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Ye ZL, Yan HJ, Guo QH, Zhang SQ, Luo S, Lian YJ, Ma YQ, Lu XG, Liu XR, Shen NX, Gao LD, Chen Z, Shi YW. NEXMIF variants are associated with epilepsy with or without intellectual disability. Seizure 2024; 116:93-99. [PMID: 37643945 DOI: 10.1016/j.seizure.2023.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/09/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023] Open
Abstract
OBJECTIVES Variants in NEXMIF had been reported associated with intellectual disability (ID) without epilepsy or developmental epileptic encephalopathy (DEE). It is unkown whether NEXMIF variants are associated with epilepsy without ID. This study aims to explore the phenotypic spectrum of NEXMIF and the genotype-phenotype correlations. MATERIALS AND METHODS Trio-based whole-exome sequencing was performed in patients with epilepsy. Previously reported NEXMIF variants were systematically reviewed to analyze the genotype-phenotype correlations. RESULTS Six variants were identified in seven unrelated cases with epilepsy, including two de novo null variants and four hemizygous missense variants. The two de novo variants were absent in all populations of gnomAD and four hemizygous missense variants were absent in male controls of gnomAD. The two patients with de novo null variants exhibited severe developmental epileptic encephalopathy. While, the patients with hemizygous missense variants had mild focal epilepsy with favorable outcome. Analysis of previously reported cases revealed that males with missense variants presented significantly higher percentage of normal intellectual development and later onset age of seizure than those with null variants, indicating a genotype-phenotype correlation. CONCLUSION This study suggested that NEXMIF variants were potentially associated with pure epilepsy with or without intellectual disability. The spectrum of epileptic phenotypes ranged from the mild epilepsy to severe developmental epileptic encephalopathy, where the epileptic phenotypes variability are potentially associated with patients' gender and variant type.
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Affiliation(s)
- Zi-Long Ye
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Hong-Jun Yan
- Epilepsy Center, Guangdong 999 Brain Hospital, Guangzhou, China
| | - Qing-Hui Guo
- Department of Pediatrics, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Shu-Qian Zhang
- Department of Pediatrics, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Sheng Luo
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Ya-Jun Lian
- Department of Pediatrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yun-Qing Ma
- Department of Pediatrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xin-Guo Lu
- Epilepsy Center and Department of Neurology, Shenzhen Children's Hospital, Shenzhen, China
| | - Xiao-Rong Liu
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Nan-Xiang Shen
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Liang-Di Gao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Zheng Chen
- Department of Pediatrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yi-Wu Shi
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China.
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2
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O'Connor M, Qiao H, Odamah K, Cerdeira PC, Man HY. Heterozygous Nexmif female mice demonstrate mosaic NEXMIF expression, autism-like behaviors, and abnormalities in dendritic arborization and synaptogenesis. Heliyon 2024; 10:e24703. [PMID: 38322873 PMCID: PMC10844029 DOI: 10.1016/j.heliyon.2024.e24703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 11/28/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with a strong genetic basis. ASDs are commonly characterized by impairments in language, restrictive and repetitive behaviors, and deficits in social interactions. Although ASD is a highly heterogeneous disease with many different genes implicated in its etiology, many ASD-associated genes converge on common cellular defects, such as aberrant neuronal morphology and synapse dysregulation. Our previous work revealed that, in mice, complete loss of the ASD-associated X-linked gene NEXMIF results in a reduction in dendritic complexity, a decrease in spine and synapse density, altered synaptic transmission, and ASD-like behaviors. Interestingly, human females of NEXMIF haploinsufficiency have recently been reported to demonstrate autistic features; however, the cellular and molecular basis for this haploinsufficiency-caused ASD remains unclear. Here we report that in the brains of Nexmif± female mice, NEXMIF shows a mosaic pattern in its expression in neurons. Heterozygous female mice demonstrate behavioral impairments similar to those of knockout male mice. In the mosaic mixture of neurons from Nexmif± mice, cells that lack NEXMIF have impairments in dendritic arborization and spine development. Remarkably, the NEXMIF-expressing neurons from Nexmif± mice also demonstrate similar defects in dendritic growth and spine formation. These findings establish a novel mouse model of NEXMIF haploinsufficiency and provide new insights into the pathogenesis of NEXMIF-dependent ASD.
