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2022

Genotype-Phenotype Comparison in POGZ-Related Neurodevelopmental Disorders by Using Clinical Scoring

Nagy D, Verheyen S, Wigby KM, Borovikov A, Sharkov A, Slegesky V, Larson A, Fagerberg C, Brasch-Andersen C, Kibæk M, Bader I, Hernan R, High FA, Chung WK, Schieving JH, Behunova J, Smogavec M, Laccone F, Witsch-Baumgartner M, Zobel J, Duba HC, Weis D.

Genes (Basel). 2022 Jan 15;13(1):154. doi: 10.3390/genes13010154. ABSTRACT POGZ-related disorders (also known as White-Sutton syndrome) encompass a wide range of neurocognitive abnormalities and other accompanying anomalies. Disease severity varies widely among POGZ patients and studies investigating genotype-phenotype association are scarce. Therefore, our aim was to collect data on previously unreported POGZ patients and perform a large-scale phenotype-genotype comparison from published data. Overall, 117 POGZ patients’ genotype and phenotype data were included in the analysis, including 12 novel patients. A severity scoring system was developed for the comparison. Mild and severe phenotypes were compared with the types and location of the variants and the predicted presence or absence of nonsense-mediated RNA decay (NMD). Missense variants were more often associated with mild phenotypes (p = 0.0421) and truncating variants predicted to escape NMD presented with more severe phenotypes (p < 0.0001). Within this group, variants in the prolin-rich region of the POGZ protein were associated with the most severe phenotypes (p = 0.0004). Our study suggests that gain-of-function or dominant negative effect through escaping NMD and the location of the variants in the prolin-rich domain of the protein may play an important role in the severity of manifestations of POGZ-associated neurodevelopmental disorders. PMID:35052493 | DOI:10.3390/genes13010154

January 15, 2022
Neurogenomics

Clinico-radiological features, molecular spectrum, and identification of prognostic factors in developmental and epileptic encephalopathy due to inosine triphosphate pyrophosphatase (ITPase) deficiency

Scala M, Wortmann SB, Kaya N, Stellingwerff MD, Pistorio A, Glamuzina E, van Karnebeek CD, Skrypnyk C, Iwanicka-Pronicka K, Piekutowska-Abramczuk D, Ciara E, Tort F, Sheidley B, Poduri A, Jayakar P, Jayakar A, Upadia J, Walano N, Haack TB, Prokisch H, Aldhalaan H, Karimiani EG, Yildiz Y, Ceylan AC, Santiago-Sim T, Dameron A, Yang H, Toosi MB, Ashrafzadeh F, Akhondian J, Imannezhad S, Mirzadeh HS, Maqbool S, Farid A, Al-Muhaizea MA, Alshwameen MO, Aldowsari L, Alsagob M, Alyousef A, AlMass R, AlHargan A, Alwadei AH, AlRasheed MM, Colak D, Alqudairy H, Khan S, Lines MA, García Cazorla MÁ, Ribes A, Morava E, Bibi F, Haider S, Ferla MP, Taylor JC, Alsaif HS, Firdous A, Hashem M, Shashkin C, Koneev K, Kaiyrzhanov R, Efthymiou S, Genomics QS, Schmitt-Mechelke T, Ziegler A, Issa MY, Elbendary HM, Striano P, Alkuraya FS, Zaki MS, Gleeson JG, Barakat TS, Bierau J, van der Knaap MS, Maroofian R, Houlden H.

