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The contribution of de novo coding mutations to meningomyelocele

Yoo-Jin Ha, Isaac Tang, Ashna Nisal, Ishani Jhamb, Cassidy Wallace, Sarah Schroeder, Chanjae Lee, Keng loi Vong, Naomi Meave, Fiza Jiwani, Chelsea Barrows, Sangmoon Lee, Nan Jiang, Arzoo Patel, Francisco A. Blanco, Seyoung Yu, Hui Su Jeong, Isaac Plutzer, Michael B. Major, Béatrice Benoit, Christian Poüs, Caleb Heffner, Zoha Kibar, Gyang Markus Bot, Hope Northrup, Kit Sing Au, Madison Strain, Allison Ashley-Koch, Richard H. Finnell, Joan T. Le, Hal Meltzer, Camila Araujo, Helio R. Machado, Roger E. Stevenson, Anna Yurrita, Sara Mumtaz, Osvaldo M. Mutchinick, José Ramón Medina-Bereciartu, Friedhelm Hildebrandt, Gia Melikishvili, Rony Marwan, Valeria Capra, Mahmoud M. Noureldeen, Aida M.S. Salem, Mahmoud Y. Issa, Maha S. Zaki, Ji Eun Lee, Anna Alkelai, Alan R. Shuldiner, Stephen F. Kingsmore, Stephen A. Murray, Heon Yung Gee, W. Todd Miller, Kimberley F. Tolias, John B. Wallingford, Spina Bifida Sequencing Consortium, Sangwoo Kim, Joseph G. Gleeson

medRxiv, March 2, 2024. ABSTRACT Meningomyelocele (MM) is considered a genetically complex disease resulting from failure of neural tube closure (NTD). Patients display neuromotor disability and frequent hydrocephalus requiring ventricular shunting. A few proposed genes contribute to disease susceptibility, but most risk remains unexplained. We postulated that de novo mutations (DNMs) under purifying selection contribute to MM risk. Here we recruited a cohort of 851 MM trios requiring shunting at birth, compared with 732 control trios, and found that de novo likely gene disrupting or damaging missense mutations occur in approximately 22.3% of subjects, 28% of which are estimated to contribute to disease risk. The 187 genes with damaging DNMs collectively define networks including actin cytoskeleton and microtubule-based processes, axon guidance, and histone modification. Gene validation demonstrates partial or complete loss of function, impaired signaling and defective neural tube closure in Xenopus embryos. Our results suggest DNMs make key contributions to MM risk, and highlight critical pathways required for neural tube closure in human embryogenesis. DOI:10.1101/2024.02.28.24303390

March 2, 2024

Loss of symmetric cell division of apical neural progenitors drives DENND5A -related developmental and epileptic encephalopathy

Banks E, Francis V, Lin SJ, Kharfallah F, Fonov V, Levesque M, Han C, Kulasekaran G, Tuznik M, Bayati A, Al-Khater R, Alkuraya FS, Argyriou L, Babaei M, Bahlo M, Bakhshoodeh B, Barr E, Bartik L, Bassiony M, Bertrand M, Braun D, Buchert R, Budetta M, Cadieux-Dion M, Calame D, Cope H, Cushing D, Efthymiou S, Elmaksoud MA, El Said HG, Froukh T, Gill HK, Gleeson JG, Gogoll L, Goh ES, Gowda VK, Haack TB, Hashem MO, Hauser S, Hoffman TL, Hogue JS, Hosokawa A, Houlden H, Huang K, Huynh S, Karimiani EG, Kaulfuß S, Korenke GC, Kritzer A, Lee H, Lupski JR, Marco EJ, McWalter K, Minassian A, Minassian BA, Murphy D, Neira-Fresneda J, Northrup H, Nyaga D, Oehl-Jaschkowitz B, Osmond M, Person R, Pehlivan D, Petree C, Sadleir LG, Saunders C, Schoels L, Shashi V, Spillman RC, Srinivasan VM, Torbati PN, Tos T; Undiagnosed Diseases Network; Zaki MS, Zhou D, Zweier C, Trempe JF, Durcan TM, Gan-Or Z, Avoli M, Alves C, Varshney GK, Maroofian R, Rudko DA, McPherson PS.