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Affiliation(s)
- Margaret O'Connor
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
| | - Hui Qiao
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
| | - KathrynAnn Odamah
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
| | | | - Heng-Ye Man
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
- Department of Pharmacology, Physiology & Biophysics, Boston University School of Medicine, 72 East Concord St., Boston, MA 02118, USA
- Center for Systems Neuroscience, Boston University, 610 Commonwealth Ave, Boston, MA 02215, USA
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3
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Zhong L, Liu C, Lin L. Infantile spasms caused by NEXMIF mutation: A case report and literature review. APPLIED NEUROPSYCHOLOGY. CHILD 2023; 12:380-385. [PMID: 37313861 DOI: 10.1080/21622965.2023.2220459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Infantile spasms are rare epileptic syndromes associated with neurodevelopment and genes. The NEXMIF gene, identified as KIDLIA, KIAA2022 or Xpn, is a gene of unknown biological identity located on the q13.2 X chromosome. CASE DESCRIPTION We presented a 4-month-old infant with a diagnosis of infantile spasms with NEXMIF mutation. Clinical manifestations include psychomotor retardation, loss of consciousness, and seizures. After oral therapy with vigabatrin, sodium valproate, and levetiracetam, the syndrome was alleviated and no recurrence was observed during one month of follow-up. CONCLUSIONS A loss-of-function mutation in the NEXMIF gene has been reported. There are few reports on this mutation worldwide. This study provides a new idea for the clinical treatment of infantile spasms.
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Affiliation(s)
- Liuming Zhong
- Department of Internal Medicine-Pediatrics, Meizhou People's Hospital, Meizhou, China
| | - Caihui Liu
- Department of Internal Medicine-Pediatrics, Meizhou People's Hospital, Meizhou, China
| | - Liang Lin
- Department of Internal Medicine-Pediatrics, Meizhou People's Hospital, Meizhou, China
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4
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Yoo J, Kim GW, Jeon YH, Kim JY, Lee SW, Kwon SH. Drawing a line between histone demethylase KDM5A and KDM5B: their roles in development and tumorigenesis. Exp Mol Med 2022; 54:2107-2117. [PMID: 36509829 PMCID: PMC9794821 DOI: 10.1038/s12276-022-00902-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/29/2022] [Accepted: 10/13/2022] [Indexed: 12/14/2022] Open
Abstract
Distinct epigenetic modifiers ensure coordinated control over genes that govern a myriad of cellular processes. Growing evidence shows that dynamic regulation of histone methylation is critical for almost all stages of development. Notably, the KDM5 subfamily of histone lysine-specific demethylases plays essential roles in the proper development and differentiation of tissues, and aberrant regulation of KDM5 proteins during development can lead to chronic developmental defects and even cancer. In this review, we adopt a unique perspective regarding the context-dependent roles of KDM5A and KDM5B in development and tumorigenesis. It is well known that these two proteins show a high degree of sequence homology, with overlapping functions. However, we provide deeper insights into their substrate specificity and distinctive function in gene regulation that at times divert from each other. We also highlight both the possibility of targeting KDM5A and KDM5B to improve cancer treatment and the limitations that must be overcome to increase the efficacy of current drugs.
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Affiliation(s)
- Jung Yoo
- grid.15444.300000 0004 0470 5454College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983 Republic of Korea
| | - Go Woon Kim
- grid.15444.300000 0004 0470 5454College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983 Republic of Korea
| | - Yu Hyun Jeon
- grid.15444.300000 0004 0470 5454College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983 Republic of Korea
| | - Ji Yoon Kim
- grid.15444.300000 0004 0470 5454College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983 Republic of Korea
| | - Sang Wu Lee
- grid.15444.300000 0004 0470 5454College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983 Republic of Korea
| | - So Hee Kwon
- grid.15444.300000 0004 0470 5454College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983 Republic of Korea
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5
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Steele JL, Morrow MM, Sarnat HB, Alkhunaizi E, Brandt T, Chitayat DA, DeFilippo CP, Douglas GV, Dubbs HA, Elloumi HZ, Glassford MR, Hannibal MC, Héron B, Kim LE, Marco EJ, Mignot C, Monaghan KG, Myers KA, Parikh S, Quinonez SC, Rajabi F, Shankar SP, Shinawi MS, van de Kamp JJP, Veerapandiyan A, Waldman AT, Graf WD. Semaphorin-Plexin Signaling: From Axonal Guidance to a New X-Linked Intellectual Disability Syndrome. Pediatr Neurol 2022; 126:65-73. [PMID: 34740135 DOI: 10.1016/j.pediatrneurol.2021.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/06/2021] [Accepted: 10/10/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Semaphorins and plexins are ligands and cell surface receptors that regulate multiple neurodevelopmental processes such as axonal growth and guidance. PLXNA3 is a plexin gene located on the X chromosome that encodes the most widely expressed plexin receptor in fetal brain, plexin-A3. Plexin-A3 knockout mice demonstrate its role in semaphorin signaling in vivo. The clinical manifestations of semaphorin/plexin neurodevelopmental disorders have been less widely explored. This study describes the neurological and neurodevelopmental phenotypes of boys with maternally inherited hemizygous PLXNA3 variants. METHODS Data-sharing through GeneDx and GeneMatcher allowed identification of individuals with autism or intellectual disabilities (autism/ID) and hemizygous PLXNA3 variants in collaboration with their physicians and genetic counselors, who completed questionnaires about their patients. In silico analyses predicted pathogenicity for each PLXNA3 variant. RESULTS We assessed 14 boys (mean age, 10.7 [range 2 to 25] years) with maternally inherited hemizygous PLXNA3 variants and autism/ID ranging from mild to severe. Other findings included fine motor dyspraxia (92%), attention-deficit/hyperactivity traits, and aggressive behaviors (63%). Six patients (43%) had seizures. Thirteen boys (93%) with PLXNA3 variants showed novel or very low allele frequencies and probable damaging/disease-causing pathogenicity in one or more predictors. We found a genotype-phenotype correlation between PLXNA3 cytoplasmic domain variants (exons 22 to 32) and more severe neurodevelopmental disorder phenotypes (P < 0.05). CONCLUSIONS We report 14 boys with maternally inherited, hemizygous PLXNA3 variants and a range of neurodevelopmental disorders suggesting a novel X-linked intellectual disability syndrome. Greater understanding of PLXNA3 variant pathogenicity in humans will require additional clinical, computational, and experimental validation.