Hum Mutat. 2022 Jan 6. doi: 10.1002/humu.24326. Online ahead of print. ABSTRACT Developmental and epileptic encephalopathy 35 (DEE 35) is a severe neurological condition caused by biallelic variants in ITPA, encoding inosine triphosphate pyrophosphatase, an essential enzyme in purine metabolism. We delineate the genotypic and phenotypic spectrum of DEE 35, analyzing possible predictors for adverse clinical outcomes. We investigated a cohort of 28 new patients and reviewed previously described cases, providing a comprehensive characterization of 40 subjects. Exome sequencing was performed to identify underlying ITPA pathogenic variants. Brain MRI (magnetic resonance imaging) scans were systematically analyzed to delineate the neuroradiological spectrum. Survival curves according to the Kaplan-Meier method and log-rank test were used to investigate outcome predictors in different subgroups of patients. We identified 18 distinct ITPA pathogenic variants, including 14 novel variants, and two deletions. All subjects showed profound developmental delay, microcephaly, and refractory epilepsy followed by neurodevelopmental regression. Brain MRI revision revealed a recurrent pattern of delayed myelination and restricted diffusion of early myelinating structures. Congenital microcephaly and cardiac involvement were statistically significant novel clinical predictors of adverse outcomes. We refined the molecular, clinical, and neuroradiological characterization of ITPase deficiency, and identified new clinical predictors which may have a potentially important impact on diagnosis, counseling, and follow-up of affected individuals. PMID:34989426 | DOI:10.1002/humu.24326

January 6, 2022
Neurogenomics

2021

Biallelic FRA10AC1 variants cause a neurodevelopmental disorder with growth retardation

von Elsner L, Chai G, Schneeberger PE, Harms FL, Casar C, Qi M, Alawi M, Abdel-Salam GMH, Zaki MS, Arndt F, Yang X, Stanley V, Hempel M, Gleeson JG, Kutsche K

Brain. 2021 Oct 25:awab403. doi: 10.1093/brain/awab403. Online ahead of print. ABSTRACT The major spliceosome mediates pre-mRNA splicing by recognizing the highly conserved sequences at the 5′ and 3′ splice sites and the branch point. More than 150 proteins participate in the splicing process and are organized in the spliceosomal A, B, and C complexes. FRA10AC1 is a peripheral protein of the spliceosomal C complex and its ortholog in the green alga facilitates recognition or interaction with splice sites. We identified biallelic pathogenic variants in FRA10AC1 in five individuals from three consanguineous families. The two unrelated patients 1 and 2 with loss-of-function variants showed developmental delay, intellectual disability, and no speech, while three siblings with the c.494_496delAAG (p.Glu165del) variant had borderline to mild intellectual disability. All patients had microcephaly, hypoplasia or agenesis of the corpus callosum, growth retardation, and craniofacial dysmorphism. FRA10AC1 transcripts and proteins were drastically reduced or absent in fibroblasts of patients 1 and 2. In a heterologous expression system, the p. Glu165del variant impacts intrinsic stability of FRA10AC1 but does not affect its nuclear localization. By co-immunoprecipitation, we found ectopically expressed HA-FRA10AC1 in complex with endogenous DGCR14, another component of the spliceosomal C complex, while the splice factors CHERP, NKAP, RED, and SF3B2 could not be co-immunoprecipitated. Using an in vitro splicing reporter assay, we did not obtain evidence for FRA10AC1 deficiency to suppress missplicing events caused by mutations in the highly conserved dinucleotides of 5′ and 3′ splice sites in an in vitro splicing assay in patient-derived fibroblasts. Our data highlight the importance of specific peripheral spliceosomal C complex proteins for neurodevelopment. It remains possible that FRA10AC1 may have other and/or additional cellular functions, such as coupling of transcription and splicing reactions. PMID:34694367 | DOI:10.1093/brain/awab403

October 26, 2021
Neurogenomics

Caenorhabditis elegans provides an efficient drug screening platform for GNAO1-related disorders and highlights the potential role of caffeine in controlling dyskinesia

Di Rocco M, Galosi S, Lanza E, Tosato F, Caprini D, Folli V, Friedman J, Bocchinfuso G, Martire A, Di Schiavi E, Leuzzi V, Martinelli S.