medRxiv. 2024 Jan 31:2022.08.23.22278845. doi: 10.1101/2022.08.23.22278845. Preprint. ABSTRACT Developmental and epileptic encephalopathies (DEEs) are a heterogenous group of epilepsies in which altered brain development leads to developmental delay and seizures, with the epileptic activity further negatively impacting neurodevelopment. Identifying the underlying cause of DEEs is essential for progress toward precision therapies. Here we describe a group of individuals with biallelic variants in DENND5A and determine that variant type is correlated with disease severity. We demonstrate that DENND5A interacts with MUPP1 and PALS1, components of the Crumbs apical polarity complex, which is required for both neural progenitor cell identity and the ability of these stem cells to divide symmetrically. Induced pluripotent stem cells lacking DENND5A fail to undergo symmetric cell division during neural induction and have an inherent propensity to differentiate into neurons, and transgenic DENND5A mice, with phenotypes like the human syndrome, have an increased number of neurons in the adult subventricular zone. Disruption of symmetric cell division following loss of DENND5A results from misalignment of the mitotic spindle in apical neural progenitors. A subset of DENND5A is localized to centrosomes, which define the spindle poles during mitosis. Cells lacking DENND5A orient away from the proliferative apical domain surrounding the ventricles, biasing daughter cells towards a more fate-committed state and ultimately shortening the period of neurogenesis. This study provides a mechanism behind DENND5A -related DEE that may be generalizable to other developmental conditions and provides variant-specific clinical information for physicians and families. PMID:38352438 | PMC:PMC10863025 | DOI:10.1101/2022.08.23.22278845

January 31, 2024

The clinical and genetic landscape of developmental and epileptic encephalopathies in Egyptian children

Elkhateeb N, Issa MY, Elbendary HM, Elnaggar W, Ramadan A, Rafat K, Kamel M, Abdel-Ghafar SF, Amer F, Hassaan HM, Trunzo R, Pereira C, Abdel-Hamid MS, D’Arco F, Bauer P, Bertoli-Avella AM, Girgis M, Gleeson JG, Zaki MS, Selim L.

Clin Genet. 2024 Jan 14. doi: 10.1111/cge.14481. Online ahead of print. ABSTRACT Developmental and epileptic encephalopathies (DEEs) are a heterogeneous group of epilepsies characterized by early-onset, refractory seizures associated with developmental regression or impairment, with a heterogeneous genetic landscape including genes implicated in various pathways and mechanisms. We retrospectively studied the clinical and genetic data of patients with genetic DEE who presented at two tertiary centers in Egypt over a 10-year period. Exome sequencing was used for genetic testing. We report 74 patients from 63 unrelated Egyptian families, with a high rate of consanguinity (58%). The most common seizure type was generalized tonic-clonic (58%) and multiple seizure types were common (55%). The most common epilepsy syndrome was early infantile DEE (50%). All patients showed variable degrees of developmental impairment. Microcephaly, hypotonia, ophthalmological involvement and neuroimaging abnormalities were common. Eighteen novel variants were identified and the phenotypes of five DEE genes were expanded with novel phenotype-genotype associations. Obtaining a genetic diagnosis had implications on epilepsy management in 17 patients with variants in 12 genes. In this study, we expand the phenotype and genotype spectrum of DEE in a large single ethnic cohort of patients. Reaching a genetic diagnosis guided precision management of epilepsy in a significant proportion of patients. PMID:38221827 | DOI:10.1111/cge.14481

January 14, 2024


Gain-of-function and loss-of-function variants in GRIA3 lead to distinct neurodevelopmental phenotypes