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Affiliation(s)
| | | | - Harvey B Sarnat
- Departments of Paediatrics, Pathology (Neuropathology), and Clinical Neurosciences, University of Calgary Cumming School of Medicine and Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
| | - Ebba Alkhunaizi
- Department of Obstetrics and Gynecology, The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | | | - David A Chitayat
- Department of Obstetrics and Gynecology, The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Colette P DeFilippo
- Division of Genomic Medicine, Department of Pediatrics, MIND Institute, University of California-Davis, Sacramento, California
| | | | - Holly A Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | - Megan R Glassford
- Division of Pediatric Genetics, Metabolism and Genomic Medicine, Department of Pediatrics, C. S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan
| | - Mark C Hannibal
- Division of Pediatric Genetics, Metabolism and Genomic Medicine, Department of Pediatrics, C. S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan
| | - Bénédicte Héron
- Hôpital Armand Trousseau, Service de Neurologie Pédiatrique, Paris, France
| | - Linda E Kim
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
| | - Elysa J Marco
- Department of Neurodevelopmental Medicine, CorticaCare, San Diego, California
| | - Cyril Mignot
- Clinical Genetic Department, Pitié Salpétrière University Hospital, Paris, France
| | | | - Kenneth A Myers
- Division of Neurology, Department of Pediatrics, McGill University Health Centre, Montreal, Canada
| | - Sumit Parikh
- Department of Mitochondrial Medicine & Genetics, Cleveland Clinic, Cleveland, Ohio
| | - Shane C Quinonez
- Division of Pediatric Genetics, Metabolism and Genomic Medicine, Department of Pediatrics, C. S. Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan
| | - Farrah Rajabi
- Division of Genetics and Genomics, Boston Children's Hospital; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Suma P Shankar
- Division of Genomic Medicine, Department of Pediatrics, MIND Institute, University of California-Davis, Sacramento, California
| | - Marwan S Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri
| | | | - Aravindhan Veerapandiyan
- Division of Neurology, Department of Pediatrics, Arkansas Children's Hospital, Little Rock, Arkansas
| | - Amy T Waldman
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - William D Graf
- Division of Neurology, Department of Pediatrics, Connecticut Children's, University of Connecticut, Farmington, Connecticut.
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6
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Kuhn T, Blades R, Gottlieb L, Knudsen K, Ashdown C, Martin-Harris L, Ghahremani D, Dang BH, Bilder RM, Bookheimer SY. Neuroanatomical differences in the memory systems of intellectual giftedness and typical development. Brain Behav 2021; 11:e2348. [PMID: 34651457 PMCID: PMC8613411 DOI: 10.1002/brb3.2348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/14/2021] [Accepted: 08/14/2021] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Studying neuro-structural markers of intellectual giftedness (IG) will inform scientific understanding of the processes helping children excel academically. METHODS Structural and diffusion-weighted MRI was used to compare regional brain shape and connectivity of 12 children with average to high average IQ and 18 IG children, defined as having IQ greater than 145. RESULTS IG had larger subcortical structures and more robust white matter microstructural organization between those structures in regions associated with explicit memory. TD had more connected, larger subcortical structures in regions associated with implicit memory. CONCLUSIONS It was found that the memory systems within brains of children with exceptional intellectual abilities are differently sized and connected compared to the brains of typically developing children. These different neurodevelopmental trajectories suggest different learning strategies. A spectrum of intelligence types is envisioned, facilitated by different ratios of implicit and explicit system, which was validated using a large external dataset.
