Astrocytes play a pivotal role in neuronal network development. Despite the well-known role of astrocytes in the pathophysiology of neurologic disorders, the utilization of induced pluripotent stem cell (iPSC)-derived astrocytes in neuronal networks remains limited. Here, we present a streamlined one-step protocol for the differentiation of iPSCs directly into functional astrocytes without the need for ectopic gene expression or neural progenitor cell generation. We found that culturing iPSCs directly in commercial astrocyte medium, was sufficient to differentiate iPSCs into functional astrocytes within 5 weeks. More than 60 iPSC lines were successfully differentiated into astrocytes by independent researchers across 10 independent laboratories. Validation of the iPSC-astrocyte cultures demonstrated consistent astrocyte differentiation with minimal batch-to-batch variability. In dept. characterization of a subset of iPSC lines confirmed astrocyte identity and functionality of the iPSC-astrocyte monocultures by immunofluorescence, flow cytometry, RNA sequencing, glutamate uptake assays and calcium signaling recordings. Optimization of the protocol enabled co-culture of iPSC-astrocytes with Ngn2 iPSC-derived neurons (iNeurons), promoting neuronal differentiation and synapse formation. Lastly, we used single-cell electrophysiology and multi-electrode arrays, by four independent researchers, to confirm robust neuronal network development in 5-week-old iPSC-astrocyte and iNeuron co-cultures. This protocol offers a rapid and efficient method to establish all-human astrocyte-neuron co-cultures, facilitating the investigation of cell-type-specific contributions to disease pathogenesis. Its validation across numerous iPSC lines in 10 independent laboratories highlights the reproducibility of the protocol and positions it as a platform for advancing disease modeling in human neural networks.

Kleefstra syndrome (KLEFS1) results from EHMT1 haploinsufficiency and is characterized by variable neurodevelopmental delays and psychopathology. Developmental regression, marked by the sudden loss of previously acquired daily life skills during late puberty or early adulthood, has emerged as a severe complication in individuals with KLEFS1. To investigate the clinical and molecular mechanisms underlying developmental regression and assess the therapeutic potential of olanzapine, we conducted a sequential study in an international cohort of 54 individuals with KLEFS1. Among 16 individuals treated with olanzapine, 10 exhibited a beneficial response based upon improvement of their adaptive functioning, and 4 showed temporary improvement. These clinical findings informed preclinical studies using human induced pluripotent stem cell-derived and ex-vivo cortical slices from a mouse model of KLEFS1. We identified hyperactivity in EHMT1+/- neuronal networks cocultured with EHMT1+/- astrocytes, a dysfunction reversible by olanzapine. Mechanistically, EHMT1+/- astrocytes displayed elevated levels of S100B, a neuroinflammatory marker contributing to neuronal network hyperactivity. Notably, olanzapine treatment reduced S100B levels, and pharmacological inhibition or genetic knockdown of S100B in EHMT1+/- astrocytes was sufficient to rescue the neuronal hyperactivity phenotype. These findings underscore a critical role for astrocytes in KLEFS1 pathophysiology and identify a potential cellular target for olanzapine in mitigating developmental regression.

Koolen-de Vries Syndrome (KdVS) is a neurodevelopmental disorder (NDD) caused by KANSL1 haploinsufficiency with no treatment options. To investigate neuronal network activity in KdVS, human induced pluripotent stem cell (hiPSC)-derived neurons from KdVS patients and controls were cultured on microelectrode arrays (MEAs). KdVS networks exhibited reduced burst rates and increased variability in burst rhythmicity. To bridge molecular and functional aspects of the syndrome, we applied MEA-seq, integrating electrophysiological recordings with high-throughput transcriptome profiling. This analysis revealed a negative correlation between the NDD-associated gene CLCN4 and network burst rate. Knockdown of CLCN4 in KdVS neurons restored network bursting toward control levels, highlighting how transcriptome profiling can identify mediators linking genetic defects to relevant physiological phenotypes. We also identified significant correlations between mitochondrial gene expression and network activity and consequently confirmed impaired mitochondrial function in KdVS hiPSC-derived neurons. Using the KdVS transcriptomic signature for computational screening against the LINCS drug perturbation database, we predicted compounds capable of reversing dysregulated gene expression. Ten candidates were prioritized for experimental validation, focusing on mitochondrial function. Among these, the antioxidant phloretin improved multiple aspects of the KdVS-related network activity phenotype, reduced reactive oxygen species, and rescued synaptic density across patient lines, revealing its potential as a therapeutic candidate. Together, these findings demonstrate that integrative MEA-seq profiling can connect molecular and electrophysiological alterations in KdVS, providing a robust framework for identifying novel drugs and druggable pathways for KdVS and potentially other neurodevelopmental disorders.

