MAB21L1 loss of function causes a syndromic neurodevelopmental disorder with distinctive cerebellar, ocular, craniofacial and genital features (COFG syndrome)
Rad A, Altunoglu U, Miller R, Maroofian R, James KN, Çağlayan AO, Najafi M, Stanley V, Boustany RM, Yeşil G, Sahebzamani A, Ercan-Sencicek G, Saeidi K, Wu K, Bauer P, Bakey Z, Gleeson JG, Hauser N, Gunel M, Kayserili H, Schmidts M.
J Med Genet. 2019 May;56(5):332-339. doi: 10.1136/jmedgenet-2018-105623. Epub 2018 Nov 28.
ABSTRACT
BACKGROUND: Putative nucleotidyltransferase MAB21L1 is a member of an evolutionarily well-conserved family of the male abnormal 21 (MAB21)-like proteins. Little is known about the biochemical function of the protein; however, prior studies have shown essential roles for several aspects of embryonic development including the eye, midbrain, neural tube and reproductive organs.
OBJECTIVE: A homozygous truncating variant in
MAB21L1 has recently been described in a male affected by intellectual disability, scrotal agenesis, ophthalmological anomalies, cerebellar hypoplasia and facial dysmorphism. We employed a combination of exome sequencing and homozygosity mapping to identify the underlying genetic cause in subjects with similar phenotypic features descending from five unrelated consanguineous families.
RESULTS: We identified four homozygous
MAB21L1 loss of function variants (p.Glu281fs*20, p.Arg287Glufs*14 p.Tyr280* and p.Ser93Serfs*48) and one missense variant (p.Gln233Pro) in 10 affected individuals from 5 consanguineous families with a distinctive autosomal recessive neurodevelopmental syndrome. Cardinal features of this syndrome include a characteristic facial gestalt, corneal dystrophy, hairy nipples, underdeveloped labioscrotal folds and scrotum/scrotal agenesis as well as cerebellar hypoplasia with ataxia and variable microcephaly.
CONCLUSION: This report defines an ultrarare but clinically recognisable Cerebello-Oculo-Facio-Genital syndrome associated with recessive
MAB21L1 variants. Additionally, our findings further support the critical role of MAB21L1 in cerebellum, lens, genitalia and as craniofacial morphogenesis.
PMID:
30487245 | PMC:
PMC6581149 | DOI:
10.1136/jmedgenet-2018-105623
November 30, 2018
Elucidating the molecular pathogenesis of glioma: integrated germline and somatic profiling of a familial glioma case series.
Jacobs DI, Fukumura K, Bainbridge MN, Armstrong GN, Tsavachidis S, Gu X, Doddapaneni HV, Hu J, Jayaseelan JC, Muzny DM, Huse JT, Bondy ML.
Neuro Oncol. 2018 Nov 12;20(12):1625-1633. doi: 10.1093/neuonc/noy119. PMID: 30165405; PMCID: PMC6231201.
Abstract
Key points: 1. Familial and sporadic gliomas display highly comparable molecular landscapes. 2. Germline and somatic molecular events target common core pathways involved in gliomagenesis. 3. Carriage of germline glioma risk variants is not associated with somatic events in the same gene.
PMID: 30165405 | PMCID: PMC6231201 | DOI: 10.1093/neuonc/noy119
November 12, 2018
Gene Discovery
A Screen Using iPSC-Derived Hepatocytes Reveals NAD+ as a Potential Treatment for mtDNA Depletion Syndrome
Jing R, Corbett JL, Cai J, Beeson GC, Beeson CC, Chan SS, Dimmock DP, Lazcares L, Geurts AM, Lemasters JJ, Duncan SA.
Cell Rep. 2018 Nov 6;25(6):1469-1484.e5. doi: 10.1016/j.celrep.2018.10.036.
ABSTRACT
Patients with mtDNA depletion syndrome 3 (MTDPS3) often die as children from liver failure caused by severe reduction in mtDNA content. The identification of treatments has been impeded by an inability to culture and manipulate MTDPS3 primary hepatocytes. Here we generated DGUOK-deficient hepatocyte-like cells using induced pluripotent stem cells (iPSCs) and used them to identify drugs that could improve mitochondrial ATP production and mitochondrial function. Nicotinamide adenine dinucleotide (NAD) was found to improve mitochondrial function in DGUOK-deficient hepatocyte-like cells by activating the peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α). NAD treatment also improved ATP production in MTDPS3-null rats and in hepatocyte-like cells that were deficient in ribonucleoside-diphosphate reductase subunit M2B (RRM2B), suggesting that it could be broadly effective. Our studies reveal that DGUOK-deficient iPSC-derived hepatocytes recapitulate the pathophysiology of MTDPS3 in culture and can be used to identify therapeutics for mtDNA depletion syndromes.