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Affiliation(s)
- Taylor Kuhn
- Department ofPsychiatry and Biobehavioral Sciences, UCLA, 635 Charles E Young Dr, South, Los Angeles, CA, 90025, USA
| | - Robin Blades
- Department ofPsychiatry and Biobehavioral Sciences, UCLA, 635 Charles E Young Dr, South, Los Angeles, CA, 90025, USA
| | - Lev Gottlieb
- Department ofPsychiatry and Biobehavioral Sciences, UCLA, 635 Charles E Young Dr, South, Los Angeles, CA, 90025, USA
| | - Kendra Knudsen
- Department ofPsychiatry and Biobehavioral Sciences, UCLA, 635 Charles E Young Dr, South, Los Angeles, CA, 90025, USA
| | - Christopher Ashdown
- Department ofPsychiatry and Biobehavioral Sciences, UCLA, 635 Charles E Young Dr, South, Los Angeles, CA, 90025, USA
| | - Laurel Martin-Harris
- Department ofPsychiatry and Biobehavioral Sciences, UCLA, 635 Charles E Young Dr, South, Los Angeles, CA, 90025, USA
| | - Dara Ghahremani
- Department ofPsychiatry and Biobehavioral Sciences, UCLA, 635 Charles E Young Dr, South, Los Angeles, CA, 90025, USA
| | - Bianca H Dang
- Department ofPsychiatry and Biobehavioral Sciences, UCLA, 635 Charles E Young Dr, South, Los Angeles, CA, 90025, USA
| | - Robert M Bilder
- Department ofPsychiatry and Biobehavioral Sciences, UCLA, 635 Charles E Young Dr, South, Los Angeles, CA, 90025, USA
| | - Susan Y Bookheimer
- Department ofPsychiatry and Biobehavioral Sciences, UCLA, 635 Charles E Young Dr, South, Los Angeles, CA, 90025, USA
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7
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Agenesis of the Corpus Callosum with Facial Dysmorphism and Intellectual Disability in Sibs Associated with Compound Heterozygous KDM5B Variants. Genes (Basel) 2021; 12:genes12091397. [PMID: 34573379 PMCID: PMC8467522 DOI: 10.3390/genes12091397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 01/14/2023] Open
Abstract
We studied a family in which the first-born child, a girl, had developmental delay, facial dysmorphism, and agenesis of the corpus callosum (ACC). The subsequent pregnancy was interrupted as the fetus was found to be also affected by ACC. Both cases were heterozygous for two KDM5B variants predicting p (Ala635Thr) and p (Ser1155AlafsTer4) that were shown to be in trans. KDM5B variants have been previously associated with moderate to severe developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), and dysmorphism in a few individuals, but the pathogenetic mechanisms are not clear yet as patients with both monoallelic and biallelic variants have been observed. Interestingly, one individual has previously been reported with ACC and severe ID in association with biallelic KDM5B variants. Together with the observations in this family, this suggests that agenesis of the corpus callosum may be part of the phenotypic spectrum associated with KDM5B variants and that the KDM5B gene should be included in gene panels to clarify the etiology of ACC both in the prenatal and postnatal setting.
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8
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Singh R, Cohen ASA, Poulton C, Hjortshøj TD, Akahira-Azuma M, Mendiratta G, Khan WA, Azmanov DN, Woodward KJ, Kirchhoff M, Shi L, Edelmann L, Baynam G, Scott SA, Jabs EW. Deletion of ERF and CIC causes abnormal skull morphology and global developmental delay. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a005991. [PMID: 34117072 PMCID: PMC8208047 DOI: 10.1101/mcs.a005991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/26/2021] [Indexed: 11/24/2022] Open
Abstract
The ETS2 repressor factor (ERF) is a transcription factor in the RAS-MEK-ERK signal transduction cascade that regulates cell proliferation and differentiation, and pathogenic sequence variants in the ERF gene cause variable craniosynostosis inherited in an autosomal dominant pattern. The reported ERF variants are largely loss-of-function, implying haploinsufficiency as a primary disease mechanism; however, ERF gene deletions have not been reported previously. Here we describe three probands with macrocephaly, craniofacial dysmorphology, and global developmental delay. Clinical genetic testing for fragile X and other relevant sequencing panels were negative; however, chromosomal microarray identified heterozygous deletions (63.7–583.2 kb) on Chromosome 19q13.2 in each proband that together included five genes associated with Mendelian diseases (ATP1A3, ERF, CIC, MEGF8, and LIPE). Parental testing indicated that the aberrations were apparently de novo in two of the probands and were inherited in the one proband with the smallest deletion. Deletion of ERF is consistent with the reported loss-of-function ERF variants, prompting clinical copy-number-variant classifications of likely pathogenic. Moreover, the recent characterization of heterozygous loss-of-function CIC sequence variants as a cause of intellectual disability and neurodevelopmental disorders inherited in an autosomal dominant pattern is also consistent with the developmental delays and intellectual disabilities identified among the two probands with CIC deletions. Taken together, this case series adds to the previously reported patients with ERF and/or CIC sequence variants and supports haploinsufficiency of both genes as a mechanism for a variable syndromic cranial phenotype with developmental delays and intellectual disability inherited in an autosomal dominant pattern.