The capacity of neurons to maintain stable activity levels through homeostatic plasticity is essential for proper brain function. Primary cilia, which are non-motile, antenna-like organelles projecting from the surface of most vertebrate cells, serve as key hubs for signal transduction, playing crucial roles in tissue development and cellular homeostasis. In this study, we identify a previously unrecognised role for primary cilia in mediating neuronal homeostatic plasticity using human induced pluripotent stem cell-derived neurons. We show that neuronal cilia exhibit dynamic, bidirectional changes in volume in response to alterations in network activity: elongating during chronic activity suppression and shortening after increased activity. To assess the functional relevance of this ciliary plasticity, we modelled ciliary dysfunction in neurons carrying homozygous loss-of-function mutations in genes associated with neuronal ciliopathies, including NPHP1 and CEP290 . Mutations affecting ciliary function either increased ciliary length or led to ciliary loss, and these mutant neurons exhibited severe impairments in homeostatic regulation across multiple domains—morphological, functional, and transcriptional. Specifically, NPHP1 and CEP290 deficient neurons failed to adapt synaptic strength, intrinsic excitability, and ciliary morphology in response to prolonged activity suppression. They also displayed dysregulated baseline network activity, and exhibited blunted gene expression changes. Together, these findings establish the primary cilium as a critical regulator of homeostatic plasticity in human neurons and provide a new framework through which to examine neurodevelopmental and neuropsychiatric disorders linked to ciliary dysfunction. Key highlights ### Competing Interest Statement The authors have declared no competing interest. European Research Council, 861329 Dutch Research Council, NWO ENW-M2, OCENW.M20.216 Simons Foundation, 890042

Pyridoxine-dependent epilepsy (PDE) is a rare neurometabolic disorder of lysine catabolism caused by bi-allelic variants in ALDH7A1. This enzyme deficiency leads to accumulation of neurotoxic metabolites, pyridoxal-phosphate inactivation, and consequently severe neurological symptoms. Current treatments, including vitamin B6 supplementation and lysine-restricted diets, partially alleviate seizures and intellectual disability but are not curative. To explore underlying mechanisms and potential therapies, we generated patient-derived human induced pluripotent stem cell (hiPSC) lines that were subsequently differentiated into astrocytes, the primary source of ALDH7A1 in the brain and key regulators of metabolic homeostasis. Metabolomic analyses confirmed elevated PDE biomarkers, and RNA sequencing revealed gene expression changes consistent with increased oxidative stress. Oxidative damage was validated by markers of DNA oxidation, increased reactive oxygen species (ROS) levels, and lipid peroxidation. In addition, dysregulated oxygen consumption rates suggested mitochondrial dysfunction in PDE astrocytes. Notably, these pathological phenotypes were alleviated by downregulating alpha-aminoadipic semialdehyde synthase (AASS), the first enzyme of the lysine catabolism, by using CRISPR-Cas9 editing or antisense oligonucleotides (AONs). This demonstrates that lysine catabolism underlies these phenotypes and highlights the therapeutic potential of AON therapy targeting AASS to reduce neurotoxic metabolite accumulation. These findings provide a promising strategy for developing targeted treatments for PDE and other rare neurometabolic disorders.