PMID:
30404003 | PMC:
PMC6289059 | DOI:
10.1016/j.celrep.2018.10.036
November 8, 2018
Copy-number variants in clinical genome sequencing: deployment and interpretation for rare and undiagnosed disease
Gross AM, Ajay SS, Rajan V, Brown C, Bluske K, Burns NJ, Chawla A, Coffey AJ, Malhotra A, Scocchia A, Thorpe E, Dzidic N, Hovanes K, Sahoo T, Dolzhenko E, Lajoie B, Khouzam A, Chowdhury S, Belmont J, Roller E, Ivakhno S, Tanner S, McEachern J, Hambuch T, Eberle M, Hagelstrom RT, Bentley DR, Perry DL, Taft RJ.
Genet Med. 2019 May;21(5):1121-1130. doi: 10.1038/s41436-018-0295-y. Epub 2018 Oct 8.
ABSTRACT
PURPOSE: Current diagnostic testing for genetic disorders involves serial use of specialized assays spanning multiple technologies. In principle, genome sequencing (GS) can detect all genomic pathogenic variant types on a single platform. Here we evaluate copy-number variant (CNV) calling as part of a clinically accredited GS test.
METHODS: We performed analytical validation of CNV calling on 17 reference samples, compared the sensitivity of GS-based variants with those from a clinical microarray, and set a bound on precision using orthogonal technologies. We developed a protocol for family-based analysis of GS-based CNV calls, and deployed this across a clinical cohort of 79 rare and undiagnosed cases.
RESULTS: We found that CNV calls from GS are at least as sensitive as those from microarrays, while only creating a modest increase in the number of variants interpreted (~10 CNVs per case). We identified clinically significant CNVs in 15% of the first 79 cases analyzed, all of which were confirmed by an orthogonal approach. The pipeline also enabled discovery of a uniparental disomy (UPD) and a 50% mosaic trisomy 14. Directed analysis of select CNVs enabled breakpoint level resolution of genomic rearrangements and phasing of de novo CNVs.
CONCLUSION: Robust identification of CNVs by GS is possible within a clinical testing environment.
PMID:
30293986 | PMC:
PMC6752263 | DOI:
10.1038/s41436-018-0295-y
October 9, 2018
Heterozygous WNT1 variant causing a variable bone phenotype
Alhamdi S, Lee YC, Chowdhury S, Byers PH, Gottschalk M, Taft RJ, Joeng KS, Lee BH, Bird LM.
Am J Med Genet A. 2018 Nov;176(11):2419-2424. doi: 10.1002/ajmg.a.40347. Epub 2018 Sep 24.
ABSTRACT
Osteogenesis imperfecta (OI) is a family of heritable disorders of bone fragility. Most individuals with OI have mutations in the genes encoding type I collagen; at least 17 other genes have been associated with OI. Biallelic loss-of-function mutations in WNT1 cause severe OI. Heterozygous missense variants in WNT1 are responsible for early-onset osteoporosis with variable bone phenotypes. Herein, we report a third-generation family with four affected individuals, some presenting with multiple low-impact fractures in childhood and others presenting with early-onset osteoporosis without a striking fracture history. A WNT1 variant (c. 1051 > C; p.Trp351Arg) was identified in the proband and segregated with a bone phenotype in three additional family members, consistent with autosomal dominant inheritance. In the proband, whole genome sequencing also revealed a de novo duplication (434 kb) of 22q11.2 that involves 25 genes, 4 of which are associated with human disease when haploinsufficient. Though smaller than the typical (1.5 Mb) 22q11.2 duplication, the duplication in the proband may be responsible for additional nonosseous aspects of his phenotype (hypotonia, developmental delay, small genitalia, strabismus, and depression in preadolescence). This case demonstrates the variability of bone phenotype conferred by a WNT1 variant and extends the spectrum of bone phenotypes associated with heterozygous WNT1 mutations.
