RARE DISEASE
FOXG1 syndrome
FOXG1 syndrome
FOXG1 syndrome
Synonyms: FOXG1-related epileptic-dyskinetic encephalopathy
Synonyms: FOXG1-related epileptic-dyskinetic encephalopathy
Synonyms: FOXG1-related epileptic-dyskinetic encephalopathy
Drug discovery
1
drug
With orphan designation
Overview
FOXG1 syndrome is a severe neurodevelopmental disorder caused by heterozygous mutations or deletions in the FOXG1 gene, critical for forebrain development. Key features include congenital microcephaly, profound global developmental delay, refractory epilepsy, hyperkinetic movement disorders (e.g., choreoathetosis, dystonia), and structural brain abnormalities (e.g., corpus callosum hypogenesis, delayed myelination). Distinguished from Rett syndrome by earlier symptom onset, lack of regression, and equal sex distribution [1][6][11][16].
Burden
Functional impact: 90% nonverbal, 80% non-ambulatory, lifelong dependency for daily care [2][6][9].
Healthcare utilization: High due to refractory seizures (53% daily episodes [9]), feeding/breathing tube dependence, and complex comorbidities [1][14].
Economic/caregiver burden: Median 4+ specialist visits annually; sleep disturbances, stereotypic behaviors, and mobility needs necessitate 24/7 care [6][9][14].
Therapies
Symptomatic management: Antiseizure medications (e.g., ACTH for infantile spasms [1][9]), dystonia treatments (e.g., levodopa [1][13]), and multidisciplinary support (gastrointestinal, respiratory, mobility) [6][14].
Emerging therapies: AAV9-mediated gene replacement therapy (preclinical success in reversing brain abnormalities [8][17]), RNAi/ASO approaches, and tRNA nonsense mutation correction [3][13].
Categories: rare genetic diseases, rare neurological diseases
Research Papers
45 drug discovery papers about FOXG1 syndrome, with 1 first-in-class and 2 next-in-class emerging drug candidates forecasted to outperform the average preclinical success rate. Recent publications:
45 drug discovery papers about FOXG1 syndrome, with 1 first-in-class and 2 next-in-class emerging drug candidates forecasted to outperform the average preclinical success rate. Recent publications:
categories:
Small molecules
proteins
2025-06-24 | The lincRNA Pantr1 is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1.
Derailed gene expression programs within the developing nervous system, encompassing both transcriptional and post-transcriptional processes, can cause diverse neurodevelopmental diseases (NDD). The NDD FOXG1-syndrome lacks full understanding of the mechanistic role of its eponymous gene product. While it is known that FOXG1 acts in part at the chromatin by binding to regulative regions, it is unclear what factors control its presence at specific sites. Long non-coding RNAs (lncRNAs) can mediate site-directed transcription factor binding, but their potential role in FOXG1-syndrome has not been described. Here, we show that FOXG1 localisation is regulated at selected loci through the lncRNA Pantr1. We identified FOXG1 as an upstream transcriptional activator of Pantr1 in human and mice. Further, we discovered that FOXG1 has the ability to associate with RNAs. Both transcriptional regulation of Pantr1 by FOXG1 and binding of both partners build up a regulative network that impacts the localisation of FOXG1 at selected genomic loci. Specifically, Pantr1 facilitates cooperative presence of FOXG1/NEUROD1 at specific sites, and Pantr1 reduction leads to redistribution of FOXG1 to comparably more generic binding sites. The rescue of impaired dendritic outgrowth upon FOXG1 reduction by simultaneous overexpression of Pantr1 underlines the importance of the FOXG1/Pantr1 regulative network.
2024-08-30 | The lincRNAPantr1is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1
ABSTRACT Derailed gene expression programs within the developing nervous system, encompassing both transcriptional and posttranscriptional processes, can cause diverse neurodevelopmental diseases (NDD). The NDD FOXG1-syndrome lacks full understanding of the mechanistic role of its eponymous gene product. While it is known that FOXG1 acts in part at the chromatin by binding to regulative regions, it is unclear what factors control its presence at specific sites. Long non-coding RNAs (lncRNAs) can mediate site-directed transcription factor binding, but their potential role in FOXG1-syndrome has not been described. Here, we show that FOXG1 localisation is regulated at selected loci through the lncRNA Pantr1 . We identified FOXG1 as an upstream transcriptional activator of Pantr1 in human and mice. Further, we discovered that FOXG1 has the ability to associate with RNAs. Both, transcriptional regulation of Pantr1 by FOXG1 and association of both partners, build up a regulative network that impacts the localisation of FOXG1 at selected genomic loci. Specifically, Pantr1 facilitates cooperative presence of FOXG1/NEUROD1 at specific sites, and Pantr1 reduction leads to redistribution of FOXG1 to comparably more generic binding sites. The rescue of impaired dendritic outgrowth upon FOXG1 reduction by simultaneous overexpression of Pantr1 underlines the importance of the FOXG1/ Pantr1 regulative network. GRAPHICAL ABSTRACT
2024-08-13 | A cleaved cytosolic FOXG1 promotes excitatory neurogenesis by modulation of mitochondrial translation – a new therapeutic target for brain disorders
Abstract Modulation of mitochondrial function is at the core of cell fate decisions and tissue homeostasis, yet the mechanisms that govern their activity are not understood. Here, we provide evidence that mitochondrial activity is controlled in a tissue-specific manner through a non-canonical cytoplasmic function of the transcription factor FOXG1. Using zebrafish and human models of the neurodevelopmental disorder, FOXG1 Syndrome, we found that FOXG1 mutations inducing a premature stop codon unexpectedly lead to the production of a short C-terminal peptide. The expression of this truncated protein is responsible for an excess of excitatory neurons and a structural, functional, and translational mitochondrial phenotype in mutants. We demonstrate that this activity is a gain of function, normally carried out by a cleavage product in wildtype. Both peptides promote the translation of mitochondrially-encoded transcripts, are preferentially transported to the mitochondria, and interact with mito-ribosomal proteins. These findings unveil a mechanism that integrates cell fate decisions with metabolic output. Adjusting the dosage of the mutant peptide rescues aspects of FOXG1 Syndrome, offering a new therapeutic avenue for the treatment of disorders involving mitochondrial dysfunctions. Graphic Abstract
2011-01-12 | FoxG1 Promotes the Survival of Postmitotic Neurons
The transcription factor FoxG1 regulates neurogenesis in the embryonic telencephalon as well as a number of other neurodevelopmental processes. While FoxG1 continues to be expressed in neurons postnatally and through adulthood, its role in fully differentiated neurons is not known. The current study demonstrates that FoxG1 promotes the survival of postmitotic neurons. In cerebellar granule neurons primed to undergo apoptosis, FoxG1 expression is reduced. Ectopic expression of FoxG1 blocks neuronal death, whereas suppression of its expression induces death in otherwise healthy neurons. The first 36 residues of FoxG1 are necessary for its survival-promoting effect, while the C-terminal half of the protein is dispensable. Mutation of Asp219, a residue necessary for DNA binding, abrogates survival promotion by FoxG1. Survival promotion is also eliminated by mutation of Thr271, a residue phosphorylated by Akt. Pharmacological inhibition of Akt blocks the survival effects of wild-type FoxG1 but not forms in which Thr271 is replaced with phosphomimetic residues. Treatment of neurons with IGF-1, a neurotrophic factor that promotes neuronal survival by activating Akt, prevents the apoptosis-associated downregulation of FoxG1 expression. Moreover, the overexpression of dominant-negative forms of FoxG1 blocks the ability of IGF-1 to maintain neuronal survival suggesting that FoxG1 is a downstream mediator of IGF-1/Akt signaling. Our study identifies a new and important function for FoxG1 in differentiated neurons.
small molecules
2026-02-03 | FOXG1 Hierarchically Shapes Synaptic Functions in Striatal iSPNs and Contributes to ASD Etiology.
Autism spectrum disorder (ASD) pathophysiology often involves striatal dysfunction, yet the underlying mechanisms remain unclear. Mutations in Forkhead box G1 (FOXG1) cause FOXG1 syndrome, a condition sharing core ASD features. Here, loss of Foxg1 in the indirect pathway spiny projection neurons (iSPNs) in mice recapitulates ASD symptoms, including social, language, and fine movement deficits. Foxg1 deficiency causes dendritic simplification, spine reduction, and impairs excitatory synaptic transmission. Transcriptome reveals that FOXG1 drives gene networks to multidimensionally control synaptic functions from spine morphogenesis, synaptic maturation, ion transmembrane transport, glutamate receptor clustering, to neurotransmitter release and synaptic transmission. Importantly, FOXG1 directly activates the transcription of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) subunits, and pharmacological potentiation of AMPAR activity normalizes synaptic function and rescues behavioral deficits. Our study provides a new perspective on the relationship between FOXG1 and ASD etiology in iSPNs and suggests the potential of AMPAR activation as a therapeutic intervention for ASD and FOXG1 Syndrome.