Haploinsufficiency of CACNA1A, encoding the pore-forming α1 subunit of P/Q-type voltage-gated calcium channels, is associated with a clinically variable phenotype ranging from cerebellar ataxia to neurodevelopmental syndromes with epilepsy and intellectual disability. To understand the pathological mechanisms of CACNA1A loss-of-function variants, we characterized a human neuronal model for CACNA1A haploinsufficiency by differentiating isogenic induced pluripotent stem cell lines into glutamatergic neurons and investigated the effect of CACNA1A haploinsufficiency on mature neuronal networks through a combination of electrophysiology, gene expression analysis and in silico modelling. We observed an altered network synchronization in CACNA1A+/- networks alongside synaptic deficits, notably marked by an augmented contribution of GluA2 subunit-lacking α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. Intriguingly, these synaptic perturbations coexisted with increased non-synaptically driven activity, as characterized by inhibition of N-methyl-D-aspartate and AMPA receptors on micro-electrode arrays. Single-cell electrophysiology and gene expression analysis corroborated this increased intrinsic excitability through reduced potassium channel function and expression. Moreover, we observed partial mitigation of the CACNA1A+/- network phenotype by 4-aminopyridine, a therapeutic intervention for episodic ataxia type 2. Positive modulation of small conductance calcium-activated potassium channels could reverse the CACNA1A+/- network electrophysiological phenotype. In summary, our study pioneers the characterization of a human induced pluripotent stem cell-derived neuronal model for CACNA1A haploinsufficiency and has unveiled new mechanistic insights. Beyond showcasing synaptic deficits, this neuronal model exhibited increased intrinsic excitability mediated by diminished potassium channel function, underscoring its potential as a therapeutic discovery platform with predictive validity.

The relatively slow pace of cortical development in humans has long been a topic of investigation. Studies seeking to understand the underlying mechanisms have mostly focused on neurogenetic comparisons with extant species. Here we ask if developmental tempo differences may have also existed between us and our extinct relatives for whom genomes are available. To do so, we nominate a sapiens-specific derived allele, virtually fixed in contemporary populations, which resides in an enhancer region active during early cortical development. The single nucleotide variant is predicted to significantly affect CHD2 expression, a chromatin remodeler known to play an important role in neural development and for which haploinsufficiency is associated with epilepsy and autism. We leverage patient induced pluripotent stem lines (iPSC) and engineered iPSCs in which we reintroduced the ancestral allele and generated heterozygous loss-of-function mutations. We reveal that CHD2 deficiency impairs lysosomal acidification and autophagosome flux. In contrast, ancestralized lines, which we find express higher levels of CHD2, exhibit enhanced lysosomal function and consequently accelerated autophagosome flux, consistent with our observations in chimpanzee and bonobo lines. This set of findings demonstrates that CHD2 dosage critically regulates the autolysosomal pathway. Through deep phenotyping of cortical organoid and neuron cultures, we show that the CHD2-modulated autolysosomal pathway impacts the timing of developmental programs, acquisition of neuronal functional properties and circuit maturation. Finally, we validate an estrogen-dependent rewiring of CHD2 regulation in the evolution of our lineage, providing a mechanistic understanding of how a single nucleotide variant in a regulatory region contributed to the modern pace of neuronal development and maturation. Together, our findings establish CHD2 as a regulator in setting neurodevelopmental tempo via the autolysosomal pathway. ### Competing Interest Statement The authors have declared no competing interest.

GABAergic inhibition is essential for balanced brain function and is frequently disrupted in neurodevelopmental disorders such as autism spectrum disorder (ASD). The inhibition is generated by a diverse population of GABAergic interneurons, which differ in subtype composition and spatial density across the brain. Here, we applied an unbiased whole-brain clearing and light-sheet imaging approach to systematically map the distribution of the three major GABAergic interneuron subtypes – Parvalbumin-positive (PV⁺), Somatostatin-positive (SST⁺), and Vasoactive Intestinal Polypeptide-positive (VIP⁺) cells – across the mouse brain in a model of Kleefstra Syndrome ( Ehmt1+/− ), a monogenic intellectual disability disorder with a strong ASD component. Analyzing 895 brain regions we identified widespread, cell type– and region-specific alterations in GABAergic populations. Notably, we observed increased VIP⁺ neuron density in the Ehmt1+/− cortex and decreased SST⁺ neuron density in sensory cortical and subcortical regions. In the basolateral amygdala (BLA), PV⁺ interneurons exhibited precocious maturation already at the juvenile stage, which persisted into adulthood and was associated with enhanced inhibitory input onto BLA principal neurons. We here demonstrate that Ehmt1 haploinsufficiency results in region– and cell-type specific changes throughout the brain. These results underscore the value of whole-brain, high-resolution mapping approaches in uncovering previously unrecognized patterns of neural vulnerability in neurodevelopmental disorders. ### Competing Interest Statement The authors have declared no competing interest. Netherlands Organization for Scientific Research, NWO-CAS grant 012.200.001, NWA.1518.22.136 SCANNER Kleefstra Foundation