PMID:
30246918 | PMC:
PMC6289778 | DOI:
10.1002/ajmg.a.40347
September 25, 2018
Developmental phosphoproteomics identifies the kinase CK2 as a driver of Hedgehog signaling and a therapeutic target in medulloblastoma
Teresa Purzner, James Purzner, Taylor Buckstaff, Giorgio Cozza, Sharareh Gholamin, Jessica M Rusert, Tom A Hartl, John Sanders, Nicholas Conley, Xuecai Ge, Marc Langan, Vijay Ramaswamy, Lauren Ellis, Ulrike Litzenburger, Sara Bolin, Johanna Theruvath, Ryan Nitta, Lin Qi, Xiao-Nan Li, Gordon Li, Michael D Taylor, Robert J Wechsler-Reya, Lorenzo A Pinna, Yoon-Jae Cho, Margaret T Fuller, Joshua E Elias, Matthew P Scott
Sci Signal. 2018 Sep 11;11(547):eaau5147. doi: 10.1126/scisignal.aau5147.
ABSTRACT
A major limitation of targeted cancer therapy is the rapid emergence of drug resistance, which often arises through mutations at or downstream of the drug target or through intrinsic resistance of subpopulations of tumor cells. Medulloblastoma (MB), the most common pediatric brain tumor, is no exception, and MBs that are driven by sonic hedgehog (SHH) signaling are particularly aggressive and drug-resistant. To find new drug targets and therapeutics for MB that may be less susceptible to common resistance mechanisms, we used a developmental phosphoproteomics approach in murine granule neuron precursors (GNPs), the developmental cell of origin of MB. The protein kinase CK2 emerged as a driver of hundreds of phosphorylation events during the proliferative, MB-like stage of GNP growth, including the phosphorylation of three of the eight proteins commonly amplified in MB. CK2 was critical to the stabilization and activity of the transcription factor GLI2, a late downstream effector in SHH signaling. CK2 inhibitors decreased the viability of primary SHH-type MB patient cells in culture and blocked the growth of murine MB tumors that were resistant to currently available Hh inhibitors, thereby extending the survival of tumor-bearing mice. Because of structural interactions, one CK2 inhibitor (CX-4945) inhibited both wild-type and mutant CK2, indicating that this drug may avoid at least one common mode of acquired resistance. These findings suggest that CK2 inhibitors may be effective for treating patients with MB and show how phosphoproteomics may be used to gain insight into developmental biology and pathology.
PMID:30206138 | PMC:PMC6475502 | DOI:10.1126/scisignal.aau5147
September 13, 2018
Neuro-Oncology
De novo truncating variants in the intronless IRF2BPL are responsible for developmental epileptic encephalopathy
Tran Mau-Them F, Guibaud L, Duplomb L, Keren B, Lindstrom K, Marey I, Mochel F, van den Boogaard MJ, Oegema R, Nava C, Masurel A, Jouan T, Jansen FE, Au M, Chen AH, Cho M, Duffourd Y, Lozier E, Konovalov F, Sharkov A, Korostelev S, Urteaga B, Dickson P, Vera M, Martínez-Agosto JA, Begemann A, Zweier M, Schmitt-Mechelke T, Rauch A, Philippe C, van Gassen K, Nelson S, Graham JM Jr, Friedman J, Faivre L, Lin HJ, Thauvin-Robinet C, Vitobello A.
Genet Med. 2019 Apr;21(4):1008-1014. doi: 10.1038/s41436-018-0143-0. Epub 2018 Aug 31.
ABSTRACT
PURPOSE: Developmental and epileptic encephalopathies (DEEs) are severe clinical conditions characterized by stagnation or decline of cognitive and behavioral abilities preceded, accompanied or followed by seizures. Because DEEs are clinically and genetically heterogeneous, next-generation sequencing, especially exome sequencing (ES), is becoming a first-tier strategy to identify the molecular etiologies of these disorders.
METHODS: We combined ES analysis and international data sharing.
RESULTS: We identified 11 unrelated individuals with DEE and de novo heterozygous truncating variants in the interferon regulatory factor 2-binding protein-like gene (IRF2BPL). The 11 individuals allowed for delineation of a consistent neurodevelopmental disorder characterized by mostly normal initial psychomotor development followed by severe global neurological regression and epilepsy with nonspecific electroencephalogram (EEG) abnormalities and variable central nervous system (CNS) anomalies. IRF2BPL, also known as enhanced at puberty protein 1 (EAP1), encodes a transcriptional regulator containing a C-terminal RING-finger domain common to E3 ubiquitin ligases. This domain is required for its repressive and transactivating transcriptional properties. The variants identified are expected to encode a protein lacking the C-terminal RING-finger domain.