2025-10-03 | Human patient-specific FOXG1 syndrome mouse model revealed FOXG1-MYCN-mediated regulation of protein homeostasis in neurodevelopmental disorder.
Neurodevelopmental disorders are characterized by disruptions in brain development, resulting in cognitive, behavioral, and neurological impairments. FOXG1 syndrome (FS), caused by heterozygous mutations in the FOXG1 gene, exemplifies a severe monogenic neurodevelopmental disorder. To investigate its pathogenesis, we generated a patient-specific W300X mouse model carrying a truncation variant of FOXG1. We found that the truncated FOXG1 protein in W300X-heterozygous (W300X-Het) mice is more abundant and more nuclear-localized than the full-length FOXG1 protein, implicating a pathogenic mechanism involving the truncated protein. Interestingly, W300X-Het mice exhibited profound abnormalities in the dentate gyrus, including disrupted neurogenesis, impaired granule cell migration, and altered dendritic morphology. Transcriptomic profiling identified broad dysregulation in protein homeostasis pathways, particularly ribosomal biogenesis, translation, and proteostasis. Disruption of the FOXG1-MYCN pathway, critical for robust protein synthesis during neural stem cell division, synaptogenesis, and synaptic plasticity, emerged as a key mechanism underlying these defects. In parallel, microglial activation and inflammation were markedly increased in the dentate gyrus, contributing to a pro-inflammatory environment that exacerbates neurogenic and structural deficits. Consistent with hippocampal dysfunction in FS patients, W300X-Het mice exhibited significant spatial learning and memory impairments. Together, our study highlights disrupted protein homeostasis and neuroinflammation as key drivers of FS pathogenesis, providing a framework for developing therapeutic strategies targeting these pathways.
2024-08-18 | Evaluation of seizure semiology, genetics, magnetic resonance imaging, and electroencephalogram findings in children with Rett syndrome: A multicenter retrospective study.
This study aimed to evaluate seizure semiology, electroencephalogram (EEG), magnetic resonance imaging (MRI), and genetic findings, as well as treatment choices in Rett syndrome (RTT). A retrospective analysis was conducted on one hundred and twenty cases diagnosed with RTT with a genetic mutation. Data were obtained from nine participating centers. In this study, 93.3 % of patients were female, with typical RTT found in 70 % of cases. Genetic etiology revealed MECP2, FoxG1, and CDKL5 in 93.8 %, 2.7 %, and 1.8 % of cases, respectively. Atypical RTT clinics were observed in 50 % of male cases, with the first EEG being normal in atypical RTT cases (p = 0.01). Generalized tonic-clonic and myoclonic epilepsy were the most common seizure semiologies, while absence and focal epilepsy were less prevalent. Valproate, levetiracetam, lamotrigine, and clobazam were the most commonly used antiepileptic drugs, affecting the severity and frequency of seizures (p = 0.015, p=<0.001, p = 0.022, and p=<0.001, respectively). No significant differences were observed in EEG findings. The initiation of anti-seizure medications significantly altered seizure characteristics (Table 4). A ketogenic diet and vagal nerve stimulation (VNS) correlated with a 50 % improvement in cognitive function, while steroid treatment showed a 60 % improvement. Remarkably, seizures were substantially reduced after VNS application. This study underscores the importance of genetic diagnosis in RTT cases with a clinical diagnosis. These preliminary results will be further validated with the inclusion of clinically diagnosed RTT cases in our ongoing study.
2024-08-13 | Drug repurposing in Rett and Rett-like syndromes: a promising yet underrated opportunity?
Rett syndrome (RTT) and Rett-like syndromes [i.e., CDKL5 deficiency disorder (CDD) and FOXG1-syndrome] represent rare yet profoundly impactful neurodevelopmental disorders (NDDs). The severity and complexity of symptoms associated with these disorders, including cognitive impairment, motor dysfunction, seizures and other neurological features significantly affect the quality of life of patients and families. Despite ongoing research efforts to identify potential therapeutic targets and develop novel treatments, current therapeutic options remain limited. Here the potential of drug repurposing (DR) as a promising avenue for addressing the unmet medical needs of individuals with RTT and related disorders is explored. Leveraging existing drugs for new therapeutic purposes, DR presents an attractive strategy, particularly suited for neurological disorders given the complexities of the central nervous system (CNS) and the challenges in blood-brain barrier penetration. The current landscape of DR efforts in these syndromes is thoroughly examined, with partiuclar focus on shared molecular pathways and potential common drug targets across these conditions.
2024-04-06 | Menin Deficiency Induces Autism-Like Behaviors by Regulating Foxg1 Transcription and Participates in Foxg1-Related Encephalopathy.
Abstract FOXG1 syndrome is a developmental encephalopathy caused by FOXG1 (Forkhead box G1) mutations, resulting in high phenotypic variability. However, the upstream transcriptional regulation of Foxg1 expression remains unclear. This report demonstrates that both deficiency and overexpression of Men1 (protein: menin, a pathogenic gene of MEN1 syndrome known as multiple endocrine neoplasia type 1) lead to autism‐like behaviors, such as social defects, increased repetitive behaviors, and cognitive impairments. Multifaceted transcriptome analyses revealed that Foxg1 signaling is predominantly altered in Men1 deficiency mice, through its regulation of the Alpha Thalassemia/Mental Retardation Syndrome X‐Linked (Atrx) factor. Atrx recruits menin to bind to the transcriptional start region of Foxg1 and mediates the regulation of Foxg1 expression by H3K4me3 (Trimethylation of histone H3 lysine 4) modification. The deficits observed in menin deficient mice are rescued by the over‐expression of Foxg1 , leading to normalized spine growth and restoration of hippocampal synaptic plasticity. These findings suggest that menin may have a putative role in the maintenance of Foxg1 expression, highlighting menin signaling as a potential therapeutic target for Foxg1 ‐related encephalopathy.
oligonucleotides
2025-11-17 | RNA-based therapies for neurodevelopmental disorders: innovative tools for molecular correction.
Modulation of RNA and protein expression to restore or normalize neuronal function has emerged as a powerful therapeutic strategy for neurodevelopmental disorders (NDDs) tailoring individual genetic mutations causing intellectual disability (ID), or autism spectrum disorder (ASD), or developmental epileptic encephalopathy (DEE). In recent years, diverse classes of RNA-based molecules have been developed with therapeutic potential, including antisense oligonucleotides (ASOs), oligonucleotides targeting natural antisense transcripts (antagoNATs), Short Interspersed Nuclear Element UP-regulating RNAs (SINEUPs), interfering RNAs (RNAi), Exon-Specific engineering U1 small nuclear RNAs (ExSpeU1s), and small-activating RNA (saRNA) This review highlights the promising advances of these RNA-based therapeutics in addressing syndromic ID, such as Fragile X syndrome, MECP2 duplication syndrome, FOXG1-gene related Rett syndrome and Angelman syndrome, which are characterized by well-defined genetic mutations with limited treatment options. Moreover, ASD-related condition linked to mutations in CHD8 is under investigation, extending the therapeutic landscape to complex behavioral and cognitive disorders. In the same way, several DEEs caused by mutations in CDKL5, DNM1, KCNT1, SCN1A, SCN2A, SCN8A, and UBA5 genes, which present severe pharmaco-resistant epilepsy, are increasingly becoming targets for RNA molecules that aim to restore neuronal excitability and network function. Together, these findings underscore the expanding therapeutic landscape enabled by RNA technologies, offering unprecedented specificity and flexibility for gene-targeted interventions in NDDs. As the field of RNA medicine continues to evolve across genomics and neuroscience, we aim to provide a resource for researchers and clinicians on promising innovative tools for molecular correction.
2024-10-16 | PLP1-Targeting Antisense Oligonucleotides Improve FOXG1 Syndrome Mice.