Astrocytes play a pivotal role in neuronal network development. Despite the well-known role of astrocytes in the pathophysiology of neurologic disorders, the utilization of human induced pluripotent stem cell (hiPSC)-derived astrocytes in neuronal networks remains limited. Here, we present a streamlined one-step protocol for the differentiation of hiPSCs directly into functional astrocytes without the need for ectopic gene expression or neural progenitor cell generation. We found that culturing hiPSCs directly in commercial astrocyte medium, was sufficient to differentiate hiPSCs into functional astrocytes within five weeks. Validation to varying extents across thirty hiPSC-lines demonstrated consistent astrocyte differentiation with minimal batch-to-batch variability. We confirmed astrocyte identity and functionality of the hiPSC-astrocyte monocultures by immunofluorescence, flowcytometry, RNA sequencing, glutamate uptake assays and calcium signaling recordings. Optimization of the protocol enabled co-culture of hiPSC-astrocytes with Ngn2 hiPSC-derived neurons (iNeurons), promoting neuronal differentiation and synapse formation. Lastly, we used single-cell electrophysiology and multi-electrode arrays to confirm robust neuronal network development in 5-week-old hiPSC-astrocyte and iNeuron co-cultures. This protocol offers a rapid and efficient method to establish all-human astrocyte-neuron co-cultures, facilitating the investigation of cell-type-specific contributions to disease pathogenesis. While validated across multiple hiPSC lines, we actively encourage researchers to test and provide feedback on this protocol to enhance its validation for future iterations.### Competing Interest StatementThe authors have declared no competing interest.

NPHP1 (Nephrocystin 1) is a protein that localizes to the transition zone of the cilium, a small organelle that projects from the plasma membrane of most cells and allows for integration and coordination of signalling pathways during development and homeostasis. Loss of NPHP1 function due to biallelic NPHP1 gene mutations can lead to the development of ciliopathies - a heterogeneous spectra of disorders characterized by ciliary dysfunction. Here we report the generation of an NPHP1-null hiPSC line (UCSFi001-A-68) via CRISPR/Cas9-mediated non-homologous end joining in the UCSFi001-A background, for study of the role that this protein plays in different tissues.

Summary Mechanisms that underlie homeostatic plasticity have been extensively investigated at single-cell levels in animal models, but are less well understood at the network level. Here, we used microelectrode arrays to characterize neuronal networks following induction of homeostatic plasticity in human induced pluripotent stem cell (hiPSC)-derived glutamatergic neurons co-cultured with rat astrocytes. Chronic suppression of neuronal activity through tetrodotoxin (TTX) elicited a time-dependent network re-arrangement. Increased expression of AMPA receptors and the elongation of axon initial segments were associated with increased network excitability following TTX treatment. Transcriptomic profiling of TTX-treated neurons revealed up-regulated genes related to extracellular matrix organization, while down-regulated genes related to cell communication; also astrocytic gene expression was found altered. Overall, our study shows that hiPSC-derived neuronal networks provide a reliable in vitro platform to measure and characterize homeostatic plasticity at network and single-cell level; this platform can be extended to investigate altered homeostatic plasticity in brain disorders.