Rinaldi B, Bayat A, Zachariassen LG, Sun JH, Ge YH, Zhao D, Bonde K, Madsen LH, Awad IAA, Bagiran D, Sbeih A, Shah SM, El-Sayed S, Lyngby SM, Pedersen MG, Stenum-Berg C, Walker LC, Krey I, Delahaye-Duriez A, Emrick LT, Sully K, Murali CN, Burrage LC, Plaud Gonzalez JA, Parnes M, Friedman J, Isidor B, Lefranc J, Redon S, Heron D, Mignot C, Keren B, Fradin M, Dubourg C, Mercier S, Besnard T, Cogne B, Deb W, Rivier C, Milani D, Bedeschi MF, Di Napoli C, Grilli F, Marchisio P, Koudijs S, Veenma D, Argilli E, Lynch SA, Au PYB, Ayala Valenzuela FE, Brown C, Masser-Frye D, Jones M, Patron Romero L, Li WL, Thorpe E, Hecher L, Johannsen J, Denecke J, McNiven V, Szuto A, Wakeling E, Cruz V, Sency V, Wang H, Piard J, Kortüm F, Herget T, Bierhals T, Condell A, Zeev BB, Kaur S, Christodoulou J, Piton A, Zweier C, Kraus C, Micalizzi A, Trivisano M, Specchio N, Lesca G, Møller RS, Tümer Z, Musgaard M, Gerard B, Lemke JR, Shi YS, Kristensen AS.

Brain. 2023 Dec 1:awad403. doi: 10.1093/brain/awad403. Online ahead of print. ABSTRACT AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) receptors (AMPARs) mediate fast excitatory neurotransmission in the brain. AMPARs form by homo- or heteromeric assembly of subunits encoded by the GRIA1-GRIA4 genes, of which only GRIA3 is X-chromosomal. Increasing numbers of GRIA3 missense variants are reported in patients with neurodevelopmental disorders (NDD), but only a few have been examined functionally. Here, we evaluated the impact on AMPAR function of one frameshift and 43 rare missense GRIA3 variants identified in patients with NDD by electrophysiological assays. Thirty-one variants alter receptor function and show loss-of-function (LoF) or gain-of-function (GoF) properties, whereas 13 appeared neutral. We collected detailed clinical data from 25 patients (from 23 families) harbouring 17 of these variants. All patients had global developmental impairment, mostly moderate (9/25) or severe (12/25). Twelve patients had seizures, including focal motor (6/12), unknown onset motor (4/12), focal impaired awareness (1/12), (atypical) absence (2/12), myoclonic (5/12), and generalized tonic-clonic (1/12) or atonic (1/12) seizures. The epilepsy syndrome was classified as developmental and epileptic encephalopathy in eight patients, developmental encephalopathy without seizures in 13 patients, and intellectual disability with epilepsy in four patients. Limb muscular hypotonia was reported in 13/25, and hypertonia in 10/25. Movement disorders were reported in 14/25, with hyperekplexia or non-epileptic erratic myoclonus being the most prevalent feature (8/25). Correlating receptor functional phenotype with clinical features revealed clinical features for GRIA3-associated NDDs and distinct NDD phenotypes for LoF and GoF variants. GoF variants were associated with more severe outcomes: patients were younger at the time of seizure onset (median age one month), hypertonic, and more often had movement disorders, including hyperekplexia. Patients with LoF variants were older at the time of seizure onset (median age 16 months), hypotonic, and had sleeping disturbances. LoF and GoF variants were disease-causing in both sexes but affected males often carried de novo or hemizygous LoF variants inherited from healthy mothers, whereas all but one affected females had de novo heterozygous GoF variants. PMID:38038360 | DOI:10.1093/brain/awad403

December 1, 2023

Sunflower Syndrome: A Survey of Provider Awareness and Management Preferences

Baumer FM, Julich K, Friedman J, Nespeca M, Thiele EA, Bhatia S, Joshi C.

