survival, renewal and cell lineage specification. Cerebrospinal fluid (CSF) is an integral part of the neurogenic niche in development as it is in direct contact with radial glial cells, and it is important in regulating proliferation and migration. Yet, the effect of CSF on neural stem cells in the subventricular zone of the adult human brain is unknown. We hypothesized a persistent stimulating effect of ventricular CSF on neural stem cells in adulthood, based on the literature, describing bulging accumulations of subventricular cells where CSF is in direct contact with the subventricular zone. Here, we show by immunohistochemistry on post-mortem adult human subventricular zone sections that neural stem cells are in close contact with CSF via protrusions through both intact and incomplete ependymal layers. We are the first to systematically quantify subventricular glial nodules denuded of ependyma and consisting of proliferating neural stem and progenitor cells, and showed that they are present from foetal age until adulthood. Neurosphere, cell motility and differentiation assays as well as analyses of RNA expression were used to assess the effects of CSF of adult humans on primary neural stem cells and a human immortalized neural stem cell line. We show that human ventricular CSF increases proliferation and decreases motility of neural stem cells. Our results also indicate that adult CSF pushes neural stem cells from a relative quiescent to a more active state and promotes neuronal over astrocytic lineage differentiation. Thus, CSF continues to stimulate neural stem cells throughout aging

The Price of Prominence: STXBP1/MUNC18-1 in brain (dys)function

Neuronal functioning and viability strongly depend on presynaptic protein MUNC18-1. In absence of MUNC18-1, mouse neurons die, which is independent from its known function in synaptic transmission. Pathogenic variants in its gene, STXBP1, are among the most common associated with developmental delay and epilepsy. The general aim of this thesis was to gain more insight in why MUNC18-1 is such an essential protein in neurons beyond synaptic transmission, and how pathogenic variants lead to disease. In Chapter 2, we investigated which cell death pathway(s) are involved in MUNC18-1 and syntaxin-1-dependent degeneration. We show that the last stages before cell death are characterized by gradual loss of neurites, which is not observed in other well-characterized forms of neuronal cell death. In the final stage, neurons express markers associated with apoptosis, yet inhibition of apoptosis is insufficient to halt cell death. We conclude that depletion of MUNC18-1 or syntaxin-1 leads to atypical cell death ultimately involving, but not driven by, apoptosis. In Chapter 3, we examined which biological pathways critically depend on MUNC18-1. We show that absence of MUNC18-1 results in extensive remodelling of the neuronal transcriptome and proteome. Dysregulated proteins are primarily involved in neuron development and synapse function. Many of the downregulated proteins are normally upregulated during early development. Thus, MUNC18-1 may act as a critical regulator of developmental and synaptic protein expression in immature neurons. In Chapter 4, we investigated whether loss of MUNC18-1 leads to defects in membrane transport routes, which may explain the observed abnormal Golgi morphology and degeneration in null neurons. We conclude that loss of MUNC18-1 leads to defects in retro- but not anterograde membrane trafficking pathways, which provides a plausible explanation for the abnormal Golgi morphology. In Chapter 5, we investigated the cellular phenotype of the first homozygous STXBP1 variant reported in patients. Neurons expressing L446F demonstrate a two-fold increase in evoked synaptic transmission. We conclude that the homozygous L446F variant leads to an opposing cellular phenotype than previously reported for heterozygous variants, yet results in comparable clinical symptoms. In Chapter 6, we developed a gene-tailored in silico classifier which predicts pathogenicity with high confidence, and outperforms currently available (generic) classifiers. Next, we examined which biological features are predictive for pathogenicity. We show in an allelic series of variants that protein instability, reduced MUNC18-1 expression levels and impaired function in SNARE fusion are shared features of pathogenic variants. The scores from the in silico classifier highly correlate to the experimental data. Thus, this extendable framework increased pathogenicity prediction of MUNC18-1 variants and improved understanding on underlying disease mechanisms. In Chapter 7, we evaluated commonly used designs involved iPSC-based disease models in terms of the research questions they address, statistical analysis and power considerations. We show that culture batch and interindividual variation contributes to overall experimental variation and should be taken into account in the statistical analysis. To foster future study designs, we deliver a web application to enable researchers to perform power analyses on their own data. In Chapter 8, we studied cellular phenotypes of iPSC-derived neurons from six STXBP1-Syndrome patients. We show that patient neurons present lower MUNC18-1 levels as well as dysregulation of many other proteins related to synapse function. Neuronal networks demonstrate altered frequency, network irregularity and synchronicity, whereas synapse physiology of single neurons is unaffected. We conclude that reduced MUNC18-1 levels, dysregulation of synaptic proteins and altered network activity are shared cellular phenotypes of STXBP1- Syndrome neurons. Taken together, we now better understand when variants in STXBP1 are disease-causing or neutral, and how these variants affect neuronal functioning