Mechanisms that underlie homeostatic plasticity have been extensively investigated at single-cell levels in animal models, but are less well understood at the network level. Here, we used microelectrode arrays to characterize neuronal networks following induction of homeostatic plasticity in human induced pluripotent stem cell (hiPSC)-derived glutamatergic neurons co-cultured with rat astrocytes. Chronic suppression of neuronal activity through tetrodotoxin (TTX) elicited a time-dependent network re-arrangement. Increased expression of AMPA receptors and the elongation of axon initial segments were associated with increased network excitability following TTX treatment. Transcriptomic profiling of TTX-treated neurons revealed up-regulated genes related to extracellular matrix organization, while down-regulated genes related to cell communication; also astrocytic gene expression was found altered. Overall, our study shows that hiPSC-derived neuronal networks provide a reliable in vitro platform to measure and characterize homeostatic plasticity at network and single-cell levels; this platform can be extended to investigate altered homeostatic plasticity in brain disorders.

Macroautophagy (hereafter referred to as autophagy) is a finely tuned process of programmed degradation and recycling of proteins and cellular components, which is crucial in neuronal function and synaptic integrity. Mounting evidence implicates chromatin remodeling in fine-tuning autophagy pathways. However, this epigenetic regulation is poorly understood in neurons. Here, we investigate the role in autophagy of KANSL1, a member of the nonspecific lethal complex, which acetylates histone H4 on lysine 16 (H4K16ac) to facilitate transcriptional activation. Loss-of-function of KANSL1 is strongly associated with the neurodevelopmental disorder Koolen-de Vries Syndrome (KdVS). Starting from KANSL1-deficient human induced-pluripotent stem cells, both from KdVS patients and genome-edited lines, we identified SOD1 (superoxide dismutase 1), an antioxidant enzyme, to be significantly decreased, leading to a subsequent increase in oxidative stress and autophagosome accumulation. In KANSL1-deficient neurons, autophagosome accumulation at excitatory synapses resulted in reduced synaptic density, reduced GRIA/AMPA receptor-mediated transmission and impaired neuronal network activity. Furthermore, we found that increased oxidative stress-mediated autophagosome accumulation leads to increased MTOR activation and decreased lysosome function, further preventing the clearing of autophagosomes. Finally, by pharmacologically reducing oxidative stress, we could rescue the aberrant autophagosome formation as well as synaptic and neuronal network activity in KANSL1-deficient neurons. Our findings thus point toward an important relation between oxidative stress-induced autophagy and synapse function, and demonstrate the importance of H4K16ac-mediated changes in chromatin structure to balance reactive oxygen species- and MTOR-dependent autophagy. Abbreviations: APO: apocynin; ATG: autophagy related; BAF: bafilomycin A1; BSO: buthionine sulfoximine; CV: coefficient of variation; DIV: days in vitro; H4K16ac: histone 4 lysine 16 acetylation; iPSC: induced-pluripotent stem cell; KANSL1: KAT8 regulatory NSL complex subunit 1; KdVS: Koolen-de Vries Syndrome; LAMP1: lysosomal associated membrane protein 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MEA: micro-electrode array; MTOR: mechanistic target of rapamycin kinase; NSL complex: nonspecific lethal complex; 8-oxo-dG: 8-hydroxydesoxyguanosine; RAP: rapamycin; ROS: reactive oxygen species; sEPSCs: spontaneous excitatory postsynaptic currents; SOD1: superoxide dismutase 1; SQSTM1/p62: sequestosome 1; SYN: synapsin; WRT: wortmannin.

Activity in the healthy brain relies on a concerted interplay of excitation (E) and inhibition (I) via balanced synaptic communication between glutamatergic and GABAergic neurons. A growing number of studies imply that disruption of this E/I balance is a commonality in many brain disorders; however, obtaining mechanistic insight into these disruptions, with translational value for the patient, has typically been hampered by methodological limitations. Cadherin-13 (CDH13) has been associated with autism and attention-deficit/hyperactivity disorder. CDH13 localizes at inhibitory presynapses, specifically of parvalbumin (PV) and somatostatin (SST) expressing GABAergic neurons. However, the mechanism by which CDH13 regulates the function of inhibitory synapses in human neurons remains unknown. Starting from human-induced pluripotent stem cells, we established a robust method to generate a homogenous population of SST and MEF2C (PV-precursor marker protein) expressing GABAergic neurons (iGABA) in vitro, and co-cultured these with glutamatergic neurons at defined E/I ratios on micro-electrode arrays. We identified functional network parameters that are most reliably affected by GABAergic modulation as such, and through alterations of E/I balance by reduced expression of CDH13 in iGABAs. We found that CDH13 deficiency in iGABAs decreased E/I balance by means of increased inhibition. Moreover, CDH13 interacts with Integrin-β1 and Integrin-β3, which play opposite roles in the regulation of inhibitory synaptic strength via this interaction. Taken together, this model allows for standardized investigation of the E/I balance in a human neuronal background and can be deployed to dissect the cell-type-specific contribution of disease genes to the E/I balance.