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Affiliation(s)
- Ram Singh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Ana S A Cohen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Cathryn Poulton
- Genetic Service of Western Australia, King Edward Memorial Hospital, Perth, Western Australia 6008, Australia
| | - Tina Duelund Hjortshøj
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Moe Akahira-Azuma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Geetu Mendiratta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Wahab A Khan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Dimitar N Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia 6009, Australia.,Pathology and Laboratory Medicine, Medical School, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Karen J Woodward
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia 6009, Australia.,Pathology and Laboratory Medicine, Medical School, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Maria Kirchhoff
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Lisong Shi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Western Australia 6008, Australia.,Faculty of Health and Medical Sciences, Division of Paediatrics and Telethon Kids Institute, University of Western Australia, Perth, Western Australia 6008, Australia.,Faculty of Medicine, University of Notre Dame, Australia, Perth, Western Australia 6160, Australia
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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9
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Stamberger H, Hammer TB, Gardella E, Vlaskamp DRM, Bertelsen B, Mandelstam S, de Lange I, Zhang J, Myers CT, Fenger C, Afawi Z, Almanza Fuerte EP, Andrade DM, Balcik Y, Ben Zeev B, Bennett MF, Berkovic SF, Isidor B, Bouman A, Brilstra E, Busk ØL, Cairns A, Caumes R, Chatron N, Dale RC, de Geus C, Edery P, Gill D, Granild-Jensen JB, Gunderson L, Gunning B, Heimer G, Helle JR, Hildebrand MS, Hollingsworth G, Kharytonov V, Klee EW, Koeleman BPC, Koolen DA, Korff C, Küry S, Lesca G, Lev D, Leventer RJ, Mackay MT, Macke EL, McEntagart M, Mohammad SS, Monin P, Montomoli M, Morava E, Moutton S, Muir AM, Parrini E, Procopis P, Ranza E, Reed L, Reif PS, Rosenow F, Rossi M, Sadleir LG, Sadoway T, Schelhaas HJ, Schneider AL, Shah K, Shalev R, Sisodiya SM, Smol T, Stumpel CTRM, Stuurman K, Symonds JD, Mau-Them FT, Verbeek N, Verhoeven JS, Wallace G, Yosovich K, Zarate YA, Zerem A, Zuberi SM, Guerrini R, Mefford HC, Patel C, Zhang YH, Møller RS, Scheffer IE. NEXMIF encephalopathy: an X-linked disorder with male and female phenotypic patterns. Genet Med 2020; 23:363-373. [PMID: 33144681 DOI: 10.1038/s41436-020-00988-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/21/2020] [Accepted: 09/21/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Pathogenic variants in the X-linked gene NEXMIF (previously KIAA2022) are associated with intellectual disability (ID), autism spectrum disorder, and epilepsy. We aimed to delineate the female and male phenotypic spectrum of NEXMIF encephalopathy. METHODS Through an international collaboration, we analyzed the phenotypes and genotypes of 87 patients with NEXMIF encephalopathy. RESULTS Sixty-three females and 24 males (46 new patients) with NEXMIF encephalopathy were studied, with 30 novel variants. Phenotypic features included developmental delay/ID in 86/87 (99%), seizures in 71/86 (83%) and multiple comorbidities. Generalized seizures predominated including myoclonic seizures and absence seizures (both 46/70, 66%), absence with eyelid myoclonia (17/70, 24%), and atonic seizures (30/70, 43%). Males had more severe developmental impairment; females had epilepsy more frequently, and varied from unaffected to severely affected. All NEXMIF pathogenic variants led to a premature stop codon or were deleterious structural variants. Most arose de novo, although X-linked segregation occurred for both sexes. Somatic mosaicism occurred in two males and a family with suspected parental mosaicism. CONCLUSION NEXMIF encephalopathy is an X-linked, generalized developmental and epileptic encephalopathy characterized by myoclonic-atonic epilepsy overlapping with eyelid myoclonia with absence. Some patients have developmental encephalopathy without epilepsy. Males have more severe developmental impairment. NEXMIF encephalopathy arises due to loss-of-function variants.
