2022
SELECTED PUBLICATIONS

AUGUST 2022

Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements

Ignacio L Ibarra, Vikram S Ratnu, Lucia Gordillo, In-Young Hwang, Luca Mariani, Kathryn Weinand, Henrik M Hammarén, Jennifer Heck, Martha L Bulyk, Mikhail M Savitski, Judith B Zaugg, Kyung-Min Noh

Neuronal stimulation induced by the brain-derived neurotrophic factor (BDNF) triggers gene expression, which is crucial for neuronal survival, differentiation, synaptic plasticity, memory formation, and neurocognitive health. However, its role in chromatin regulation is unclear. Here, using temporal profiling of chromatin accessibility and transcription in mouse primary cortical neurons upon either BDNF stimulation or depolarization (KCl), we identify features that define BDNF-specific chromatin-to-gene expression programs. Enhancer activation is an early event in the regulatory control of BDNF-treated neurons, where the bZIP motif-binding Fos protein pioneered chromatin opening and cooperated with co-regulatory transcription factors (Homeobox, EGRs, and CTCF) to induce transcription. Deleting cis-regulatory sequences affect BDNF-mediated Arc expression, a regulator of synaptic plasticity. BDNF-induced accessible regions are linked to preferential exon usage by neurodevelopmental disorder-related genes and the heritability of neuronal complex traits, which were validated in human iPSC-derived neurons. Thus, we provide a comprehensive view of BDNF-mediated genome regulatory features using comparative genomic approaches to dissect mammalian neuronal stimulation.

Autoinhibition of the GEF activity of cytoskeletal regulatory protein Trio is disrupted in neurodevelopmental disorder-related genetic variants.

Josie E. Bircher, Ellen E. Corcoran, TuKiet T. Lam, Michael J. Trnka, Anthony J. Koleske

TRIO encodes a cytoskeletal regulatory protein with three catalytic domains – two guanine exchange factor (GEF) domains, GEF1 and GEF2, and a kinase domain – as well as several accessory domains that have not been extensively studied. Function-damaging variants in the TRIO gene are known to be enriched in individuals with neurodevelopmental disorders (NDDs). Disease variants in the GEF1 domain or the nine adjacent spectrin repeats (SRs) are enriched in NDDs, suggesting that dysregulated GEF1 activity is linked to these disorders. We provide evidence here that the Trio SRs interact intramolecularly with the GEF1 domain to inhibit its enzymatic activity. We demonstrate that SRs 6-9 decrease GEF1 catalytic activity both in vitro and in cells and show that NDD-associated variants in the SR8 and GEF1 domains relieve this autoinhibitory constraint. Our results from chemical cross-linking and BioLayer Interferometry indicate that the SRs primarily contact the pleckstrin homology (PH) region of the GEF1 domain, reducing GEF1 binding to the small GTPase Rac1. Together, our findings reveal a key regulatory mechanism that is commonly disrupted in multiple NDDs and may offer a new target for therapeutic intervention for TRIO-associated NDDs.

Key role of Rho GTPases in motor disorders associated with neurodevelopmental pathologies

David I. Anderson; Evelyne Bloch-Gallego

Growing evidence suggests that Rho GTPases and molecules involved in their signaling pathways play a major role in the development of the central nervous system (CNS). Whole exome sequencing (WES) and de novo examination of mutations, including SNP (Single Nucleotide Polymorphism) in genes coding for the molecules of their signaling cascade, has allowed the recent discovery of dominant autosomic mutations and duplication or deletion of candidates in the field of neurodevelopmental diseases (NDD). Epidemiological studies show that the co-occurrence of several of these neurological pathologies may indeed be the rule. The regulators of Rho GTPases have often been considered for cognitive diseases such as intellectual disability (ID) and autism. But, in a remarkable way, mild to severe motor symptoms are now reported in autism and other cognitive NDD. Although a more abundant litterature reports the involvement of Rho GTPases and signaling partners in cognitive development, molecular investigations on their roles in central nervous system (CNS) development or degenerative CNS pathologies also reveal their role in embryonic and perinatal motor wiring through axon guidance and later in synaptic plasticity. Thus, Rho family small GTPases have been revealed to play a key role in brain functions including learning and memory but their precise role in motor development and associated symptoms in NDD has been poorly scoped so far, despite increasing clinical data highlighting the links between cognition and motor development. Indeed, early impairements in fine or gross motor performance is often an associated feature of NDDs, which then impact social communication, cognition, emotion, and behavior. We review here recent insights derived from clinical developmental neurobiology in the field of Rho GTPases and NDD (autism spectrum related disorder (ASD), ID, schizophrenia, hypotonia, spastic paraplegia, bipolar disorder and dyslexia), with a specific focus on genetic alterations affecting Rho GTPases that are involved in motor circuit development.

