Neurogenomics

Research

Cracking
the Code

Identifying the cause of neurological disorders and early intervention are key to reducing the devastating brain damage that can occur. 

Neurological disorders can be caused both by inherited and random gene variations. Often, the first sign of a disorder in a newborn is unexplained seizures. 

RCIGM is involved in both foundational and translational research.

Neurodevelopmental Genetics

RCIGM investigations into inherited brain disorders focus on poorly understood conditions in neuronal development where the application of human genetics, wet-lab disease modeling and cell biology can be used to develop new treatments.
190227RadySeminar

Joseph Gleeson, MD

RCIGM Director of Neurodevelopmental Genetics Endowed Chair

Joseph Gleeson, MD, is the RCIGM Director of Neurodevelopmental Genetics Endowed Chair. Among his current research projects is a genetic investigation of the genetic mechanisms underlying spina bifida, the most common structural defect of the central nervous system.

In 2020 Dr. Gleeson along with other researchers at UC San Diego School of Medicine, in collaboration with Rady Children’s Institute for Genomic Medicine, were awarded an $8.3 million grant from the National Institutes of Health’s Eunice Kennedy Shriver National Institute of Child Health and Human Development to further illuminate the causes of spina bifida.

Dr. Gleeson also heads the Neurogenetics Laboratory at UC San Diego and is the Director of the Center for Brain Development. He is the 2020 recipient of the Bernard Sachs Award from the Child Neurology Society. In 2017, he was the first recipient of the Constance Lieber Prize for Innovation in Developmental Neuroscience.

Publications

The ClinGen Syndromic Disorders Gene Curation Expert Panel: Assessing the Clinical Validity of 111 Gene-Disease Relationships

  • Broeren E, Gitau V, Byrne A, Ajuyah P, Balzotti M, Berg J, Bluske K, Bowen BM, Brown MP, Buchanan A, Burns B, Burns NJ, Chandrasekhar A, Chawla A, Chong J, Chopra M, Clause A, DiStefano M, DiTroia S, Elnagheeb M, Girod A, Goel H, Golden-Grant K, Ha T, Hamosh A, Huang J, Hughes M, Jamuar S, Kam S, Kesari A, Koh AL, Lassiter R, Leigh S, Lemire G, Lim JY, Malhotra A, McCurry H, Milewski B, Moosa S, Murray S, Owens E, Palmer E, Palus B, Patel M, Rajkumar R, Ratliff J, Raymond FL, Assis BDRR, Sajan S, Schlachetzki Z, Schmidt S, Stark Z, Strom S, Taylor J, Thaxton C, Thrush D, Toro S, Tshering K, Vasilevsky N, Wayburn B, Webb R, O'Donnell-Luria A, Coffey AJ. The ClinGen Syndromic Disorders Gene Curation Expert Panel: Assessing the Clinical Validity of 111 Gene-Disease Relationships. medRxiv [Preprint]. 2024 Nov 20:2024

medRxiv [Preprint]. 2024 Nov 20:2024.11.19.24317561. doi: 10.1101/2024.11.19.24317561.

ABSTRACT

PURPOSE: The Clinical Genome Resource (ClinGen) Gene Curation Expert Panels (GCEPs) have historically focused on specific organ systems or phenotypes; thus, the ClinGen Syndromic Disorders GCEP (SD-GCEP) was formed to address an unmet need.

METHODS: The SD-GCEP applied ClinGen’s framework to evaluate the clinical validity of genes associated with rare syndromic disorders. 111 Gene-Disease Relationships (GDRs) associated with 100 genes spanning the clinical spectrum of syndromic disorders were curated.

RESULTS: From April 2020 through March 2024, 38 precurations were performed on genes with multiple disease relationships and were reviewed to determine if the disorders were part of a spectrum or distinct entities. 14 genes were lumped into a single disease entity and 24 were split into separate entities, of which 11 were curated by the SD-GCEP. A full review of 111 GDRs for 100 genes followed, with 78 classified as Definitive, 9 as Strong, 15 as Moderate, and 9 as Limited highlighting where further data are needed. All diseases involved two or more organ systems, while the majority (88/111 GDRs, 79.2%) had five or more organ systems affected.