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Affiliation(s)
- Hannah Stamberger
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia.,Applied and Translational Neurogenomics group, Center for Molecular Neurology, VIB, and Department of Neurology, University Hospital of Antwerp, University of Antwerp, Antwerpen, Belgium
| | - Trine B Hammer
- Department of Epilepsy Genetics, Danish Epilepsy Centre Filadelfia, Dianalund, Denmark.,Clinical Genetic Department, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Elena Gardella
- Department of Epilepsy Genetics, Danish Epilepsy Centre Filadelfia, Dianalund, Denmark.,Institute for Regional Health Services Research, University of Southern Denmark, Odense, Denmark
| | - Danique R M Vlaskamp
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia.,University of Groningen, University Medical Center Groningen, Department of Neurology, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Birgitte Bertelsen
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Simone Mandelstam
- Royal Children's Hospital, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia.,Department of Radiology, University of Melbourne, Melbourne, VIC, Australia.,Florey Institute of Neuroscience and Mental Health, Melbourne, VIC, Australia
| | - Iris de Lange
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jing Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Candace T Myers
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Christina Fenger
- Department of Epilepsy Genetics, Danish Epilepsy Centre Filadelfia, Dianalund, Denmark
| | - Zaid Afawi
- Tel Aviv University Medical School, Tel Aviv, Israel
| | - Edith P Almanza Fuerte
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Danielle M Andrade
- Division of Neurology, Toronto Western Hospital, University of Toronto, Toronto, ON, Canada
| | - Yunus Balcik
- Epilepsy Center Frankfurt Rhine-Main, Center of Neurology and Neurosurgery, University Hospital Frankfurt, and Center for Personalized Translational Epilepsy Research (CePTER), Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Bruria Ben Zeev
- Edmond and Lily Safra Children's Hospital, Pediatric Neurology Unit, Tel-Hashomer, Israel.,Tel Aviv University, Sackler School of Medicine, Tel Aviv, Israel
| | - Mark F Bennett
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia.,The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology University of Melbourne, Melbourne, VIC, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia
| | | | - Arjan Bouman
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Eva Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Øyvind L Busk
- Section for Medical Genetics, Telemark Hospital, Skien, Norway
| | - Anita Cairns
- Department of Neurosciences, Queensland Children's Hospital, Brisbane, QLD, Australia
| | - Roseline Caumes
- Service de Neuropédiatrie, Pôle de Médecine et Spécialités Médicales, CHRU de Lille, Lille, France
| | - Nicolas Chatron
- Lyon University Hospitals, Departments of Genetics, Lyon, France
| | - Russell C Dale
- T.Y. Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Christa de Geus
- University Medical Centre Groningen, Department of Genetics, Groningen, The Netherlands
| | - Patrick Edery
- Lyon University Hospitals, Departments of Genetics, Lyon, France.,INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Bron, France
| | - Deepak Gill
- T.Y. Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | | | - Lauren Gunderson
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Gali Heimer
- Edmond and Lily Safra Children's Hospital, Pediatric Neurology Unit, Tel-Hashomer, Israel.,Tel Aviv University, Sackler School of Medicine, Tel Aviv, Israel
| | - Johan R Helle
- Section for Medical Genetics, Telemark Hospital, Skien, Norway
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Georgie Hollingsworth
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia
| | | | - Eric W Klee
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Bobby P C Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Korff
- Pediatric Neurology Unit, University Hospitals, Geneva, Switzerland
| | - Sébastien Küry
- Service de génétique médicale, CHU Nantes, Nantes, France
| | - Gaetan Lesca
- Lyon University Hospitals, Departments of Genetics, Lyon, France
| | - Dorit Lev
- Tel Aviv University, Sackler School of Medicine, Tel Aviv, Israel.,Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Richard J Leventer
- Royal Children's Hospital, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Mark T Mackay
- Royal Children's Hospital, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Meriel McEntagart
- Medical Genetics, St George's University Hospitals NHS FT, Cranmer Tce, London, United Kingdom
| | - Shekeeb S Mohammad
- T.Y. Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Pauline Monin
- Lyon University Hospitals, Departments of Genetics, Lyon, France
| | - Martino Montomoli
- Department of Neuroscience, Pharmacology and Child Health, Children's Hospital A. Meyer and University of Florence, Florence, Italy
| | - Eva Morava
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sebastien Moutton
- CPDPN, Pôle mère enfant, Maison de Santé Protestante Bordeaux Bagatelle, Talence, France.,INSERM UMR1231 GAD, FHU-TRANSLAD, Université de Bourgogne, Dijon, France
| | - Alison M Muir
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Elena Parrini
- Department of Neuroscience, Pharmacology and Child Health, Children's Hospital A. Meyer and University of Florence, Florence, Italy
| | - Peter Procopis
- T.Y. Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, Sydney, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Laura Reed
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Philipp S Reif
- Epilepsy Center Frankfurt Rhine-Main, Center of Neurology and Neurosurgery, University Hospital Frankfurt, and Center for Personalized Translational Epilepsy Research (CePTER), Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Felix Rosenow
- Epilepsy Center Frankfurt Rhine-Main, Center of Neurology and Neurosurgery, University Hospital Frankfurt, and Center for Personalized Translational Epilepsy Research (CePTER), Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Massimiliano Rossi
- Lyon University Hospitals, Departments of Genetics, Lyon, France.,INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Bron, France
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Tara Sadoway