Pediatr Neurol. 2023 Nov 30;152:177-183. doi: 10.1016/j.pediatrneurol.2023.11.013. Online ahead of print. ABSTRACT BACKGROUND: Sunflower syndrome is a rare photosensitive pediatric epilepsy characterized by stereotyped hand-waving in response to bright lights. These stereotyped movements with maintained awareness can be mistaken for a movement disorder. This study assessed neurology providers’ diagnostic reasoning, evaluation, and treatment of Sunflower syndrome. METHODS: A 32-question anonymized electronic survey, including a clinical vignette and video of hand-waving in sunlight, was distributed to child neurology providers to assess (1) initial diagnosis and evaluation based on clinical information, (2) updated diagnosis and management after electroencephalography (EEG), and (3) prior experience with Sunflower syndrome. RESULTS: Among 277 viewed surveys, 211 respondents provided information about initial diagnosis and evaluation, 200 about updated diagnosis, 191 about management, and 189 about prior clinical experience. Most providers (135, 64%) suspected seizure, whereas fewer suspected movement disorders (29, 14%) or were unsure of the diagnosis (37, 22%). EEG was recommended by 180 (85%). After EEG, 189 (95%) diagnosed epilepsy, 111 of whom specifically diagnosed Sunflower syndrome. The majority (149, 78%) recommended antiseizure medications (ASMs) and sun avoidance (181, 95%). Only 103 (55%) had managed Sunflower syndrome. Epileptologists and those with prior clinical experience were more likely to suspect a seizure, order an EEG, and offer ASMs than those without prior experience. CONCLUSIONS: Although many providers had not managed Sunflower syndrome, the majority recognized this presentation as concerning for epilepsy. Epilepsy training and prior clinical experience are associated with improved recognition and appropriate treatment. Educational initiatives that increase awareness of Sunflower syndrome may improve patient care. PMID:38295719 | DOI:10.1016/j.pediatrneurol.2023.11.013

November 30, 2023
Genetic Neurologic DiseaseNeurogenomics

Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases

Garrison MA, Jang Y, Bae T, Cherskov A, Emery SB, Fasching L, Jones A, Moldovan JB, Molitor C, Pochareddy S, Peters MA, Shin JH, Wang Y, Yang X, Akbarian S, Chess A, Gage FH, Gleeson JG, Kidd JM, McConnell M, Mills RE, Moran JV, Park PJ, Sestan N, Urban AE, Vaccarino FM, Walsh CA, Weinberger DR, Wheelan SJ, Abyzov A; BSMN Consortium.

Sci Data. 2023 Nov 20;10(1):813. doi: 10.1038/s41597-023-02645-7. ABSTRACT Somatic mosaicism is defined as an occurrence of two or more populations of cells having genomic sequences differing at given loci in an individual who is derived from a single zygote. It is a characteristic of multicellular organisms that plays a crucial role in normal development and disease. To study the nature and extent of somatic mosaicism in autism spectrum disorder, bipolar disorder, focal cortical dysplasia, schizophrenia, and Tourette syndrome, a multi-institutional consortium called the Brain Somatic Mosaicism Network (BSMN) was formed through the National Institute of Mental Health (NIMH). In addition to genomic data of affected and neurotypical brains, the BSMN also developed and validated a best practices somatic single nucleotide variant calling workflow through the analysis of reference brain tissue. These resources, which include >400 terabytes of data from 1087 subjects, are now available to the research community via the NIMH Data Archive (NDA) and are described here. PMID:37985666 | DOI:10.1038/s41597-023-02645-7

November 20, 2023

Bi-allelic loss-of-function variants in WBP4, encoding a spliceosome protein, result in a variable neurodevelopmental syndrome

Engal E, Oja KT, Maroofian R, Geminder O, Le TL, Marzin P, Guimier A, Mor E, Zvi N, Elefant N, Zaki MS, Gleeson JG, Muru K, Pajusalu S, Wojcik MH, Pachat D, Elmaksoud MA, Chan Jeong W, Lee H, Bauer P, Zifarelli G, Houlden H, Daana M, Elpeleg O, Amiel J, Lyonnet S, Gordon CT, Harel T, Õunap K, Salton M, Mor-Shaked H.