FOXG1 syndrome is a rare neurodevelopmental disorder of the telencephalon, for which there is no cure. Underlying heterozygous pathogenic variants in the Forkhead Box G1 (FOXG1) gene with resulting impaired or loss of FOXG1 function lead to severe neurological impairments. Here, we report a patient with a de novo pathogenic single nucleotide deletion c.946del (p.Leu316Cysfs*10) of the FOXG1 gene that causes a premature protein truncation. To study this variant in vivo, we generated and characterized Foxg1 c946del mice that recapitulate hallmarks of the human disorder. Accordingly, heterozygous Foxg1 c946del mice display neurological symptoms with aberrant neuronal networks and increased seizure susceptibility. Gene expression profiling identified increased oligodendrocyte- and myelination-related gene clusters. Specifically, we showed that expression of the c946del mutant and of other pathogenic FOXG1 variants correlated with overexpression of proteolipid protein 1 (Plp1), a gene linked to white matter disorders. Postnatal administration of Plp1-targeting antisense oligonucleotides (ASOs) in Foxg1 c946del mice improved neurological deficits. Our data suggest Plp1 as a new target for therapeutic strategies mitigating disease phenotypes in FOXG1 syndrome patients.
2019-04-30 | Enhancing Neuronogenesis and Counteracting Neuropathogenic Gene Haploinsufficiencies by RNA Gene Activation.
Small activating RNAs (saRNAs), targeting endogenous genes and stimulating their transcription, are a promising tool for implementing a variety of neurotherapeutic strategies. Among these there is the stimulation of select histogenetic subroutines for purposes of cell-based brain repair, as well as the therapeutic treatment of gene expression deficits underlying severe neurological disorders.We employed RNA activation (RNAa) to transactivate the Emx2 transcription factor gene in embryonic cortico-cerebral precursor cells. This led to enhanced self-renewal, delayed differentiation, and reduced death of neuronally committed precursors, resulting in a remarkable expansion of the neuronogenic precursors pool. These results are of paramount interest for purposes of gene-promoted brain repair. As such, RNAa makes therapeutic stimulation of neuronogenesis via Emx2 overexpression a feasible goal, preventing the drawbacks of exogenous gene copies introduction.Moreover, we employed RNAa to achieve a gentle transactivation of the Foxg1 transcription factor gene, specifically in cortico-cerebral cells. This manipulation led to an appreciable biological outcome, while complying with endogenous gene tuning linked to early central nervous system regionalization and late activity of neocortical projection neurons. Foxg1-activating miRNAs stimulated RNApolII recruitment, possibly via Ago1. One of them worked promisingly in vivo. As such, RNAa can be a valuable approach for therapeutic treatment of the FOXG1-haploinsufficiency-linked variant of the Rett syndrome. Remarkably, hemizygosity for specific genes and polygenic chromosomal segments underlies a huge number of neuropathological entities for which no cure is presently available. Based on the results reported above, RNAa might be a simple and scalable approach for fixing this class of problems.
2016-12-30 | Clinical Utility of a Comprehensive, Whole Genome CMA Testing Platform in Pediatrics: A Prospective Randomized Controlled Trial of Simulated Patients in Physician Practices
Developmental disorders (DD), including autism spectrum disorder (ASD) and intellectual disability (ID), are a common group of clinical manifestations caused by a variety of genetic abnormalities. Genetic testing, including chromosomal microarray (CMA), plays an important role in diagnosing these conditions, but CMA can be limited by incomplete coverage of genetic abnormalities and lack of guidance for conditions rarely seen by treating physicians.We conducted a longitudinal, randomized controlled trial investigating the impact of a higher resolution 2.8 million (MM) probe-CMA test on the quality of care delivered by practicing general pediatricians and specialists. To overcome the twin problems of finding an adequate sample size of multiple rare conditions and under/incorrect diagnoses, we used standardized simulated patients known as CPVs. Physicians, randomized into control and intervention groups, cared for the CPV pediatric patients with DD/ASD/ID. Care responses were scored against evidence-based criteria. In round one, participants could order diagnostic tests including existing CMA tests. In round two, intervention physicians could order the 2.8MM probe-CMA test. Outcome measures included overall quality of care and quality of the diagnosis and treatment plan.Physicians ordering CMA testing had 5.43% (p<0.001) higher overall quality scores than those who did not. Intervention physicians ordering the 2.8MM probe-CMA test had 7.20% (p<0.001) higher overall quality scores. Use of the 2.8MM probe-CMA test led to a 10.9% (p<0.001) improvement in the diagnosis and treatment score. Introduction of the 2.8MM probe-CMA test led to significant improvements in condition-specific interventions including an 8.3% (p = 0.04) improvement in evaluation and therapy for gross motor delays caused by Hunter syndrome, a 27.5% (p = 0.03) increase in early cognitive intervention for FOXG1-related disorder, and an 18.2% (p<0.001) improvement in referrals to child neurology for Dravet syndrome.Physician use of the 2.8MM probe-CMA test significantly improves overall quality as well as diagnosis and treatment quality for simulated cases of pediatric DD/ASD/ID patients, and delivers additional clinical utility over existing CMA tests.
2016-12-20 | RNA activation of haploinsufficient Foxg1 gene in murine neocortex
Abstract More than one hundred distinct gene hemizygosities are specifically linked to epilepsy, mental retardation, autism, schizophrenia and neuro-degeneration. Radical repair of these gene deficits via genome engineering is hardly feasible. The same applies to therapeutic stimulation of the spared allele by artificial transactivators. Small activating RNAs (saRNAs) offer an alternative, appealing approach. As a proof-of-principle, here we tested this approach on the Rett syndrome-linked, haploinsufficient, Foxg1 brain patterning gene. We selected a set of artificial small activating RNAs (saRNAs) upregulating it in neocortical precursors and their derivatives. Expression of these effectors achieved a robust biological outcome. saRNA-driven activation (RNAa) was limited to neural cells which normally express Foxg1 and did not hide endogenous gene tuning. saRNAs recognized target chromatin through a ncRNA stemming from it. Gene upregulation required Ago1 and was associated to RNApolII enrichment throughout the Foxg1 locus. Finally, saRNA delivery to murine neonatal brain replicated Foxg1 -RNAa in vivo .
gene therapies
2025-11-27 | Temporal lobe-predominant cortical dysplasia with mild cortical thickening in FOXG1 syndrome
Forkhead box G1 ( FOXG1 ) gene syndrome is a neurodevelopmental disorder characterized by severe developmental delays, microcephaly, autistic features, epilepsy, and complex hyperkinetic-dyskinetic movement disorders. We present the case of a Japanese patient with microcephaly, cortical dysplasia with irregular gyri and mild cortical thickening in the temporal and frontal lobes, and a de novo heterozygous missense variant in FOXG1 . The patient was an 11-year-old Japanese boy who presented with microcephaly at 3 months of age. At 2 years and 10 months of age, he presented with frequent tonic seizures of unknown onset. Physical examination revealed microcephaly and dysmorphic features. He exhibited severe developmental delays and generalized hypotonia. Brain magnetic resonance imaging (MRI) revealed anterior hypogenesis of the corpus callosum, decreased cerebral volume, mildly delayed myelination, and cortical dysplasia with irregular gyri and mild cortical thickening, particularly in the temporal lobes. His seizures resolved after administering carbamazepine. Trio-based whole-exome sequencing analysis of the patient and his parents revealed a de novo heterozygous missense variant, NM_005249.5:c.688C>T p.(Arg230Cys), located in the forkhead DNA-binding domain of FOXG1 , a recurrent variant that was finally diagnosed as FOXG1 syndrome. Cortical malformation in FOXG1 syndrome is often observed in the frontal lobe. The cortical dysplasia and mild cortical thickening observed in our patient was predominantly in the temporal cortex, suggesting distinctive findings. These results provide new insights into brain malformations associated with FOXG1 syndrome.
2025-05-23 | The patient-specific mouse model with Foxg1 frameshift mutation provides insights into the pathophysiology of FOXG1 syndrome.
Single allelic mutations in the FOXG1 gene lead to FOXG1 syndrome (FS). To understand the pathophysiology of FS, which vary depending on FOXG1 mutation types, patient-specific animal models are critical. Here, we report a patient-specific Q84Pfs heterozygous (Q84Pfs-Het) mouse model, which recapitulates various FS phenotypes across cellular, brain structural, and behavioral levels. Q84Pfs-Het cortex shows dysregulations of genes controlling cell proliferation, neuronal projection and migration, synaptic assembly, and synaptic vesicle transport. The Q84Pfs allele produces the N-terminal fragment of FOXG1 (Q84Pfs protein) in Q84Pfs-Het mouse brains, which forms intracellular speckles, interacts with FOXG1 full-length protein, and triggers the sequestration of FOXG1 to distinct subcellular domains. Q84Pfs protein promotes the radial glial cell identity and suppresses neuronal migration in the cortex. Our study uncovers the role of the FOXG1 fragment from FS-causing FOXG1 variants and identifies the genes involved in FS-like cellular and behavioral phenotypes, providing insights into the pathophysiology of FS.