CONCLUSIONS: These data support the causative role of truncating IRF2BPL variants in pediatric neurodegeneration and expand the spectrum of transcriptional regulators identified as molecular factors implicated in genetic developmental and epileptic encephalopathies.
PMID:
30166628 | DOI:
10.1038/s41436-018-0143-0
September 1, 2018
Genetic variants in components of the NALCN-UNC80-UNC79 ion channel complex cause a broad clinical phenotype (NALCN channelopathies)
Bramswig NC, Bertoli-Avella AM, Albrecht B, Al Aqeel AI, Alhashem A, Al-Sannaa N, Bah M, Bröhl K, Depienne C, Dorison N, Doummar D, Ehmke N, Elbendary HM, Gorokhova S, Héron D, Horn D, James K, Keren B, Kuechler A, Ismail S, Issa MY, Marey I, Mayer M, McEvoy-Venneri J, Megarbane A, Mignot C, Mohamed S, Nava C, Philip N, Ravix C, Rolfs A, Sadek AA, Segebrecht L, Stanley V, Trautman C, Valence S, Villard L, Wieland T, Engels H, Strom TM, Zaki MS, Gleeson JG, Lüdecke HJ, Bauer P, Wieczorek D.
Hum Genet. 2018 Sep;137(9):753-768. doi: 10.1007/s00439-018-1929-5. Epub 2018 Aug 23.
ABSTRACT
NALCN is a conserved cation channel, which conducts a permanent sodium leak current and regulates resting membrane potential and neuronal excitability. It is part of a large ion channel complex, the “NALCN channelosome”, consisting of multiple proteins including UNC80 and UNC79. The predominant neuronal expression pattern and its function suggest an important role in neuronal function and disease. So far, biallelic NALCN and UNC80 variants have been described in a small number of individuals leading to infantile hypotonia, psychomotor retardation, and characteristic facies 1 (IHPRF1, OMIM 615419) and 2 (IHPRF2, OMIM 616801), respectively. Heterozygous de novo NALCN missense variants in the S5/S6 pore-forming segments lead to congenital contractures of the limbs and face, hypotonia, and developmental delay (CLIFAHDD, OMIM 616266) with some clinical overlap. In this study, we present detailed clinical information of 16 novel individuals with biallelic NALCN variants, 1 individual with a heterozygous de novo NALCN missense variant and an interesting clinical phenotype without contractures, and 12 individuals with biallelic UNC80 variants. We report for the first time a missense NALCN variant located in the predicted S6 pore-forming unit inherited in an autosomal-recessive manner leading to mild IHPRF1. We show evidence of clinical variability, especially among IHPRF1-affected individuals, and discuss differences between the IHPRF1- and IHPRF2 phenotypes. In summary, we provide a comprehensive overview of IHPRF1 and IHPRF2 phenotypes based on the largest cohort of individuals reported so far and provide additional insights into the clinical phenotypes of these neurodevelopmental diseases to help improve counseling of affected families.
PMID:
30167850 | PMC:
PMC6671679 | DOI:
10.1007/s00439-018-1929-5
September 1, 2018
Paroxysmal motor disorders: expanding phenotypes lead to coalescing genotypes
Zima L, Ceulemans S, Reiner G, Galosi S, Chen D, Sahagian M, Haas RH, Hyland K, Friedman J.
Ann Clin Transl Neurol. 2018 Jul 17;5(8):996-1010. doi: 10.1002/acn3.597. eCollection 2018 Aug.
ABSTRACT
Paroxysmal movement disorders encompass varied motor phenomena. Less recognized features and wide phenotypic and genotypic heterogeneity are impediments to straightforward molecular diagnosis. We describe a family with episodic ataxia type 1, initially mis-characterized as paroxysmal dystonia to illustrate this diagnostic challenge. We summarize clinical features in affected individuals to highlight underappreciated aspects and provide comprehensive phenotypic description of the rare familial KCNA1 mutation. Delayed diagnosis in this family is emblematic of the broader challenge of diagnosing other paroxysmal motor disorders. We summarize genotypic and phenotypic overlap and provide a suggested diagnostic algorithm for approaching patients with these conditions.
PMID:30128325 | PMC:PMC6093839 | DOI:10.1002/acn3.597
August 22, 2018
Genetic Neurologic DiseaseNeurogenomics