Autophagy is a finely tuned process of programmed degradation and recycling of proteins and cellular components, which is crucial in neuronal function and synaptic integrity. Mounting evidence implicates chromatin remodelling in fine-tuning autophagy pathways. However, this epigenetic regulation is poorly understood in neurons. Here, we investigate the role in autophagy of KANSL1, a member of the nonspecific lethal complex, which acetylates histone H4 on lysine 16 (H4K16ac) to facilitate transcriptional activation. Loss-of-function of KANSL1 is strongly associated with the neurodevelopmental disorder Koolen-de Vries Syndrome (KdVS). Starting from KANSL1-deficient human induced-pluripotent stem cells, both from KdVS patients and genome-edited lines, we identified superoxide dismutase 1, an antioxidant enzyme, to be significantly decreased, leading to a subsequent increase in oxidative stress and autophagosome accumulation. In KANSL1-deficient neurons, autophagosome accumulation at excitatory synapses resulted in reduced synaptic density, reduced AMPA receptor-mediated transmission and impaired neuronal network activity. Furthermore, we found that increased oxidative stress-mediated autophagosome accumulation leads to increased mTOR activation and decreased lysosome function, further preventing the clearing of autophagosomes. Finally, by pharmacologically reducing oxidative stress, we could rescue the aberrant autophagosome formation as well as synaptic and neuronal network activity in KANSL1-deficient neurons. Our findings thus point towards an important relation between oxidative stress-induced autophagy and synapse function, and demonstrate the importance of H4K16ac-mediated changes in chromatin structure to balance reactive oxygen species- and mTOR-dependent autophagy. ### Competing Interest Statement The authors have declared no competing interest.

Pathogenic mutations in either one of the epigenetic modifiers EHMT1, MBD5, MLL3, or SMARCB1 have been identified to be causative for Kleefstra syndrome spectrum (KSS), a neurodevelopmental disorder with clinical features of both intellectual disability (ID) and autism spectrum disorder (ASD). To understand how these variants lead to the phenotypic convergence in KSS, we employ a loss-of-function approach to assess neuronal network development at the molecular, single-cell, and network activity level. KSS-gene-deficient neuronal networks all develop into hyperactive networks with altered network organization and excitatory-inhibitory balance. Interestingly, even though transcriptional data reveal distinct regulatory mechanisms, KSS target genes share similar functions in regulating neuronal excitability and synaptic function, several of which are associated with ID and ASD. Our results show that KSS genes mainly converge at the level of neuronal network communication, providing insights into the pathophysiology of KSS and phenotypically congruent disorders.

Kleefstra syndrome (KS) is a neurodevelopmental disorder caused by mutations in the histone methyltransferase EHMT1. To study the impact of decreased EHMT1 function in human cells, we generated excitatory cortical neurons from induced pluripotent stem (iPS) cells derived from KS patients. Neuronal networks of patient-derived cells exhibit network bursting with a reduced rate, longer duration, and increased temporal irregularity compared to control networks. We show that these changes are mediated by upregulation of NMDA receptor (NMDAR) subunit 1 correlating with reduced deposition of the repressive H3K9me2 mark, the catalytic product of EHMT1, at the GRIN1 promoter. In mice EHMT1 deficiency leads to similar neuronal network impairments with increased NMDAR function. Finally, we rescue the KS patient-derived neuronal network phenotypes by pharmacological inhibition of NMDARs. Summarized, we demonstrate a direct link between EHMT1 deficiency and NMDAR hyperfunction in human neurons, providing a potential basis for more targeted therapeutic approaches for KS.