Hum Mol Genet. 2021 Oct 8:ddab296. doi: 10.1093/hmg/ddab296. Online ahead of print. ABSTRACT Dominant GNAO1 mutations cause an emerging group of childhood-onset neurological disorders characterized by developmental delay, intellectual disability, movement disorders, drug-resistant seizures, and neurological deterioration. GNAO1 encodes the α-subunit of an inhibitory GTP/GDP-binding protein regulating ion channel activity and neurotransmitter release. The pathogenic mechanisms underlying GNAO1-related disorders remain largely elusive and there are no effective therapies. Here, we assessed the functional impact of two disease-causing variants associated with distinct clinical features, c.139A > G (p.S47G) and c.662C > A (p.A221D), using Caenorhabditis elegans as a model organism. The c.139A > G change was introduced into the orthologous position of the C. elegans gene via CRISPR/Cas9, whereas a knock-in strain carrying the p.A221D variant was already available. Like null mutants, homozygous knock-in animals showed increased egg laying and were hypersensitive to aldicarb, an inhibitor of acetylcholinesterase, suggesting excessive neurotransmitter release by different classes of motor neurons. Automated analysis of C. elegans locomotion indicated that goa-1 mutants move faster than control animals, with more frequent body bends and a higher reversal rate, and display uncoordinated locomotion. Phenotypic profiling of heterozygous animals revealed a strong hypomorphic effect of both variants, with a partial dominant-negative activity for the p.A221D allele. Finally, caffeine was shown to rescue aberrant motor function in C. elegans harboring the goa-1 variants; this effect is mainly exerted through adenosine receptor antagonism. Overall, our findings establish a suitable platform for drug discovery, which may assist in accelerating the development of new therapies for this devastating condition, and highlight the potential role of caffeine in controlling GNAO1-related dyskinesia. PMID:34622282 | DOI:10.1093/hmg/ddab296

October 8, 2021
Neurogenomics

YY1: A New Gene for Childhood Onset Dystonia with Prominent Oromandibular-Laryngeal Involvement?

Ferng A, Thulin P, Walsh E, Weissbrod PA, Friedman J.

Mov Disord. 2021 Oct 7. doi: 10.1002/mds.28813. Online ahead of print. NO ABSTRACT PMID:34618373 | DOI:10.1002/mds.28813

October 8, 2021
Gene DiscoveryNeurogenomics

Dual orexin receptor antagonists for insomnia in youth with neurodevelopmental disorders: a case series and review

Besterman AD, Jeste SS

Eur Child Adolesc Psychiatry. 2021 Oct 5. doi: 10.1007/s00787-021-01883-7. Online ahead of print. ABSTRACT Insomnia is a common, impairing, and difficult-to-treat comorbidity in children with neurodevelopmental disorders (NDDs). Behavioral interventions can be challenging because of developmental and behavioral features that interfere with treatment. Medication management also can be difficult due to a high burden of side effects, a high rate of paradoxical responses, and frequent treatment resistance. Therefore, new treatment options for insomnia in children with NDDs are needed. Dual orexin receptor antagonists (DORAs) are a relatively new class of pharmacotherapeutics that induce sleep by inhibiting the orexin signaling pathway. To date, there is little safety or efficacy data on the use of DORAs in children with NDDs. We present four patients with NDDs and insomnia that we treated with the DORA, suvorexant. We found that patients had a wide range of responses, with one patient displaying a robust improvement in sleep onset and maintenance, while another had significant improvement in insomnia symptoms on combination therapy with trazodone. Our final two patients had mild or no benefit from suvorexant therapy. Further research is necessary to establish the safety and efficacy of DORAs in this population and to identify predictive factors, such as specific neurogenetic diagnoses or clinical features, of a positive treatment response. PMID:34611728 | DOI:10.1007/s00787-021-01883-7

October 6, 2021
Neurogenomics

Biallelic variants in SLC38A3 encoding a glutamine transporter cause epileptic encephalopathy

Marafi D, Fatih JM, Kaiyrzhanov R, Ferla MP, Gijavanekar C, Al-Maraghi A, Liu N, Sites E, Alsaif HS, Al-Owain M, Zakkariah M, El-Anany E, Guliyeva U, Guliyeva S, Gaba C, Haseeb A, Alhashem AM, Danish E, Karageorgou V, Beetz C, Subhi AA, Mullegama SV, Torti E, Sebastin M, Breilyn MS, Duberstein S, Abdel-Hamid MS, Mitani T, Du H, Rosenfeld JA, Jhangiani SN, Coban Akdemir Z, Gibbs RA, Taylor JC, Fakhro KA, Hunter JV, Pehlivan D, Zaki MS, Gleeson JG, Maroofian R, Houlden H, Posey JE, Sutton VR, Alkuraya FS, Elsea SH, Lupski JR