- Division of Neurology, Toronto Western Hospital, University of Toronto, Toronto, ON, Canada
| | | | - Amy L Schneider
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia
| | | | - Ruth Shalev
- Neuropaediatric Unit, Shaare Zedek Medical Centre, Hebrew University School of Medicine, Jerusalem, Israel
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, United Kingdom and Chalfont Centre for Epilepsy, Bucks, UK
| | - Thomas Smol
- Institut de Génétique Médicale, Hopital Jeanne de Flandre, Lille University Hospital, Lille, France
| | - Connie T R M Stumpel
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Kyra Stuurman
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Joseph D Symonds
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK.,College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Frederic Tran Mau-Them
- UF Innovation en diagnostic genomique des maladies rares, CHU Dijon Bourgogne, Dijon, France.,INSERM UMR1231 GAD, Dijon, France
| | - Nienke Verbeek
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Judith S Verhoeven
- Academic Center for Epileptology, Kempenhaege, Department of Neurology, Heeze, The Netherlands
| | - Geoffrey Wallace
- Department of Neurosciences, Queensland Children's Hospital, Brisbane, QLD, Australia.,School of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Keren Yosovich
- Molecular Genetics Lab, Wolfson Medical Center, Holon, Israel
| | - Yuri A Zarate
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Little Rock, AR, USA
| | - Ayelet Zerem
- Tel Aviv University, Sackler School of Medicine, Tel Aviv, Israel.,White Matter Disease Care, Pediatric Neurology Unit, Dana-Dwak Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Sameer M Zuberi
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK.,College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Renzo Guerrini
- Department of Neuroscience, Pharmacology and Child Health, Children's Hospital A. Meyer and University of Florence, Florence, Italy
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Yue-Hua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Rikke S Møller
- Department of Epilepsy Genetics, Danish Epilepsy Centre Filadelfia, Dianalund, Denmark.,Institute for Regional Health Services Research, University of Southern Denmark, Odense, Denmark
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, VIC, Australia. .,Royal Children's Hospital, Melbourne, VIC, Australia. .,Murdoch Children's Research Institute, Melbourne, VIC, Australia. .,Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia. .,Florey Institute of Neuroscience and Mental Health, Melbourne, VIC, Australia.
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10
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Ogasawara M, Nakagawa E, Takeshita E, Hamanaka K, Miyatake S, Matsumoto N, Sasaki M. Clonazepam as an Effective Treatment for Epilepsy in a Female Patient with NEXMIF Mutation: Case Report. Mol Syndromol 2020; 11:232-237. [PMID: 33224018 DOI: 10.1159/000510172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/01/2020] [Indexed: 12/13/2022] Open
Abstract
The NEXMIF (KIAA2022) gene is located in the X chromosome, and hemizygous mutations in NEXMIF cause X-linked intellectual disability in male patients. Female patients with heterozygous mutations in NEXMIF also show similar, but milder, intellectual disability. Most female patients demonstrate intractable epilepsy compared with male patients, and the treatment strategy for epilepsy is still uncertain. Thus far, 24 female patients with NEXMIF mutations have been reported. Of these 24 patients, 20 also have epilepsy. Until now, epilepsy has been controlled in only 2 of these female patients. We report a female patient with a heterozygous de novo mutation, NM_001008537.2:c.1123del (p.Glu375Argfs*21), in NEXMIF. The patient showed mild intellectual disability, facial dysmorphism, obesity, generalized tonic-clonic seizures, and nonconvulsive status epilepticus. Sodium valproate was effective but caused secondary amenorrhea. We successfully treated her epilepsy with clonazepam without side effects, indicating that clonazepam might be a good choice to treat epilepsy in patients with NEXMIF mutations.
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Affiliation(s)
- Masashi Ogasawara
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Genome Medicine Development, Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Eiji Nakagawa
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Eri Takeshita
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masayuki Sasaki
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
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11
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Abay-Nørgaard S, Attianese B, Boreggio L, Salcini AE. Regulators of H3K4 methylation mutated in neurodevelopmental disorders control axon guidance in Caenorhabditis elegans. Development 2020; 147:dev.190637. [PMID: 32675280 PMCID: PMC7420840 DOI: 10.1242/dev.190637] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022]
Abstract
Post-translational histone modifications regulate chromatin compaction and gene expression to control many aspects of development. Mutations in genes encoding regulators of H3K4 methylation are causally associated with neurodevelopmental disorders characterized by intellectual disability and deficits in motor functions. However, it remains unclear how H3K4 methylation influences nervous system development and contributes to the aetiology of disease. Here, we show that the catalytic activity of set-2, the Caenorhabditis elegans homologue of the H3K4 methyltransferase KMT2F/G (SETD1A/B) genes, controls embryonic transcription of neuronal genes and is required for establishing proper axon guidance, and for neuronal functions related to locomotion and learning. Moreover, we uncover a striking correlation between components of the H3K4 regulatory machinery mutated in neurodevelopmental disorders and the process of axon guidance in C. elegans. Thus, our study supports an epigenetic-based model for the aetiology of neurodevelopmental disorders, based on an aberrant axon guidance process originating from deregulated H3K4 methylation. Summary: Analysis of mutants lacking many known H3K4 regulators reveals the role of H3K4 methylation in C. elegans neuronal functions and suggests that aberrant axon guidance is a shared trait in neurodevelopmental diseases.