An intriguing question in medical biology is how mutations in functionally distinct genes can lead to similar clinical phenotypes. For example, patients with mutations in distinct epigenetic regulators EHMT1, MBD5, MLL3 or SMARCB1 share the core clinical features of intellectual disability (ID), autism spectrum disorder (ASD) and facial dysmorphisms. To elucidate how these phenotypic similarities are reflected by convergence at the molecular, cellular and neuronal network level, we directly compared the effects of their loss of function in neurons. Interestingly, knockdown of each gene resulted in hyperactive neuronal networks with altered patterns of synchronized activity. At the single-cell level, we found genotype-specific changes in intrinsic excitability and excitatory-inhibitory balance, but in all cases leading to increased excitability. Congruent with our physiological findings, we identified dysregulated genes that converge on biological and cellular pathways related to neuronal excitability and synaptic function, including genes previously implicated in ID/ASD. Yet, our data suggests that the common cellular phenotypes depend on the ensemble of dysregulated genes engaged in neuronal excitability rather than the direction of transcriptional changes of individual genes. The demonstration of increasing convergence from molecular pathways to neuronal networks may be a paradigm for other types of ID/ASD.

Homeostatic plasticity, a form of synaptic plasticity, maintains the fine balance between overall excitation and inhibition in developing and mature neuronal networks. Although the synaptic mechanisms of homeostatic plasticity are well characterized, the associated transcriptional program remains poorly understood. We show that the Kleefstra-syndrome-associated protein EHMT1 plays a critical and cell-autonomous role in synaptic scaling by responding to attenuated neuronal firing or sensory drive. Chronic activity deprivation increased the amount of neuronal dimethylated H3 at lysine 9 (H3K9me2), the catalytic product of EHMT1 and an epigenetic marker for gene repression. Genetic knockdown and pharmacological blockade of EHMT1 or EHMT2 prevented the increase of H3K9me2 and synaptic scaling up. Furthermore, BDNF repression was preceded by EHMT1/2-mediated H3K9me2 deposition at the Bdnf promoter during synaptic scaling up, both in vitro and in vivo. Our findings suggest that H3K9me2-mediated changes in chromatin structure govern a repressive program that controls synaptic scaling.

Haploinsufficiency of Euchromatin histone methyltransferase 1 (EHMT1), a chromatin modifying enzyme, is the cause of Kleefstra syndrome (KS). KS is an intellectual disability (ID) syndrome, with general developmental delay, hypotonia, and craniofacial dysmorphisms as additional core features. Recent studies have been focused on the role of EHMT1 in learning and memory, linked to the ID phenotype of KS patients. In this study we used the Ehmt1(+/-) mouse model, and investigated whether the core features of KS were mimicked in these mice. When comparing Ehmt1(+/-) mice to wildtype littermates we observed delayed postnatal growth, eye opening, ear opening, and upper incisor eruption, indicating a delayed postnatal development Furthermore, tests for muscular strength and motor coordination showed features of hypotonia in young Ehmt1(+/-) mice. Lastly, we found that Ehmt1(+/-) mice showed brachycephalic crania, a shorter or bent nose, and hypertelorism, reminiscent of the craniofacial dysmorphisms seen in KS. In addition, gene expression analysis revealed a significant upregulation of the mRNA levels of Runx2 and several other bone tissue related genes in P28 Ehmt1(+/-) mice. Runx2 immunostaining also appeared to be increased. The mRNA upregulation was associated with decreased histone H3 lysine 9 dimethylation (H3K9me2) levels, the epigenetic mark deposited by Ehmt1, in the promoter region of these genes. Together, Ehmt1(+/-) mice indeed recapitulate KS core features and can be used as an animal model for Kleefstra syndrome. The increased expression of bone developmental genes in the Ehmt1(+/-) mice likely contributes to their cranial dysmorphisms and might be explained by diminished Ehmt1-induced H3K9 dimethylation. (C) 2013 Elsevier Inc. All rights reserved.