CONCLUSION: The SD-GCEP addresses a critical gap in gene curation efforts, enabling inclusion of genes for syndromic disorders in clinical testing and contributing to keeping pace with the rapid discovery of new genetic syndromes.

PMID:39606380 | PMC:PMC11601709 | DOI:10.1101/2024.11.19.24317561

Consolidating the Role of Mutated ATP2B2 in Neurodevelopmental and Cerebellar Pathologies

  • Stehr AM, Lenberg J, Friedman J, Dobbelaere D, Imbard A, Levy J, Donoghue S, Derive N, Stoeva R, Gueguen P, Zech M. Consolidating the Role of Mutated ATP2B2 in Neurodevelopmental and Cerebellar Pathologies. Clin Genet. 2024

Clin Genet. 2024 Oct 5. doi: 10.1111/cge.14622. Online ahead of print.

ABSTRACT

Plasma membrane calcium ATPases (PMCAs) encoded by ATP2B genes have been implicated in Mendelian diseases with ataxia, dystonia, and intellectual disability. Work to date has shown that ATP2B2 (encoding PMCA2) is required for synaptic function and Purkinje-cell integrity in the cerebellum. A recent case series has linked ATP2B2 to a novel entity, characterized by neurodevelopmental and movement phenotypes, in only seven individuals. We called for collaboration to collect five unpublished families affected by the new rare ATP2B2-related condition. Exome-/genome sequencing-identified genotypes included four likely pathogenic/pathogenic heterozygous de novo missense variants and one dominantly inherited end-truncating frameshift allele. The six affected individuals shared features with the described patients including developmental delay, cognitive disturbances, epilepsy, autistic traits, and motor disorders. Striking cerebellar atrophy was observed in one affected individual. In association with hearing loss and movement abnormalities, we report a recurrent p.(Glu457Lys) substitution, previously documented in a neurologically impaired ATP2B2 mouse mutant. Our study further delineates the mutational spectrum and presentation of a human syndrome caused by ATP2B2 variants, confirming the importance of PMCA2 in neurotypical and cerebellar development.

PMID:39367743 | DOI:10.1111/cge.14622

Biallelic variants in ERLIN1: a series of 13 individuals with spastic paraparesis

  • Cogan G, Zaki MS, Issa M, Keren B, Guillaud-Bataille M, Renaldo F, Isapof A, Lallemant P, Stevanin G, Guillot-Noel L, Courtin T, Buratti J, Freihuber C, Gleeson JG, Howarth R, Durr A, de Sainte Agathe JM, Mignot C. Biallelic variants in ERLIN1: a series of 13 individuals with spastic paraparesis. Hum Genet. 2024 Nov;14

Abstract
Biallelic variants in the ERLIN1 gene were recently reported as the cause of two motor neuron degeneration diseases, SPG62 and a recessive form of amyotrophic lateral sclerosis. However, only 12 individuals from five pedigrees have been identified so far. Thus, the description of the disease remains limited. Following the discovery of a homozygous pathogenic variant in a girl with SPG62, presenting with intellectual disability, and epilepsy, we gathered the largest series of SPG62 cases reported so far (13 individuals) to better understand the phenotype associated with ERLIN1. We collected molecular and clinical data for 13 individuals from six families with ERLIN1 biallelic variants. We performed RNA-seq analyses to characterize intronic variants and used Alphafold and a transcripts database to characterize the molecular consequences of the variants. We identified three new variants suspected to alter the bell-shaped ring formed by the ERLIN1/ERLIN2 complex. Affected individuals had childhood-onset paraparesis with slow progression. Six individuals presented with gait ataxia and three had superficial sensory loss. Aside from our proband, none had intellectual disability or epilepsy. Biallelic pathogenic ERLIN1 variants induce a rare, predominantly pure, spastic paraparesis, with possible cerebellar and peripheral nerve involvement.

PMID: 39367212 | DOI: 10.1007/s00439-024-02702-0

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Genetic Neurologic Disease

Neurologic Movement Disorders

RCIGM focuses on translational research in pediatric neurologic movement disorders, particularly those resulting from genetic or metabolic conditions. 