2025-04-17 | A modular CRISPRa system for molecular therapy of FOXG1 syndrome
Abstract To date, there is an unmet need for novel approaches that address haploinsufficiency disorders in a targeted and robust manner. Here, we developed a novel, modular tool for transcriptional regulation of genes involved in neurodevelopmental disease in the absence of creating double-stranded breaks. We utilized this novel platform technology to identify single guide RNA (sgRNAs) that efficiently regulate expression of the intellectual disability gene FOXG1 that utilizes an optimized protein intein system. Using a modular assembly of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) trans-activators, including single and dual VP64 (tetramer of herpes simplex virus VP16 peptide) dCas9 fusion proteins, sgRNA-mediated MS2 p65 HSF (MPH) recruitment or the addition of the VPR tripartite effector (VP64, p65, and Rta) can induce dynamic gene regulation. We further increased messenger RNA (mRNA) levels of FOXG1 using duplexed sgRNAs paired with different combinations of transcriptional activators. We demonstrate that FOXG1 gene upregulation results in a significant increase in FoxG1 protein translation. Following treatment of mutant FOXG1 neural stem cells with the CRISPR activators, we observed a significant increase in FOXG1 expression with no-off targets as determined by in silico sgRNA binding prediction paired with RNA-sequencing. This approach holds great promise as a modular platform technology that is readily adapted for gene therapy delivery for those affected by rare genetic conditions.
2020-06-15 | AAV-mediated FOXG1 gene editing in human Rett primary cells
Variations in the Forkhead Box G1 (FOXG1) gene cause FOXG1 syndrome spectrum, including the congenital variant of Rett syndrome, characterized by early onset of regression, Rett-like and jerky movements, and cortical visual impairment. Due to the largely unknown pathophysiological mechanisms downstream the impairment of this transcriptional regulator, a specific treatment is not yet available. Since both haploinsufficiency and hyper-expression of FOXG1 cause diseases in humans, we reasoned that adding a gene under nonnative regulatory sequences would be a risky strategy as opposed to a genome editing approach where the mutated gene is reversed into wild-type. Here, we demonstrate that an adeno-associated viruses (AAVs)-coupled CRISPR/Cas9 system is able to target and correct FOXG1 variants in patient-derived fibroblasts, induced Pluripotent Stem Cells (iPSCs) and iPSC-derived neurons. Variant-specific single-guide RNAs (sgRNAs) and donor DNAs have been selected and cloned together with a mCherry/EGFP reporter system. Specific sgRNA recognition sequences were inserted upstream and downstream Cas9 CDS to allow self-cleavage and inactivation. We demonstrated that AAV serotypes vary in transduction efficiency depending on the target cell type, the best being AAV9 in fibroblasts and iPSC-derived neurons, and AAV2 in iPSCs. Next-generation sequencing (NGS) of mCherry+/EGFP+ transfected cells demonstrated that the mutated alleles were repaired with high efficiency (20–35% reversion) and precision both in terms of allelic discrimination and off-target activity. The genome editing strategy tested in this study has proven to precisely repair FOXG1 and delivery through an AAV9-based system represents a step forward toward the development of a therapy for Rett syndrome.
2019-09-04 | Knockdown of Foxg1 in supporting cells increases the trans-differentiation of supporting cells into hair cells in the neonatal mouse cochlea
Foxg1 is one of the forkhead box genes that are involved in morphogenesis, cell fate determination, and proliferation, and Foxg1 was previously reported to be required for morphogenesis of the mammalian inner ear. However, Foxg1 knock-out mice die at birth, and thus the role of Foxg1 in regulating hair cell (HC) regeneration after birth remains unclear. Here we used Sox2CreER/+ Foxg1loxp/loxp mice and Lgr5-EGFPCreER/+ Foxg1loxp/loxp mice to conditionally knock down Foxg1 specifically in Sox2+ SCs and Lgr5+ progenitors, respectively, in neonatal mice. We found that Foxg1 conditional knockdown (cKD) in Sox2+ SCs and Lgr5+ progenitors at postnatal day (P)1 both led to large numbers of extra HCs, especially extra inner HCs (IHCs) at P7, and these extra IHCs with normal hair bundles and synapses could survive at least to P30. The EdU assay failed to detect any EdU+ SCs, while the SC number was significantly decreased in Foxg1 cKD mice, and lineage tracing data showed that much more tdTomato+ HCs originated from Sox2+ SCs in Foxg1 cKD mice compared to the control mice. Moreover, the sphere-forming assay showed that Foxg1 cKD in Lgr5+ progenitors did not significantly change their sphere-forming ability. All these results suggest that Foxg1 cKD promotes HC regeneration and leads to large numbers of extra HCs probably by inducing direct trans-differentiation of SCs and progenitors to HCs. Real-time qPCR showed that cell cycle and Notch signaling pathways were significantly down-regulated in Foxg1 cKD mice cochlear SCs. Together, this study provides new evidence for the role of Foxg1 in regulating HC regeneration from SCs and progenitors in the neonatal mouse cochlea.
other
2022-05-02 | FOXG1 dose tunes cell proliferation dynamics in human forebrain progenitor cells.
Heterozygous loss-of-function mutations in Forkhead box G1 (FOXG1), a uniquely brain-expressed gene, cause microcephaly, seizures, and severe intellectual disability, whereas increased FOXG1 expression is frequently observed in glioblastoma. To investigate the role of FOXG1 in forebrain cell proliferation, we modeled FOXG1 syndrome using cells from three clinically diagnosed cases with two sex-matched healthy parents and one unrelated sex-matched control. Cells with heterozygous FOXG1 loss showed significant reduction in cell proliferation, increased ratio of cells in G0/G1 stage of the cell cycle, and increased frequency of primary cilia. Engineered loss of FOXG1 recapitulated this effect, while isogenic repair of a patient mutation reverted output markers to wild type. An engineered inducible FOXG1 cell line derived from a FOXG1 syndrome case demonstrated that FOXG1 dose-dependently affects all cell proliferation outputs measured. These findings provide strong support for the critical importance of FOXG1 levels in controlling human brain cell growth in health and disease.
2019-05-01 | WNT/NOTCH Pathway Is Essential for the Maintenance and Expansion of Human MGE Progenitors
Medial ganglionic eminence (MGE)-like cells yielded from human pluripotent stem cells (hPSCs) hold great potentials for cell therapies of related neurological disorders. However, cues that orchestrate the maintenance versus differentiation of human MGE progenitors, and ways for large-scale expansion of these cells have not been investigated. Here, we report that WNT/CTNNB1 signaling plays an essential role in maintaining MGE-like cells derived from hPSCs. Ablation of CTNNB1 in MGE cells led to precocious cell-cycle exit and advanced neuronal differentiation. Activation of WNT signaling through genetic or chemical approach was sufficient to maintain MGE cells in an expandable manner with authentic neuronal differentiation potencies through activation of endogenous NOTCH signaling. Our findings reveal that WNT/NOTCH signaling cascade is a key player in governing the maintenance versus terminal differentiation of MGE progenitors in humans. Large-scale expansion of functional MGE progenitors for cell therapies can therefore be achieved by modifying WNT/NOTCH pathway.
2016-04-01 | Forced cell cycle exit and modulation of GABAA, CREB, and GSK3β signaling promote functional maturation of induced pluripotent stem cell-derived neurons.
Although numerous protocols have been developed for differentiation of neurons from a variety of pluripotent stem cells, most have concentrated on being able to specify effectively appropriate neuronal subtypes and few have been designed to enhance or accelerate functional maturity. Of those that have, most employ time courses of functional maturation that are rather protracted, and none have fully characterized all aspects of neuronal function, from spontaneous action potential generation through to postsynaptic receptor maturation. Here, we describe a simple protocol that employs the sequential addition of just two supplemented media that have been formulated to separate the two key phases of neural differentiation, the neurogenesis and synaptogenesis, each characterized by different signaling requirements. Employing these media, this new protocol synchronized neurogenesis and enhanced the rate of maturation of pluripotent stem cell-derived neural precursors. Neurons differentiated using this protocol exhibited large cell capacitance with relatively hyperpolarized resting membrane potentials; moreover, they exhibited augmented: 1) spontaneous electrical activity; 2) regenerative induced action potential train activity; 3) Na + current availability, and 4) synaptic currents. This was accomplished by rapid and uniform development of a mature, inhibitory GABA A receptor phenotype that was demonstrated by Ca 2+ imaging and the ability of GABA A receptor blockers to evoke seizurogenic network activity in multielectrode array recordings. Furthermore, since this protocol can exploit expanded and frozen prepatterned neural progenitors to deliver mature neurons within 21 days, it is both scalable and transferable to high-throughput platforms for the use in functional screens.