Cognitive benefits of the ketogenic diet in patients with epilepsy: A systematic overview

The ketogenic diet (KD) has been found to be effective in reducing seizures in patients with treatment-refractory epilepsy. Less attention has been paid to additional cognitive benefits of KD. The aim of the present paper was to provide a comprehensive overview of the studies reporting effects on cognition after KD treatment in adults and children with epilepsy. To address this aim, the clinical literature on cognitive effects of KD in patients with epilepsy was reviewed using a systematic approach. We conclude that using subjective assessments of the patient's experience, cognitive improvements are frequently reported during KD treatment in the domains of alertness, attention, and global cognition. Studies that used objective neuropsychological tests confirmed benefits on alertness but found no improvement in global cognition. There are indications that these improvements are caused by both seizure reduction and direct effects of KD on cognition. The improvements appear to be unrelated to medication reduction, age when KD is started, type of KD, and sleep improvement. The findings in the present overview contribute to a better understanding of the beneficial effects of KD in patients with epilepsy

An Atypical, Staged Cell Death Pathway Induced by Depletion of SNARE-Proteins MUNC18-1 or Syntaxin-1

The presynaptic proteins MUNC18-1, syntaxin-1, and SNAP25 drive SNARE-mediated synaptic vesicle fusion and are also required for neuronal viability. Their absence triggers rapid, cell-autonomous, neuron-specific degeneration, unrelated to synaptic vesicle deficits. The underlying cell death pathways remain poorly understood. Here, we show that hippocampi of munc18-1 null mice (unknown sex) express apoptosis hallmarks cleaved caspase 3 (CC-3) and phosphorylated p53, and have condensed nuclei. However, side-by-side in vitro comparison with classical apoptosis induced by camptothecin uncovered striking differences to syntaxin-1 and MUNC18-1 depleted neurons. First, live-cell imaging revealed consecutive neurite retraction hours before cell death in MUNC18-1 or syntaxin-1 depleted neurons, whereas all neurites retracted at once, directly before cell death in classical apoptosis. Second, CC-3 activation was observed only after loss of all neurites and cellular breakdown, whereas CC-3 is activated before any neurite loss in classical apoptosis. Third, a pan-caspase inhibitor and a p53 inhibitor both arrested classical apoptosis, as expected, but not cell death in MUNC18-1 or syntaxin-1 depleted neurons. Neuron-specific cell death, consecutive neurite retraction, and late CC-3 activation were conserved in syntaxin-1 depleted human neurons. Finally, no indications were observed for involvement of other established cell death pathways, including necroptosis, Wallerian degeneration, autophagic cell death, and pyroptosis. Together, these data show that depletion of presynaptic proteins MUNC18-1 or syntaxin-1 triggers an atypical, staged cell death pathway characterized by consecutive neurite retraction, ultimately leading to, but not driven by, apoptosis

An Atypical, Staged Cell Death Pathway Induced by Depletion of SNARE-Proteins MUNC18-1 or Syntaxin-1

The presynaptic proteins MUNC18-1, syntaxin-1, and SNAP25 drive SNARE-mediated synaptic vesicle fusion and are also required for neuronal viability. Their absence triggers rapid, cell-autonomous, neuron-specific degeneration, unrelated to synaptic vesicle deficits. The underlying cell death pathways remain poorly understood. Here, we show that hippocampi of munc18-1 null mice (unknown sex) express apoptosis hallmarks cleaved caspase 3 (CC-3) and phosphorylated p53, and have condensed nuclei. However, side-by-side in vitro comparison with classical apoptosis induced by camptothecin uncovered striking differences to syntaxin-1 and MUNC18-1 depleted neurons. First, live-cell imaging revealed consecutive neurite retraction hours before cell death in MUNC18-1 or syntaxin-1 depleted neurons, whereas all neurites retracted at once, directly before cell death in classical apoptosis. Second, CC-3 activation was observed only after loss of all neurites and cellular breakdown, whereas CC-3 is activated before any neurite loss in classical apoptosis. Third, a pan-caspase inhibitor and a p53 inhibitor both arrested classical apoptosis, as expected, but not cell death in MUNC18-1 or syntaxin-1 depleted neurons. Neuron-specific cell death, consecutive neurite retraction, and late CC-3 activation were conserved in syntaxin-1 depleted human neurons. Finally, no indications were observed for involvement of other established cell death pathways, including necroptosis, Wallerian degeneration, autophagic cell death, and pyroptosis. Together, these data show that depletion of presynaptic proteins MUNC18-1 or syntaxin-1 triggers an atypical, staged cell death pathway characterized by consecutive neurite retraction, ultimately leading to, but not driven by, apoptosis.SIGNIFICANCE STATEMENT Neuronal cell death can occur via a multitude of pathways and plays an important role in the developing nervous system as well as neurodegenerative diseases. One poorly understood pathway to neuronal cell death takes place on depletion of presynaptic SNARE proteins syntaxin-1, SNAP25, or MUNC18-1. The current study demonstrates that MUNC18-1 or syntaxin-1 depleted neurons show a new, atypical, staged cell death that does not resemble any of the established cell death pathways in neurons. Cell death on MUNC18-1 or syntaxin-1 depletion is characterized by consecutive neurite retraction, ultimately involving, but not driven by, classical apoptosis