Investigations into genetic underpinnings of neurologic movement disorders is led by Jennifer Friedman, MD. Her work involves sequencing children with unexplained neurologic disease to identify diagnosis and treatment options.

Dr. Friedman’s research is aimed at ending the diagnostic odyssey by bringing diagnoses to patients and families; shortening the therapeutic odyssey by delivering precision neurologic care and identifying novel genes for rare neurologic disorders.

headshot of Dr. Jenni Friedman

Jennifer Friedman, MD

Dr. Jennifer Friedman is the Translational Medicine Director for the Precision Medicine Clinic at Rady Children’s Hospital, where she is also a senior staff neurologist. In addition, she serves as clinical professor in the UC San Diego Departments of Neurosciences and Pediatrics. 

Dr. Friedman is a diplomate of the American Board of Psychiatry and Neurology. She is a member of the American Academy of Neurology, the Movement Disorder Society, the Tourette Syndrome Association, and the Phi Beta Kappa National Honor Society. 

Publications

Biallelic variants in GTF3C3 result in an autosomal recessive disorder with intellectual disability

  • De Hayr L, Blok LER, Dias KR, Long J, Begemann A, Moir RD, Willis IM, Mocera M, Siegel G, Steindl K, Evans CA, Zhu Y, Zhang F, Field M, Ma A, Adès L, Josephi-Taylor S, Pfundt R, Zaki MS, Tomoum H, Gregor A, Laube J, Reis A, Maddirevula S, Hashem MO, Zweier M, Alkuraya FS, Maroofian R, Buckley MF, Gleeson JG, Zweier C, Coll-Tané M, Koolen DA, Rauch A, Roscioli T, Schenck A, Harvey RJ. Biallelic variants in GTF3C3 result in an autosomal recessive disorder with intellectual disability. Genet Med. 2024 Nov 7

Genet Med. 2024 Nov 7:101253. doi: 10.1016/j.gim.2024.101253. Online ahead of print.

ABSTRACT

PURPOSE: This study details a novel syndromic form of autosomal recessive intellectual disability resulting from recessive variants in GTF3C3, encoding a key component of the DNA-binding transcription factor IIIC, which has a conserved role in RNA polymerase III-mediated transcription.

METHODS: Exome sequencing, minigene analysis, molecular modeling, RNA polymerase III reporter gene assays, and Drosophila knockdown models were utilized to characterize GTF3C3 variants.

RESULTS: Twelve affected individuals from 7 unrelated families were identified with homozygous or compound heterozygous missense variants in GTF3C3 including c.503C>T p.(Ala168Val), c.1268T>C p.(Leu423Pro), c.1436A>G p.(Tyr479Cys), c.2419C>T p.(Arg807Cys), and c.2420G>A p.(Arg807His). The cohort presented with intellectual disability, variable nonfamilial facial features, motor impairments, seizures, and cerebellar/corpus callosum malformations. Consistent with disruptions in intra- and intermolecular interactions observed in molecular modeling, RNA polymerase III reporter assays confirmed that the majority of missense variants resulted in a loss of function. Minigene analysis of the recurrent c.503C>T p.(Ala168Val) variant confirmed the introduction of a cryptic donor site into exon 4, resulting in mRNA missplicing. Consistent with the clinical features of this cohort, neuronal loss of Gtf3c3 in Drosophila induced seizure-like behavior, motor impairment, and learning deficits.

CONCLUSION: These findings confirm that GTF3C3 variants result in an autosomal recessive form of syndromic intellectual disability.

PMID:39636576 | DOI:10.1016/j.gim.2024.101253

Monoallelic loss-of-function variants in GSK3B lead to autism and developmental delay

  • Tan S, Zhang Q, Zhan R, Luo S, Han Y, Yu B, Muss C, Pingault V, Marlin S, Delahaye A, Peters S, Perne C, Kreiß M, Spataro N, Trujillo-Quintero JP, Racine C, Tran-Mau-Them F, Phornphutkul C, Besterman AD, Martinez J, Wang X, Tian X, Srivastava S, Urion DK, Madden JA, Saif HA, Morrow MM, Begtrup A, Li X, Jurgensmeyer S, Leahy P, Zhou S, Li F, Hu Z, Tan J, Xia K, Guo H. Monoallelic loss-of-function variants in GSK3B lead to autism and developmental delay. Mol Psychiatry. 2024 Oct 29

Mol Psychiatry. 2024 Oct 29. doi: 10.1038/s41380-024-02806-z. Online ahead of print.