2013-06-01 | Rapid Single-Step Induction of Functional Neurons from Human Pluripotent Stem Cells
Available methods for differentiating human embryonic stem cells (ESCs) and induced pluripotent cells (iPSCs) into neurons are often cumbersome, slow, and variable. Alternatively, human fibroblasts can be directly converted into induced neuronal (iN) cells. However, with present techniques conversion is inefficient, synapse formation is limited, and only small amounts of neurons can be generated. Here, we show that human ESCs and iPSCs can be converted into functional iN cells with nearly 100% yield and purity in less than 2 weeks by forced expression of a single transcription factor. The resulting ES-iN or iPS-iN cells exhibit quantitatively reproducible properties independent of the cell line of origin, form mature pre- and postsynaptic specializations, and integrate into existing synaptic networks when transplanted into mouse brain. As illustrated by selected examples, our approach enables large-scale studies of human neurons for questions such as analyses of human diseases, examination of human-specific genes, and drug screening.
proteins
2025-06-24 | The lincRNA Pantr1 is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1.
Derailed gene expression programs within the developing nervous system, encompassing both transcriptional and post-transcriptional processes, can cause diverse neurodevelopmental diseases (NDD). The NDD FOXG1-syndrome lacks full understanding of the mechanistic role of its eponymous gene product. While it is known that FOXG1 acts in part at the chromatin by binding to regulative regions, it is unclear what factors control its presence at specific sites. Long non-coding RNAs (lncRNAs) can mediate site-directed transcription factor binding, but their potential role in FOXG1-syndrome has not been described. Here, we show that FOXG1 localisation is regulated at selected loci through the lncRNA Pantr1. We identified FOXG1 as an upstream transcriptional activator of Pantr1 in human and mice. Further, we discovered that FOXG1 has the ability to associate with RNAs. Both transcriptional regulation of Pantr1 by FOXG1 and binding of both partners build up a regulative network that impacts the localisation of FOXG1 at selected genomic loci. Specifically, Pantr1 facilitates cooperative presence of FOXG1/NEUROD1 at specific sites, and Pantr1 reduction leads to redistribution of FOXG1 to comparably more generic binding sites. The rescue of impaired dendritic outgrowth upon FOXG1 reduction by simultaneous overexpression of Pantr1 underlines the importance of the FOXG1/Pantr1 regulative network.
2024-08-30 | The lincRNAPantr1is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1
ABSTRACT Derailed gene expression programs within the developing nervous system, encompassing both transcriptional and posttranscriptional processes, can cause diverse neurodevelopmental diseases (NDD). The NDD FOXG1-syndrome lacks full understanding of the mechanistic role of its eponymous gene product. While it is known that FOXG1 acts in part at the chromatin by binding to regulative regions, it is unclear what factors control its presence at specific sites. Long non-coding RNAs (lncRNAs) can mediate site-directed transcription factor binding, but their potential role in FOXG1-syndrome has not been described. Here, we show that FOXG1 localisation is regulated at selected loci through the lncRNA Pantr1 . We identified FOXG1 as an upstream transcriptional activator of Pantr1 in human and mice. Further, we discovered that FOXG1 has the ability to associate with RNAs. Both, transcriptional regulation of Pantr1 by FOXG1 and association of both partners, build up a regulative network that impacts the localisation of FOXG1 at selected genomic loci. Specifically, Pantr1 facilitates cooperative presence of FOXG1/NEUROD1 at specific sites, and Pantr1 reduction leads to redistribution of FOXG1 to comparably more generic binding sites. The rescue of impaired dendritic outgrowth upon FOXG1 reduction by simultaneous overexpression of Pantr1 underlines the importance of the FOXG1/ Pantr1 regulative network. GRAPHICAL ABSTRACT
2024-08-13 | A cleaved cytosolic FOXG1 promotes excitatory neurogenesis by modulation of mitochondrial translation – a new therapeutic target for brain disorders
Abstract Modulation of mitochondrial function is at the core of cell fate decisions and tissue homeostasis, yet the mechanisms that govern their activity are not understood. Here, we provide evidence that mitochondrial activity is controlled in a tissue-specific manner through a non-canonical cytoplasmic function of the transcription factor FOXG1. Using zebrafish and human models of the neurodevelopmental disorder, FOXG1 Syndrome, we found that FOXG1 mutations inducing a premature stop codon unexpectedly lead to the production of a short C-terminal peptide. The expression of this truncated protein is responsible for an excess of excitatory neurons and a structural, functional, and translational mitochondrial phenotype in mutants. We demonstrate that this activity is a gain of function, normally carried out by a cleavage product in wildtype. Both peptides promote the translation of mitochondrially-encoded transcripts, are preferentially transported to the mitochondria, and interact with mito-ribosomal proteins. These findings unveil a mechanism that integrates cell fate decisions with metabolic output. Adjusting the dosage of the mutant peptide rescues aspects of FOXG1 Syndrome, offering a new therapeutic avenue for the treatment of disorders involving mitochondrial dysfunctions. Graphic Abstract
2011-01-12 | FoxG1 Promotes the Survival of Postmitotic Neurons
The transcription factor FoxG1 regulates neurogenesis in the embryonic telencephalon as well as a number of other neurodevelopmental processes. While FoxG1 continues to be expressed in neurons postnatally and through adulthood, its role in fully differentiated neurons is not known. The current study demonstrates that FoxG1 promotes the survival of postmitotic neurons. In cerebellar granule neurons primed to undergo apoptosis, FoxG1 expression is reduced. Ectopic expression of FoxG1 blocks neuronal death, whereas suppression of its expression induces death in otherwise healthy neurons. The first 36 residues of FoxG1 are necessary for its survival-promoting effect, while the C-terminal half of the protein is dispensable. Mutation of Asp219, a residue necessary for DNA binding, abrogates survival promotion by FoxG1. Survival promotion is also eliminated by mutation of Thr271, a residue phosphorylated by Akt. Pharmacological inhibition of Akt blocks the survival effects of wild-type FoxG1 but not forms in which Thr271 is replaced with phosphomimetic residues. Treatment of neurons with IGF-1, a neurotrophic factor that promotes neuronal survival by activating Akt, prevents the apoptosis-associated downregulation of FoxG1 expression. Moreover, the overexpression of dominant-negative forms of FoxG1 blocks the ability of IGF-1 to maintain neuronal survival suggesting that FoxG1 is a downstream mediator of IGF-1/Akt signaling. Our study identifies a new and important function for FoxG1 in differentiated neurons.
small molecules
2026-02-03 | FOXG1 Hierarchically Shapes Synaptic Functions in Striatal iSPNs and Contributes to ASD Etiology.
Autism spectrum disorder (ASD) pathophysiology often involves striatal dysfunction, yet the underlying mechanisms remain unclear. Mutations in Forkhead box G1 (FOXG1) cause FOXG1 syndrome, a condition sharing core ASD features. Here, loss of Foxg1 in the indirect pathway spiny projection neurons (iSPNs) in mice recapitulates ASD symptoms, including social, language, and fine movement deficits. Foxg1 deficiency causes dendritic simplification, spine reduction, and impairs excitatory synaptic transmission. Transcriptome reveals that FOXG1 drives gene networks to multidimensionally control synaptic functions from spine morphogenesis, synaptic maturation, ion transmembrane transport, glutamate receptor clustering, to neurotransmitter release and synaptic transmission. Importantly, FOXG1 directly activates the transcription of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) subunits, and pharmacological potentiation of AMPAR activity normalizes synaptic function and rescues behavioral deficits. Our study provides a new perspective on the relationship between FOXG1 and ASD etiology in iSPNs and suggests the potential of AMPAR activation as a therapeutic intervention for ASD and FOXG1 Syndrome.
2025-10-03 | Human patient-specific FOXG1 syndrome mouse model revealed FOXG1-MYCN-mediated regulation of protein homeostasis in neurodevelopmental disorder.
Neurodevelopmental disorders are characterized by disruptions in brain development, resulting in cognitive, behavioral, and neurological impairments. FOXG1 syndrome (FS), caused by heterozygous mutations in the FOXG1 gene, exemplifies a severe monogenic neurodevelopmental disorder. To investigate its pathogenesis, we generated a patient-specific W300X mouse model carrying a truncation variant of FOXG1. We found that the truncated FOXG1 protein in W300X-heterozygous (W300X-Het) mice is more abundant and more nuclear-localized than the full-length FOXG1 protein, implicating a pathogenic mechanism involving the truncated protein. Interestingly, W300X-Het mice exhibited profound abnormalities in the dentate gyrus, including disrupted neurogenesis, impaired granule cell migration, and altered dendritic morphology. Transcriptomic profiling identified broad dysregulation in protein homeostasis pathways, particularly ribosomal biogenesis, translation, and proteostasis. Disruption of the FOXG1-MYCN pathway, critical for robust protein synthesis during neural stem cell division, synaptogenesis, and synaptic plasticity, emerged as a key mechanism underlying these defects. In parallel, microglial activation and inflammation were markedly increased in the dentate gyrus, contributing to a pro-inflammatory environment that exacerbates neurogenic and structural deficits. Consistent with hippocampal dysfunction in FS patients, W300X-Het mice exhibited significant spatial learning and memory impairments. Together, our study highlights disrupted protein homeostasis and neuroinflammation as key drivers of FS pathogenesis, providing a framework for developing therapeutic strategies targeting these pathways.