Am J Hum Genet. 2023 Nov 13:S0002-9297(23)00366-X. doi: 10.1016/j.ajhg.2023.10.013. Online ahead of print. ABSTRACT Over two dozen spliceosome proteins are involved in human diseases, also referred to as spliceosomopathies. WW domain-binding protein 4 (WBP4) is part of the early spliceosomal complex and has not been previously associated with human pathologies in the Online Mendelian Inheritance in Man (OMIM) database. Through GeneMatcher, we identified ten individuals from eight families with a severe neurodevelopmental syndrome featuring variable manifestations. Clinical manifestations included hypotonia, global developmental delay, severe intellectual disability, brain abnormalities, musculoskeletal, and gastrointestinal abnormalities. Genetic analysis revealed five different homozygous loss-of-function variants in WBP4. Immunoblotting on fibroblasts from two affected individuals with different genetic variants demonstrated a complete loss of protein, and RNA sequencing analysis uncovered shared abnormal splicing patterns, including in genes associated with abnormalities of the nervous system, potentially underlying the phenotypes of the probands. We conclude that bi-allelic variants in WBP4 cause a developmental disorder with variable presentations, adding to the growing list of human spliceosomopathies. PMID:37963460 | DOI:10.1016/j.ajhg.2023.10.013

November 13, 2023

Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders

Kaiyrzhanov R, Rad A, Lin SJ, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G, Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R.

Brain. 2023 Nov 10:awad380. doi: 10.1093/brain/awad380. Online ahead of print. ABSTRACT The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders. PMID:37951597 | DOI:10.1093/brain/awad380

November 10, 2023

Post-zygotic brain mosaicism as a result of partial reversion of pre-zygotic aneuploidy

Chung C, Yang X, Gleeson JG.

Nat Genet. 2023 Oct 23. doi: 10.1038/s41588-023-01552-2. Online ahead of print. NO ABSTRACT PMID:37872451 DOI:10.1038/s41588-023-01552-2

October 23, 2023

Cell-type-resolved somatic mosaicism reveals clonal dynamics of the human forebrain

Chung C, Yang X, Hevner RF, Kennedy K, Vong KI, Liu Y, Patel A, Nedunuri R, Barton ST, Barrows C, Stanley V, Mittal S, Breuss MW, Schlachetzki JCM, Gleeson JG.

bioRxiv. 2023 Oct 26:2023.10.24.563814. doi: 10.1101/2023.10.24.563814. Preprint. ABSTRACT Debate remains around anatomic origins of specific brain cell subtypes and lineage relationships within the human forebrain. Thus, direct observation in the mature human brain is critical for a complete understanding of the structural organization and cellular origins. Here, we utilize brain mosaic variation within specific cell types as distinct indicators for clonal dynamics, denoted as cell-type-specific Mosaic Variant Barcode Analysis. From four hemispheres from two different human neurotypical donors, we identified 287 and 780 mosaic variants (MVs), respectively that were used to deconvolve clonal dynamics. Clonal spread and allelic fractions within the brain reveal that local hippocampal excitatory neurons are more lineage-restricted compared with resident neocortical excitatory neurons or resident basal ganglia GABAergic inhibitory neurons. Furthermore, simultaneous genome-transcriptome analysis at both a cell-type-specific and single-cell level suggests a dorsal neocortical origin for a subgroup of DLX1 + inhibitory neurons that disperse radially from an origin shared with excitatory neurons. Finally, the distribution of MVs across 17 locations within one parietal lobe reveals restrictions of clonal spread in the anterior-posterior axis precedes that of the dorsal-ventral axis for both excitatory and inhibitory neurons. Thus cell-type resolved somatic mosaicism can uncover lineage relationships governing the development of the human forebrain. PMID:37961480 | PMC:PMC10634852 | DOI:10.1101/2023.10.24.563814

October 15, 2023

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