Hemimegalencephaly and Epileptic Encephalopathy Associated with a Variant of Uncertain Significance of the TRIO Gene

Eugenia ROZA, Ramona ANDREI, Raluca Ioana TELEANU

Electrical status epilepticus during sleep (ESES) is a type of EEG pattern seen in children with childhood-onset epileptic seizures and cognitive, language and motor regression. ESES has been associated with different etiologies, with or without structural abnormalities of the brain. To replace the term “ESES”, the recent Position Paper of the ILAE Taskforce on Nosology and Definitions introduced the term Epileptic Encephalopathy with Spike-Wave Activity during Sleep (EE-SWAS), which represents an activation of epileptiform activity, typically 1.5-2.5 Hz during NREM sleep, in a previously normal child and leads to cognitive and motor regression. Pathogenic variants in the TRIO gene are associated with autosomal dominant mental retardation type 44 (MRD44), which is characterized by mildly delayed global development resulting in variable intellectual deficits, learning difficulties, and variable dysmorphic features mostly represented by facial asymmetry, microcephaly, abnormalities of the fingers, and dental anomalies.

JULY 2022

Bridging between Mouse and Human Enhancer-Promoter Long-Range Interactions in Neural Stem Cells, to Understand Enhancer Function in Neurodevelopmental Disease

Romina D’Aurizio, Orazio Catona, Mattia Pitasi, Yang Eric Li, Bing Ren and Silvia Kirsten Nicolis

Non-coding variation in complex human disease has been well established by genome-wide association studies, and is thought to involve regulatory elements, such as enhancers, whose variation affects the expression of the gene responsible for the disease. The regulatory elements often lie far from the gene they regulate, or within introns of genes differing from the regulated gene, making it difficult to identify the gene whose function is affected by a given enhancer variation. Enhancers are connected to their target gene promoters via long-range physical interactions (loops). In our study, we re-mapped, onto the human genome, more than 10,000 enhancers connected to promoters via long-range interactions, that we had previously identified in mouse brain-derived neural stem cells by RNApolII-ChIA-PET analysis, coupled to ChIP-seq mapping of DNA/chromatin regions carrying epigenetic enhancer marks.

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A recent study including individuals with pathogenic variants of the TRIO gene highlighted a good genotype–phenotype correlation: missense mutations in the RAC1-activating GEF domain cause mild intellectual disability and microcephaly, missense mutations in the seventh spectrin repeat at the N-terminus underlie a phenotype characterized by severe intellectual disability and macrocephaly, while non-sense mutations in the TRIO sequence give rise to a more variable phenotype; interestingly, 31% of patients with pathogenic variants of the TRIO gene showed autistic traits …..

Variant-specific changes in RAC3 function disrupt corticogenesis in neurodevelopmental phenotypes

Marcello Scala, Masashi Nishikawa, Hidenori Ito, Hidenori Tabata, Tayyaba Khan, Andrea Accogli, Laura Davids, Anna Ruiz, Pietro Chiurazzi, Gabriella Cericola, Björn Schulte, Kristin G Monaghan, Amber Begtrup, Annalaura Torella, Michele Pinelli, Anne Sophie Denommé-Pichon, Antonio Vitobello, Caroline Racine, Maria Margherita Mancardi, Courtney Kiss, Andrea Guerin, Wendy Wu, Elisabeth Gabau Vila, Bryan C Mak, Julian A Martinez-Agosto, Michael B Gorin, Bugrahan Duz, Yavuz Bayram, Claudia M B Carvalho, Jaime E Vengoechea, David Chitayat, Tiong Yang Tan, Bert Callewaert, Bernd Kruse, Lynne M Bird, Laurence Faivre, Marcella Zollino, Saskia Biskup, Undiagnosed Diseases Network , Telethon Undiagnosed Diseases Program , Pasquale Striano, Vincenzo Nigro, Mariasavina Severino, Valeria Capra, Gregory Costain, Koh-ichi Nagata

Variants in RAC3, encoding a small GTPase RAC3 which is critical for the regulation of actin cytoskeleton and intracellular signal transduction, are associated with a rare neurodevelopmental disorder with structural brain anomalies and facial dysmorphism.