2024-08-18 | Evaluation of seizure semiology, genetics, magnetic resonance imaging, and electroencephalogram findings in children with Rett syndrome: A multicenter retrospective study.
This study aimed to evaluate seizure semiology, electroencephalogram (EEG), magnetic resonance imaging (MRI), and genetic findings, as well as treatment choices in Rett syndrome (RTT). A retrospective analysis was conducted on one hundred and twenty cases diagnosed with RTT with a genetic mutation. Data were obtained from nine participating centers. In this study, 93.3 % of patients were female, with typical RTT found in 70 % of cases. Genetic etiology revealed MECP2, FoxG1, and CDKL5 in 93.8 %, 2.7 %, and 1.8 % of cases, respectively. Atypical RTT clinics were observed in 50 % of male cases, with the first EEG being normal in atypical RTT cases (p = 0.01). Generalized tonic-clonic and myoclonic epilepsy were the most common seizure semiologies, while absence and focal epilepsy were less prevalent. Valproate, levetiracetam, lamotrigine, and clobazam were the most commonly used antiepileptic drugs, affecting the severity and frequency of seizures (p = 0.015, p=<0.001, p = 0.022, and p=<0.001, respectively). No significant differences were observed in EEG findings. The initiation of anti-seizure medications significantly altered seizure characteristics (Table 4). A ketogenic diet and vagal nerve stimulation (VNS) correlated with a 50 % improvement in cognitive function, while steroid treatment showed a 60 % improvement. Remarkably, seizures were substantially reduced after VNS application. This study underscores the importance of genetic diagnosis in RTT cases with a clinical diagnosis. These preliminary results will be further validated with the inclusion of clinically diagnosed RTT cases in our ongoing study.
2024-08-13 | Drug repurposing in Rett and Rett-like syndromes: a promising yet underrated opportunity?
Rett syndrome (RTT) and Rett-like syndromes [i.e., CDKL5 deficiency disorder (CDD) and FOXG1-syndrome] represent rare yet profoundly impactful neurodevelopmental disorders (NDDs). The severity and complexity of symptoms associated with these disorders, including cognitive impairment, motor dysfunction, seizures and other neurological features significantly affect the quality of life of patients and families. Despite ongoing research efforts to identify potential therapeutic targets and develop novel treatments, current therapeutic options remain limited. Here the potential of drug repurposing (DR) as a promising avenue for addressing the unmet medical needs of individuals with RTT and related disorders is explored. Leveraging existing drugs for new therapeutic purposes, DR presents an attractive strategy, particularly suited for neurological disorders given the complexities of the central nervous system (CNS) and the challenges in blood-brain barrier penetration. The current landscape of DR efforts in these syndromes is thoroughly examined, with partiuclar focus on shared molecular pathways and potential common drug targets across these conditions.
2024-04-06 | Menin Deficiency Induces Autism-Like Behaviors by Regulating Foxg1 Transcription and Participates in Foxg1-Related Encephalopathy.
Abstract FOXG1 syndrome is a developmental encephalopathy caused by FOXG1 (Forkhead box G1) mutations, resulting in high phenotypic variability. However, the upstream transcriptional regulation of Foxg1 expression remains unclear. This report demonstrates that both deficiency and overexpression of Men1 (protein: menin, a pathogenic gene of MEN1 syndrome known as multiple endocrine neoplasia type 1) lead to autism‐like behaviors, such as social defects, increased repetitive behaviors, and cognitive impairments. Multifaceted transcriptome analyses revealed that Foxg1 signaling is predominantly altered in Men1 deficiency mice, through its regulation of the Alpha Thalassemia/Mental Retardation Syndrome X‐Linked (Atrx) factor. Atrx recruits menin to bind to the transcriptional start region of Foxg1 and mediates the regulation of Foxg1 expression by H3K4me3 (Trimethylation of histone H3 lysine 4) modification. The deficits observed in menin deficient mice are rescued by the over‐expression of Foxg1 , leading to normalized spine growth and restoration of hippocampal synaptic plasticity. These findings suggest that menin may have a putative role in the maintenance of Foxg1 expression, highlighting menin signaling as a potential therapeutic target for Foxg1 ‐related encephalopathy.
oligonucleotides
2025-11-17 | RNA-based therapies for neurodevelopmental disorders: innovative tools for molecular correction.
Modulation of RNA and protein expression to restore or normalize neuronal function has emerged as a powerful therapeutic strategy for neurodevelopmental disorders (NDDs) tailoring individual genetic mutations causing intellectual disability (ID), or autism spectrum disorder (ASD), or developmental epileptic encephalopathy (DEE). In recent years, diverse classes of RNA-based molecules have been developed with therapeutic potential, including antisense oligonucleotides (ASOs), oligonucleotides targeting natural antisense transcripts (antagoNATs), Short Interspersed Nuclear Element UP-regulating RNAs (SINEUPs), interfering RNAs (RNAi), Exon-Specific engineering U1 small nuclear RNAs (ExSpeU1s), and small-activating RNA (saRNA) This review highlights the promising advances of these RNA-based therapeutics in addressing syndromic ID, such as Fragile X syndrome, MECP2 duplication syndrome, FOXG1-gene related Rett syndrome and Angelman syndrome, which are characterized by well-defined genetic mutations with limited treatment options. Moreover, ASD-related condition linked to mutations in CHD8 is under investigation, extending the therapeutic landscape to complex behavioral and cognitive disorders. In the same way, several DEEs caused by mutations in CDKL5, DNM1, KCNT1, SCN1A, SCN2A, SCN8A, and UBA5 genes, which present severe pharmaco-resistant epilepsy, are increasingly becoming targets for RNA molecules that aim to restore neuronal excitability and network function. Together, these findings underscore the expanding therapeutic landscape enabled by RNA technologies, offering unprecedented specificity and flexibility for gene-targeted interventions in NDDs. As the field of RNA medicine continues to evolve across genomics and neuroscience, we aim to provide a resource for researchers and clinicians on promising innovative tools for molecular correction.
2024-10-16 | PLP1-Targeting Antisense Oligonucleotides Improve FOXG1 Syndrome Mice.
FOXG1 syndrome is a rare neurodevelopmental disorder of the telencephalon, for which there is no cure. Underlying heterozygous pathogenic variants in the Forkhead Box G1 (FOXG1) gene with resulting impaired or loss of FOXG1 function lead to severe neurological impairments. Here, we report a patient with a de novo pathogenic single nucleotide deletion c.946del (p.Leu316Cysfs*10) of the FOXG1 gene that causes a premature protein truncation. To study this variant in vivo, we generated and characterized Foxg1 c946del mice that recapitulate hallmarks of the human disorder. Accordingly, heterozygous Foxg1 c946del mice display neurological symptoms with aberrant neuronal networks and increased seizure susceptibility. Gene expression profiling identified increased oligodendrocyte- and myelination-related gene clusters. Specifically, we showed that expression of the c946del mutant and of other pathogenic FOXG1 variants correlated with overexpression of proteolipid protein 1 (Plp1), a gene linked to white matter disorders. Postnatal administration of Plp1-targeting antisense oligonucleotides (ASOs) in Foxg1 c946del mice improved neurological deficits. Our data suggest Plp1 as a new target for therapeutic strategies mitigating disease phenotypes in FOXG1 syndrome patients.
2019-04-30 | Enhancing Neuronogenesis and Counteracting Neuropathogenic Gene Haploinsufficiencies by RNA Gene Activation.