Brain. 2021 Oct 4:awab369. doi: 10.1093/brain/awab369. Online ahead of print. ABSTRACT The solute carrier (SLC) superfamily encompasses >400 transmembrane transporters involved in the exchange of amino acids, nutrients, ions, metals, neurotransmitters and metabolites across biological membranes. SLCs are highly expressed in the mammalian brain; defects in nearly 100 unique SLC-encoding genes (OMIM: https://www.omim.org) are associated with rare Mendelian disorders including developmental and epileptic encephalopathy (DEE) and severe neurodevelopmental disorders (NDDs). Exome sequencing and family-based rare variant analyses on a cohort with NDD identified two siblings with DEE and a shared deleterious homozygous splicing variant in SLC38A3. The gene encodes SNAT3, a sodium-coupled neutral amino acid transporter and a principal transporter of the amino acids asparagine, histidine, and glutamine, the latter being the precursor for the neurotransmitters GABA and glutamate. Additional subjects with a similar DEE phenotype and biallelic predicted-damaging SLC38A3 variants were ascertained through GeneMatcher and collaborations with research and clinical molecular diagnostic laboratories. Untargeted metabolomic analysis was performed to identify novel metabolic biomarkers. Ten individuals from seven unrelated families from six different countries with deleterious biallelic variants in SLC38A3 were identified. Global developmental delay, intellectual disability, hypotonia, and absent speech were common features while microcephaly, epilepsy, and visual impairment were present in the majority. Epilepsy was drug-resistant in half. Metabolomic analysis revealed perturbations of glutamate, histidine, and nitrogen metabolism in plasma, urine, and cerebrospinal fluid of selected subjects, potentially representing biomarkers of disease. Our data support the contention that SLC38A3 is a novel disease gene for DEE and illuminate the likely pathophysiology of the disease as perturbations in glutamine homeostasis. PMID:34605855 | DOI:10.1093/brain/awab369

October 5, 2021
Neurogenomics

ABHD16A deficiency causes a complicated form of hereditary spastic paraplegia associated with intellectual disability and cerebral anomalies

Lemire G, Ito YA, Marshall AE, Chrestian N, Stanley V, Brady L, Tarnopolsky M, Curry CJ, Hartley T, Mears W, Derksen A, Rioux N, Laflamme N, Hutchison HT, Pais LS, Zaki MS, Sultan T, Dane AD; Care4Rare Canada Consortium, Gleeson JG, Vaz FM, Kernohan KD, Bernard G, Boycott KM

Am J Hum Genet. 2021 Sep 21:S0002-9297(21)00341-4. doi: 10.1016/j.ajhg.2021.09.005. Online ahead of print. ABSTRACT ABHD16A (abhydrolase domain-containing protein 16A, phospholipase) encodes the major phosphatidylserine (PS) lipase in the brain. PS lipase synthesizes lysophosphatidylserine, an important signaling lipid that functions in the mammalian central nervous system. ABHD16A has not yet been associated with a human disease. In this report, we present a cohort of 11 affected individuals from six unrelated families with a complicated form of hereditary spastic paraplegia (HSP) who carry bi-allelic deleterious variants in ABHD16A. Affected individuals present with a similar phenotype consisting of global developmental delay/intellectual disability, progressive spasticity affecting the upper and lower limbs, and corpus callosum and white matter anomalies. Immunoblot analysis on extracts from fibroblasts from four affected individuals demonstrated little to no ABHD16A protein levels compared to controls. Our findings add ABHD16A to the growing list of lipid genes in which dysregulation can cause complicated forms of HSP and begin to describe the molecular etiology of this condition. PMID:34587489 | DOI:10.1016/j.ajhg.2021.09.005