We investigated a cohort of 10 unrelated participants presenting with global psychomotor delay, hypotonia, behavioural disturbances, stereotyped movements, dysmorphic features, seizures and musculoskeletal abnormalities. MRI of brain revealed a complex pattern of variable brain malformations, including callosal abnormalities, white matter thinning, grey matter heterotopia, polymicrogyria/dysgyria, brainstem anomalies and cerebellar dysplasia.

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In this context, pathogenic variants in TRIO, encoding a GEF which activates RAC1 through the first GEF domain (GEFD1), were shown to cause neurodevelopmental impairment, behavioural disturbances, microcephaly or macrocephaly and skeletal features [autosomal dominant intellectual developmental disorder with microcephaly (MRD44, OMIM 617061) or macrocephaly (MRD63, OMIM 618825)].62,63 Affected individuals with variations in TRIO present with variable neurodevelopmental phenotypes.

JUNE 2022

Trio and Kalirin as unique enactors of Rho/Rac spatiotemporal precision

M.J. Grubisha, R.A. DeGiosio, Z.P. Wills, R.A. Sweet

Rac1 and RhoA are among the most widely studied small GTPases. The classic dogma surrounding their biology has largely focused on their activity as an “on/off switch” of sorts. However, the advent of more sophisticated techniques, such as genetically-encoded FRET-based sensors, has afforded the ability to delineate the spatiotemporal regulation of Rac1 and RhoA. As a result, there has been a shift from this simplistic global view to one incorporating the precision of spatiotemporal modularity. This review summarizes emerging data surrounding the roles of Rac1 and RhoA as cytoskeletal regulators and examines how these new data have led to a revision of the traditional dogma which placed Rac1 and RhoA in antagonistic pathways. This more recent evidence suggests that rather than absolute activity levels, it is the tight spatiotemporal regulation of Rac1 and RhoA across multiple roles, from oppositional to complementary, that is necessary to execute coordinated cytoskeletal processes affecting cell structure, function, and migration. We focus on how Kalirin and Trio, as dual GEFs that target Rac1 and RhoA, are uniquely designed to provide the spatiotemporally-precise shifts in Rac/Rho balance which mediate changes in neuronal structure and function, particularly by way of cytoskeletal rearrangements. Finally, we review how alterations in Trio and/or Kalirin function are associated with cellular abnormalities and neuropsychiatric disease.

May 2022

RhoA Signaling in Neurodegenerative Diseases

Sissel Ida Schmidt, Morten Blaabjerg, Kristine Freude and Morten Meyer

Ras homolog gene family member A (RhoA) is a small GTPase of the Rho family involved in regulating multiple signal transduction pathways that influence a diverse range of cellular functions. RhoA and many of its downstream effector proteins are highly expressed in the nervous system, implying an important role for RhoA signaling in neurons and glial cells. Indeed, emerging evidence points toward a role of aberrant RhoA signaling in neurodegenerative diseases such as Parkinson’s disease, Alzheimer’s disease, Huntington’s disease, and amyotrophic lateral sclerosis. In this review, we summarize the current knowledge of RhoA regulation and downstream cellular functions with an emphasis on the role of RhoA signaling in neurodegenerative diseases and the therapeutic potential of RhoA inhibition in neurodegeneration

February 2022

Phenotype and genotype spectrum of variants in guanine nucleotide exchange factor genes in a broad cohort of Iranian patients

Meysam Mosallaei, Naeim Ehtesham, Maryam Beheshtian, Shahrouz Khoshbakht, Behzad Davarnia, Kimia Kahrizi, Hossein Najmabadi

Guanine nucleotide exchange factors (GEFs) play pivotal roles in neuronal cell functions by exchanging GDP to GTP nucleotide and activation of GTPases. We aimed to determine the genotype and phenotype spectrum of GEF mutations by collecting data from a large Iranian cohort with intellectual disability (ID) and/or developmental delay (DD).