Small activating RNAs (saRNAs), targeting endogenous genes and stimulating their transcription, are a promising tool for implementing a variety of neurotherapeutic strategies. Among these there is the stimulation of select histogenetic subroutines for purposes of cell-based brain repair, as well as the therapeutic treatment of gene expression deficits underlying severe neurological disorders.We employed RNA activation (RNAa) to transactivate the Emx2 transcription factor gene in embryonic cortico-cerebral precursor cells. This led to enhanced self-renewal, delayed differentiation, and reduced death of neuronally committed precursors, resulting in a remarkable expansion of the neuronogenic precursors pool. These results are of paramount interest for purposes of gene-promoted brain repair. As such, RNAa makes therapeutic stimulation of neuronogenesis via Emx2 overexpression a feasible goal, preventing the drawbacks of exogenous gene copies introduction.Moreover, we employed RNAa to achieve a gentle transactivation of the Foxg1 transcription factor gene, specifically in cortico-cerebral cells. This manipulation led to an appreciable biological outcome, while complying with endogenous gene tuning linked to early central nervous system regionalization and late activity of neocortical projection neurons. Foxg1-activating miRNAs stimulated RNApolII recruitment, possibly via Ago1. One of them worked promisingly in vivo. As such, RNAa can be a valuable approach for therapeutic treatment of the FOXG1-haploinsufficiency-linked variant of the Rett syndrome. Remarkably, hemizygosity for specific genes and polygenic chromosomal segments underlies a huge number of neuropathological entities for which no cure is presently available. Based on the results reported above, RNAa might be a simple and scalable approach for fixing this class of problems.
2016-12-30 | Clinical Utility of a Comprehensive, Whole Genome CMA Testing Platform in Pediatrics: A Prospective Randomized Controlled Trial of Simulated Patients in Physician Practices
Developmental disorders (DD), including autism spectrum disorder (ASD) and intellectual disability (ID), are a common group of clinical manifestations caused by a variety of genetic abnormalities. Genetic testing, including chromosomal microarray (CMA), plays an important role in diagnosing these conditions, but CMA can be limited by incomplete coverage of genetic abnormalities and lack of guidance for conditions rarely seen by treating physicians.We conducted a longitudinal, randomized controlled trial investigating the impact of a higher resolution 2.8 million (MM) probe-CMA test on the quality of care delivered by practicing general pediatricians and specialists. To overcome the twin problems of finding an adequate sample size of multiple rare conditions and under/incorrect diagnoses, we used standardized simulated patients known as CPVs. Physicians, randomized into control and intervention groups, cared for the CPV pediatric patients with DD/ASD/ID. Care responses were scored against evidence-based criteria. In round one, participants could order diagnostic tests including existing CMA tests. In round two, intervention physicians could order the 2.8MM probe-CMA test. Outcome measures included overall quality of care and quality of the diagnosis and treatment plan.Physicians ordering CMA testing had 5.43% (p<0.001) higher overall quality scores than those who did not. Intervention physicians ordering the 2.8MM probe-CMA test had 7.20% (p<0.001) higher overall quality scores. Use of the 2.8MM probe-CMA test led to a 10.9% (p<0.001) improvement in the diagnosis and treatment score. Introduction of the 2.8MM probe-CMA test led to significant improvements in condition-specific interventions including an 8.3% (p = 0.04) improvement in evaluation and therapy for gross motor delays caused by Hunter syndrome, a 27.5% (p = 0.03) increase in early cognitive intervention for FOXG1-related disorder, and an 18.2% (p<0.001) improvement in referrals to child neurology for Dravet syndrome.Physician use of the 2.8MM probe-CMA test significantly improves overall quality as well as diagnosis and treatment quality for simulated cases of pediatric DD/ASD/ID patients, and delivers additional clinical utility over existing CMA tests.
2016-12-20 | RNA activation of haploinsufficient Foxg1 gene in murine neocortex
Abstract More than one hundred distinct gene hemizygosities are specifically linked to epilepsy, mental retardation, autism, schizophrenia and neuro-degeneration. Radical repair of these gene deficits via genome engineering is hardly feasible. The same applies to therapeutic stimulation of the spared allele by artificial transactivators. Small activating RNAs (saRNAs) offer an alternative, appealing approach. As a proof-of-principle, here we tested this approach on the Rett syndrome-linked, haploinsufficient, Foxg1 brain patterning gene. We selected a set of artificial small activating RNAs (saRNAs) upregulating it in neocortical precursors and their derivatives. Expression of these effectors achieved a robust biological outcome. saRNA-driven activation (RNAa) was limited to neural cells which normally express Foxg1 and did not hide endogenous gene tuning. saRNAs recognized target chromatin through a ncRNA stemming from it. Gene upregulation required Ago1 and was associated to RNApolII enrichment throughout the Foxg1 locus. Finally, saRNA delivery to murine neonatal brain replicated Foxg1 -RNAa in vivo .
gene therapies
2025-11-27 | Temporal lobe-predominant cortical dysplasia with mild cortical thickening in FOXG1 syndrome
Forkhead box G1 ( FOXG1 ) gene syndrome is a neurodevelopmental disorder characterized by severe developmental delays, microcephaly, autistic features, epilepsy, and complex hyperkinetic-dyskinetic movement disorders. We present the case of a Japanese patient with microcephaly, cortical dysplasia with irregular gyri and mild cortical thickening in the temporal and frontal lobes, and a de novo heterozygous missense variant in FOXG1 . The patient was an 11-year-old Japanese boy who presented with microcephaly at 3 months of age. At 2 years and 10 months of age, he presented with frequent tonic seizures of unknown onset. Physical examination revealed microcephaly and dysmorphic features. He exhibited severe developmental delays and generalized hypotonia. Brain magnetic resonance imaging (MRI) revealed anterior hypogenesis of the corpus callosum, decreased cerebral volume, mildly delayed myelination, and cortical dysplasia with irregular gyri and mild cortical thickening, particularly in the temporal lobes. His seizures resolved after administering carbamazepine. Trio-based whole-exome sequencing analysis of the patient and his parents revealed a de novo heterozygous missense variant, NM_005249.5:c.688C>T p.(Arg230Cys), located in the forkhead DNA-binding domain of FOXG1 , a recurrent variant that was finally diagnosed as FOXG1 syndrome. Cortical malformation in FOXG1 syndrome is often observed in the frontal lobe. The cortical dysplasia and mild cortical thickening observed in our patient was predominantly in the temporal cortex, suggesting distinctive findings. These results provide new insights into brain malformations associated with FOXG1 syndrome.
2025-05-23 | The patient-specific mouse model with Foxg1 frameshift mutation provides insights into the pathophysiology of FOXG1 syndrome.
Single allelic mutations in the FOXG1 gene lead to FOXG1 syndrome (FS). To understand the pathophysiology of FS, which vary depending on FOXG1 mutation types, patient-specific animal models are critical. Here, we report a patient-specific Q84Pfs heterozygous (Q84Pfs-Het) mouse model, which recapitulates various FS phenotypes across cellular, brain structural, and behavioral levels. Q84Pfs-Het cortex shows dysregulations of genes controlling cell proliferation, neuronal projection and migration, synaptic assembly, and synaptic vesicle transport. The Q84Pfs allele produces the N-terminal fragment of FOXG1 (Q84Pfs protein) in Q84Pfs-Het mouse brains, which forms intracellular speckles, interacts with FOXG1 full-length protein, and triggers the sequestration of FOXG1 to distinct subcellular domains. Q84Pfs protein promotes the radial glial cell identity and suppresses neuronal migration in the cortex. Our study uncovers the role of the FOXG1 fragment from FS-causing FOXG1 variants and identifies the genes involved in FS-like cellular and behavioral phenotypes, providing insights into the pathophysiology of FS.
2025-04-17 | A modular CRISPRa system for molecular therapy of FOXG1 syndrome
Abstract To date, there is an unmet need for novel approaches that address haploinsufficiency disorders in a targeted and robust manner. Here, we developed a novel, modular tool for transcriptional regulation of genes involved in neurodevelopmental disease in the absence of creating double-stranded breaks. We utilized this novel platform technology to identify single guide RNA (sgRNAs) that efficiently regulate expression of the intellectual disability gene FOXG1 that utilizes an optimized protein intein system. Using a modular assembly of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) trans-activators, including single and dual VP64 (tetramer of herpes simplex virus VP16 peptide) dCas9 fusion proteins, sgRNA-mediated MS2 p65 HSF (MPH) recruitment or the addition of the VPR tripartite effector (VP64, p65, and Rta) can induce dynamic gene regulation. We further increased messenger RNA (mRNA) levels of FOXG1 using duplexed sgRNAs paired with different combinations of transcriptional activators. We demonstrate that FOXG1 gene upregulation results in a significant increase in FoxG1 protein translation. Following treatment of mutant FOXG1 neural stem cells with the CRISPR activators, we observed a significant increase in FOXG1 expression with no-off targets as determined by in silico sgRNA binding prediction paired with RNA-sequencing. This approach holds great promise as a modular platform technology that is readily adapted for gene therapy delivery for those affected by rare genetic conditions.