ABSTRACT

De novo variants adjacent to the canonical splicing sites or in the well-defined splicing-related regions are more likely to impair splicing but remain under-investigated in autism spectrum disorder (ASD). By analyzing large, recent ASD genome sequencing cohorts, we find a significant burden of de novo potential splicing-disrupting variants (PSDVs) in 5048 probands compared to 4090 unaffected siblings. We identified 55 genes with recurrent de novo PSDVs that were highly intolerant to variation. Forty-six of these genes have not been strongly implicated in ASD or other neurodevelopmental disorders previously, including GSK3B. Through international, multicenter collaborations, we assembled genotype and phenotype data for 15 individuals with GSK3B variants and identified common phenotypes including developmental delay, ASD, sleeping disturbance, and aggressive behavior. Using available single-cell transcriptomic data, we show that GSK3B is enriched in dorsal progenitors and intermediate forms of excitatory neurons in the developing brain. We showed that Gsk3b knockdown in mouse excitatory neurons interferes with dendrite arborization and spine maturation which could not be rescued by de novo missense variants identified from affected individuals. In summary, our findings suggest that PSDVs may play an important role in the genetic etiology of ASD and allow for the prioritization of new ASD candidate genes. Importantly, we show that genetic variation resulting in GSK3B loss-of-function can lead to a neurodevelopmental disorder with core features of ASD and developmental delay.

PMID:39472663 | DOI:10.1038/s41380-024-02806-z

Clinical factors associated with genetic diagnosis in suspected neurogenetic disorders in a tertiary care clinic

  • Wong NR, Klomhaus A, Adams DJ, Schneider BN, Mehta S, DiStefano C, Wilson RB, Martinez-Agosto JA, Jeste SS, Besterman AD. Clinical factors associated with genetic diagnosis in suspected neurogenetic disorders in a tertiary care clinic. Genet Med. 2024 Oct 10

Genet Med. 2024 Oct 10:101252. doi: 10.1016/j.gim.2024.101252. Online ahead of print.

ABSTRACT

PURPOSE: This study aimed to identify phenotypic factors associated with genetic diagnoses in patients with neurodevelopmental disorders and generate a decision tree to assist clinicians in identifying patients most likely to receive a positive result on genetic testing.

METHODS: We retrospectively reviewed the charts of 316 patients evaluated in a neurodevelopmental clinic between 2014 and 2019. Patients were categorized based on genetic test results. Analyses were performed to identify variables that discriminate between patients with and without a genetic diagnosis.

RESULTS: Patients with a genetic diagnosis were more likely to be female and have a history of motor delay, hypotonia, congenital heart disease, and early intervention. Classification and regression tree analysis revealed that 75% of patients with motor delay had a genetic diagnosis. In patients without motor delay, hypotonia, age of walking, and age at initial evaluation were important indicators of a genetic diagnosis.

CONCLUSION: Our findings suggest that motor delay and hypotonia are associated with genetic diagnoses in children with neurodevelopmental disorders. The decision tree highlights patient subsets at greater risk and suggests possible phenotypic screens. Future studies could develop validated decision trees based on phenotypic data to assist clinicians in stratifying patients for genetic testing.

PMID:39395029 | DOI:10.1016/j.gim.2024.101252

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Discovery of Endocannabinoid Gene Mutation Leads to Identification of  New, Rare Pediatric Neurological Disease

In a study published in the October 2022 issue of BRAIN, researchers from Rady Children’s Institute for Genomic Medicine (RCIGM®) and the University of California San Diego School of Medicine describe their discovery of a new clinical syndrome, Neuro-Ocular DAGLA-related Syndrome (NODRS), in children with termination variants in the diacylglycerol lipase alpha (DAGLA) gene which encodes an enzyme in the brain that is involved in the signaling pathway of the endocannabinoid (eCB) system.

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