September 30, 2021
Neurogenomics

A Human Pleiotropic Multiorgan Condition Caused by Deficient Wnt Secretion

Chai G, Szenker-Ravi E, Chung C, Li Z, Wang L, Khatoo M, Marshall T, Jiang N, Yang X, McEvoy-Venneri J, Stanley V, Anzenberg P, Lang N, Wazny V, Yu J, Virshup DM, Nygaard R, Mancia F, Merdzanic R, Toralles MBP, Pitanga PML, Puri RD, Hernan R, Chung WK, Bertoli-Avella AM, Al-Sannaa N, Zaki MS, Willert K, Reversade B, Gleeson JG

N Engl J Med. 2021 Sep 30;385(14):1292-1301. doi: 10.1056/NEJMoa2033911. ABSTRACT BACKGROUND: Structural birth defects occur in approximately 3% of live births; most such defects lack defined genetic or environmental causes. Despite advances in surgical approaches, pharmacologic prevention remains largely out of reach. METHODS: We queried worldwide databases of 20,248 families that included children with neurodevelopmental disorders and that were enriched for parental consanguinity. Approximately one third of affected children in these families presented with structural birth defects or microcephaly. We performed exome or genome sequencing of samples obtained from the children, their parents, or both to identify genes with biallelic pathogenic or likely pathogenic mutations present in more than one family. After identifying disease-causing variants, we generated two mouse models, each with a pathogenic variant “knocked in,” to study mechanisms and test candidate treatments. We administered a small-molecule Wnt agonist to pregnant animals and assessed their offspring. RESULTS: We identified homozygous mutations in WLS, which encodes the Wnt ligand secretion mediator (also known as Wntless or WLS) in 10 affected persons from 5 unrelated families. (The Wnt ligand secretion mediator is essential for the secretion of all Wnt proteins.) Patients had multiorgan defects, including microcephaly and facial dysmorphism as well as foot syndactyly, renal agenesis, alopecia, iris coloboma, and heart defects. The mutations affected WLS protein stability and Wnt signaling. Knock-in mice showed tissue and cell vulnerability consistent with Wnt-signaling intensity and individual and collective functions of Wnts in embryogenesis. Administration of a pharmacologic Wnt agonist partially restored embryonic development. CONCLUSIONS: Genetic variations affecting a central Wnt regulator caused syndromic structural birth defects. Results from mouse models suggest that what we have named Zaki syndrome is a potentially preventable disorder. (Funded by the National Institutes of Health and others.). PMID:34587386 | DOI:10.1056/NEJMoa2033911

September 30, 2021
Neurogenomics

Insights into the expanding phenotypic spectrum of inherited disorders of biogenic amines

Kuseyri Hübschmann O, Horvath G, Cortès-Saladelafont E, Yıldız Y, Mastrangelo M, Pons R, Friedman J, Mercimek-Andrews S, Wong SN, Pearson TS, Zafeiriou DI, Kulhánek J, Kurian MA, López-Laso E, Oppebøen M, Kılavuz S, Wassenberg T, Goez H, Scholl-Bürgi S, Porta F, Honzík T, Santer R, Burlina A, Sivri HS, Leuzzi V, Hoffmann GF, Jeltsch K, Hübschmann D, Garbade SF; iNTD Registry Study Group, García-Cazorla A, Opladen T.

Nat Commun. 2021 Sep 20;12(1):5529. doi: 10.1038/s41467-021-25515-5. ABSTRACT Inherited disorders of neurotransmitter metabolism are rare neurodevelopmental diseases presenting with movement disorders and global developmental delay. This study presents the results of the first standardized deep phenotyping approach and describes the clinical and biochemical presentation at disease onset as well as diagnostic approaches of 275 patients from the registry of the International Working Group on Neurotransmitter related Disorders. The results reveal an increased rate of prematurity, a high risk for being small for gestational age and for congenital microcephaly in some disorders. Age at diagnosis and the diagnostic delay are influenced by the diagnostic methods applied and by disease-specific symptoms. The timepoint of investigation was also a significant factor: delay to diagnosis has decreased in recent years, possibly due to novel diagnostic approaches or raised awareness. Although each disorder has a specific biochemical pattern, we observed confounding exceptions to the rule. The data provide comprehensive insights into the phenotypic spectrum of neurotransmitter disorders. PMID:34545092 | DOI:10.1038/s41467-021-25515-5

September 23, 2021
NeurogenomicsRare Disease