2020-06-15 | AAV-mediated FOXG1 gene editing in human Rett primary cells
Variations in the Forkhead Box G1 (FOXG1) gene cause FOXG1 syndrome spectrum, including the congenital variant of Rett syndrome, characterized by early onset of regression, Rett-like and jerky movements, and cortical visual impairment. Due to the largely unknown pathophysiological mechanisms downstream the impairment of this transcriptional regulator, a specific treatment is not yet available. Since both haploinsufficiency and hyper-expression of FOXG1 cause diseases in humans, we reasoned that adding a gene under nonnative regulatory sequences would be a risky strategy as opposed to a genome editing approach where the mutated gene is reversed into wild-type. Here, we demonstrate that an adeno-associated viruses (AAVs)-coupled CRISPR/Cas9 system is able to target and correct FOXG1 variants in patient-derived fibroblasts, induced Pluripotent Stem Cells (iPSCs) and iPSC-derived neurons. Variant-specific single-guide RNAs (sgRNAs) and donor DNAs have been selected and cloned together with a mCherry/EGFP reporter system. Specific sgRNA recognition sequences were inserted upstream and downstream Cas9 CDS to allow self-cleavage and inactivation. We demonstrated that AAV serotypes vary in transduction efficiency depending on the target cell type, the best being AAV9 in fibroblasts and iPSC-derived neurons, and AAV2 in iPSCs. Next-generation sequencing (NGS) of mCherry+/EGFP+ transfected cells demonstrated that the mutated alleles were repaired with high efficiency (20–35% reversion) and precision both in terms of allelic discrimination and off-target activity. The genome editing strategy tested in this study has proven to precisely repair FOXG1 and delivery through an AAV9-based system represents a step forward toward the development of a therapy for Rett syndrome.
2019-09-04 | Knockdown of Foxg1 in supporting cells increases the trans-differentiation of supporting cells into hair cells in the neonatal mouse cochlea
Foxg1 is one of the forkhead box genes that are involved in morphogenesis, cell fate determination, and proliferation, and Foxg1 was previously reported to be required for morphogenesis of the mammalian inner ear. However, Foxg1 knock-out mice die at birth, and thus the role of Foxg1 in regulating hair cell (HC) regeneration after birth remains unclear. Here we used Sox2CreER/+ Foxg1loxp/loxp mice and Lgr5-EGFPCreER/+ Foxg1loxp/loxp mice to conditionally knock down Foxg1 specifically in Sox2+ SCs and Lgr5+ progenitors, respectively, in neonatal mice. We found that Foxg1 conditional knockdown (cKD) in Sox2+ SCs and Lgr5+ progenitors at postnatal day (P)1 both led to large numbers of extra HCs, especially extra inner HCs (IHCs) at P7, and these extra IHCs with normal hair bundles and synapses could survive at least to P30. The EdU assay failed to detect any EdU+ SCs, while the SC number was significantly decreased in Foxg1 cKD mice, and lineage tracing data showed that much more tdTomato+ HCs originated from Sox2+ SCs in Foxg1 cKD mice compared to the control mice. Moreover, the sphere-forming assay showed that Foxg1 cKD in Lgr5+ progenitors did not significantly change their sphere-forming ability. All these results suggest that Foxg1 cKD promotes HC regeneration and leads to large numbers of extra HCs probably by inducing direct trans-differentiation of SCs and progenitors to HCs. Real-time qPCR showed that cell cycle and Notch signaling pathways were significantly down-regulated in Foxg1 cKD mice cochlear SCs. Together, this study provides new evidence for the role of Foxg1 in regulating HC regeneration from SCs and progenitors in the neonatal mouse cochlea.
other
2022-05-02 | FOXG1 dose tunes cell proliferation dynamics in human forebrain progenitor cells.
Heterozygous loss-of-function mutations in Forkhead box G1 (FOXG1), a uniquely brain-expressed gene, cause microcephaly, seizures, and severe intellectual disability, whereas increased FOXG1 expression is frequently observed in glioblastoma. To investigate the role of FOXG1 in forebrain cell proliferation, we modeled FOXG1 syndrome using cells from three clinically diagnosed cases with two sex-matched healthy parents and one unrelated sex-matched control. Cells with heterozygous FOXG1 loss showed significant reduction in cell proliferation, increased ratio of cells in G0/G1 stage of the cell cycle, and increased frequency of primary cilia. Engineered loss of FOXG1 recapitulated this effect, while isogenic repair of a patient mutation reverted output markers to wild type. An engineered inducible FOXG1 cell line derived from a FOXG1 syndrome case demonstrated that FOXG1 dose-dependently affects all cell proliferation outputs measured. These findings provide strong support for the critical importance of FOXG1 levels in controlling human brain cell growth in health and disease.
2019-05-01 | WNT/NOTCH Pathway Is Essential for the Maintenance and Expansion of Human MGE Progenitors
Medial ganglionic eminence (MGE)-like cells yielded from human pluripotent stem cells (hPSCs) hold great potentials for cell therapies of related neurological disorders. However, cues that orchestrate the maintenance versus differentiation of human MGE progenitors, and ways for large-scale expansion of these cells have not been investigated. Here, we report that WNT/CTNNB1 signaling plays an essential role in maintaining MGE-like cells derived from hPSCs. Ablation of CTNNB1 in MGE cells led to precocious cell-cycle exit and advanced neuronal differentiation. Activation of WNT signaling through genetic or chemical approach was sufficient to maintain MGE cells in an expandable manner with authentic neuronal differentiation potencies through activation of endogenous NOTCH signaling. Our findings reveal that WNT/NOTCH signaling cascade is a key player in governing the maintenance versus terminal differentiation of MGE progenitors in humans. Large-scale expansion of functional MGE progenitors for cell therapies can therefore be achieved by modifying WNT/NOTCH pathway.
2016-04-01 | Forced cell cycle exit and modulation of GABAA, CREB, and GSK3β signaling promote functional maturation of induced pluripotent stem cell-derived neurons.
Although numerous protocols have been developed for differentiation of neurons from a variety of pluripotent stem cells, most have concentrated on being able to specify effectively appropriate neuronal subtypes and few have been designed to enhance or accelerate functional maturity. Of those that have, most employ time courses of functional maturation that are rather protracted, and none have fully characterized all aspects of neuronal function, from spontaneous action potential generation through to postsynaptic receptor maturation. Here, we describe a simple protocol that employs the sequential addition of just two supplemented media that have been formulated to separate the two key phases of neural differentiation, the neurogenesis and synaptogenesis, each characterized by different signaling requirements. Employing these media, this new protocol synchronized neurogenesis and enhanced the rate of maturation of pluripotent stem cell-derived neural precursors. Neurons differentiated using this protocol exhibited large cell capacitance with relatively hyperpolarized resting membrane potentials; moreover, they exhibited augmented: 1) spontaneous electrical activity; 2) regenerative induced action potential train activity; 3) Na + current availability, and 4) synaptic currents. This was accomplished by rapid and uniform development of a mature, inhibitory GABA A receptor phenotype that was demonstrated by Ca 2+ imaging and the ability of GABA A receptor blockers to evoke seizurogenic network activity in multielectrode array recordings. Furthermore, since this protocol can exploit expanded and frozen prepatterned neural progenitors to deliver mature neurons within 21 days, it is both scalable and transferable to high-throughput platforms for the use in functional screens.
2013-06-01 | Rapid Single-Step Induction of Functional Neurons from Human Pluripotent Stem Cells
Available methods for differentiating human embryonic stem cells (ESCs) and induced pluripotent cells (iPSCs) into neurons are often cumbersome, slow, and variable. Alternatively, human fibroblasts can be directly converted into induced neuronal (iN) cells. However, with present techniques conversion is inefficient, synapse formation is limited, and only small amounts of neurons can be generated. Here, we show that human ESCs and iPSCs can be converted into functional iN cells with nearly 100% yield and purity in less than 2 weeks by forced expression of a single transcription factor. The resulting ES-iN or iPS-iN cells exhibit quantitatively reproducible properties independent of the cell line of origin, form mature pre- and postsynaptic specializations, and integrate into existing synaptic networks when transplanted into mouse brain. As illustrated by selected examples, our approach enables large-scale studies of human neurons for questions such as analyses of human diseases, examination of human-specific genes, and drug screening.
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Drug Discovery Landscape
1 orphan drug designation for FOXG1 syndrome.
1 orphan drug designation for FOXG1 syndrome.
Drug | Therapy type | Regulator | Orphan designation | Approval | Sponsor |
|---|---|---|---|---|---|
AAV9/hFOXG1 construct harboring the human Synapsin 1 promoter designed to predominantly drive human FOXG1 expression in neurons | gene therapies | FDA | 2025-09-26 | — | FOXG1 Research Foundation |
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