Loss of MUNC18-1 leads to retrograde transport defects in neurons

Loss of the exocytic Sec1/MUNC18 protein MUNC18-1 or its target-SNARE partners SNAP25 and syntaxin-1 results in rapid, cell-autonomous and unexplained neurodegeneration, which is independent of their known role in synaptic vesicle exocytosis. cis-Golgi abnormalities are the earliest cellular phenotypes before degeneration occurs. Here, we investigated whether loss of MUNC18-1 causes defects in intracellular membrane transport pathways in primary murine neurons that may explain neurodegeneration. Electron, confocal and super resolution microscopy confirmed that loss of MUNC18-1 expression results in a smaller cis-Golgi. In addition, we now show that medial-Golgi and the trans-Golgi Network are also affected. However, stacking and cisternae ultrastructure of the Golgi were normal. Overall, ultrastructure of null mutant neurons was remarkably normal just hours before cell death occurred. By synchronizing protein trafficking by conditional cargo retention in the endoplasmic reticulum using selective hooks (RUSH) and immunocytochemistry, we show that anterograde Endoplasmic Reticulum-to-Golgi and Golgi exit of endogenous and exogenous proteins were normal. In contrast, loss of MUNC18-1 caused reduced retrograde Cholera Toxin B-subunit transport from the plasma membrane to the Golgi. In addition, MUNC18-1-deficiency resulted in abnormalities in retrograde TrkB trafficking in an antibody uptake assay. We conclude that MUNC18-1 deficient neurons have normal anterograde but reduced retrograde transport to the Golgi. The impairments in retrograde pathways suggest a role of MUNC18-1 in endosomal SNARE-dependent fusion and provide a plausible explanation for the observed Golgi abnormalities and cell death in MUNC18-1 deficient neurons. (Figure presented.)

Homozygous STXBP1 variant causes encephalopathy and gain-of-function in synaptic transmission

none8siHeterozygous mutations in the STXBP1 gene encoding the presynaptic protein MUNC18-1 cause STXBP1 encephalopathy, characterized by developmental delay, intellectual disability and epilepsy. Impaired mutant protein stability leading to reduced synaptic transmission is considered the main underlying pathogenetic mechanism. Here, we report the first two cases carrying a homozygous STXBP1 mutation, where their heterozygous siblings and mother are asymptomatic. Both cases were diagnosed with Lennox-Gastaut syndrome. In Munc18-1 null mouse neurons, protein stability of the disease variant (L446F) is less dramatically affected than previously observed for heterozygous disease mutants. Neurons expressing Munc18L446F showed minor changes in morphology and synapse density. However, patch clamp recordings demonstrated that L446F causes a 2-fold increase in evoked synaptic transmission. Conversely, paired pulse plasticity was reduced and recovery after stimulus trains also. Spontaneous release frequency and amplitude, the readily releasable vesicle pool and the kinetics of short-term plasticity were all normal. Hence, the homozygous L446F mutation causes a gain-of-function phenotype regarding release probability and synaptic transmission while having less impact on protein levels than previously reported (heterozygous) mutations. These data show that STXBP1 mutations produce divergent cellular effects, resulting in different clinical features, while sharing the overarching encephalopathic phenotype (developmental delay, intellectual disability and epilepsy).mixedLammertse H.C.A.; Van Berkel A.A.; Iacomino M.; Toonen R.F.; Striano P.; Gambardella A.; Verhage M.; Zara FLammertse, H. C. A.; Van Berkel, A. A.; Iacomino, M.; Toonen, R. F.; Striano, P.; Gambardella, A.; Verhage, M.; Zara,

Age-related loss of axonal regeneration is reflected by the level of local translation.

Regeneration capacity is reduced as CNS axons mature. Using laser-mediated axotomy, proteomics and puromycin-based tagging of newly-synthesized proteins in a human embryonic stem cell-derived neuron culture system that allows isolation of axons from cell bodies, we show here that efficient regeneration in younger axons (d45 in culture) is associated with local axonal protein synthesis (local translation). Enhanced regeneration, promoted by co-culture with human glial precursor cells, is associated with increased axonal synthesis of proteins, including those constituting the translation machinery itself. Reduced regeneration, as occurs with the maturation of these axons by d65 in culture, correlates with reduced levels of axonal proteins involved in translation and an inability to respond by increased translation of regeneration promoting axonal mRNAs released from stress granules. Together, our results provide evidence that, as in development and in the PNS, local translation contributes to CNS axon regeneration