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Affiliation(s)
- Steffen Abay-Nørgaard
- BRIC, University of Copenhagen, Biotech Research and Innovation Centre, Ole Maaloes vej 5, 2200, Copenhagen, Denmark
| | - Benedetta Attianese
- BRIC, University of Copenhagen, Biotech Research and Innovation Centre, Ole Maaloes vej 5, 2200, Copenhagen, Denmark
| | - Laura Boreggio
- BRIC, University of Copenhagen, Biotech Research and Innovation Centre, Ole Maaloes vej 5, 2200, Copenhagen, Denmark
| | - Anna Elisabetta Salcini
- BRIC, University of Copenhagen, Biotech Research and Innovation Centre, Ole Maaloes vej 5, 2200, Copenhagen, Denmark
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12
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Bamodu O, Chao TY. Dissecting the functional pleiotropism of lysine demethylase 5B in physiology and pathology. JOURNAL OF CANCER RESEARCH AND PRACTICE 2020. [DOI: 10.4103/jcrp.jcrp_5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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13
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Simón-Carrasco L, Jiménez G, Barbacid M, Drosten M. The Capicua tumor suppressor: a gatekeeper of Ras signaling in development and cancer. Cell Cycle 2019; 17:702-711. [PMID: 29578365 DOI: 10.1080/15384101.2018.1450029] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The transcriptional repressor Capicua (CIC) has emerged as an important rheostat of cell growth regulated by RAS/MAPK signaling. Cic was originally discovered in Drosophila, where it was shown to be inactivated by MAPK signaling downstream of the RTKs Torso and EGFR, which results in signal-dependent responses that are required for normal cell fate specification, proliferation and survival of developing and adult tissues. CIC is highly conserved in mammals, where it is also negatively regulated by MAPK signaling. Here, we review the roles of CIC during mammalian development, tissue homeostasis, tumor formation and therapy resistance. Available data indicate that CIC is involved in multiple biological processes, including lung development, liver homeostasis, autoimmunity and neurobehavioral processes. Moreover, CIC has been shown to be involved in tumor development as a tumor suppressor, both in human as well as in mouse models. Finally, several lines of evidence implicate CIC as a determinant of sensitivity to EGFR and MAPK pathway inhibitors, suggesting that CIC may play a broader role in human cancer than originally anticipated.
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Affiliation(s)
- Lucía Simón-Carrasco
- a Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO) , Melchor Fernández Almagro 3, Madrid , Spain
| | - Gerardo Jiménez
- b Institut de Biologia Molecular de Barcelona-CSIC , Parc Científic de Barcelona, Barcelona , Spain.,c ICREA , Pg. Lluís Companys 23, Barcelona , Spain
| | - Mariano Barbacid
- a Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO) , Melchor Fernández Almagro 3, Madrid , Spain
| | - Matthias Drosten
- a Molecular Oncology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO) , Melchor Fernández Almagro 3, Madrid , Spain
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14
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Miolo G, Giuffrida MG, Corona G, Capalbo A, Pivetta B, Tessitori G, Bernardini L. A novel mosaic 1q32.1 microduplication identified through Chromosome Microarray Analysis: narrowing the smallest critical region including KDM5B gene found associated with neurodevelopmetal disorders. Eur J Med Genet 2019; 62:103558. [PMID: 31405577 DOI: 10.1016/j.ejmg.2018.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 10/03/2018] [Accepted: 10/24/2018] [Indexed: 01/07/2023]
Abstract
Microduplications involving 1q32.1 chromosomal region have been rarely reported in literature. Patients with these microduplications suffer from intellectual disability, developmental delay and a number of dysmorphic features, although no clear karyotype/phenotype correlation has yet been determined. In this case report we describe two monochorionic-diamniotic twins with intellectual disability, abnormality of coordination and dysmorphic features associated with a de novo 280 kb mosaic microduplication of 1q32.1 chromosomal region, identified using a Chromosome Microarray Analysis (CMA) and confirmed by quantitative PCR analysis. The duplicated region encompassed entirely three OMIM genes KDM5B (*605393), KLHL12 (*614522), RABIF (*603417) and involved partially SYT2 (*600104). This unique case report allows to redefine the critical 1q32.1 microduplicated region implicated in the ethiopathogenesis of intellectual disability and developmental delay. Furthermore, it suggests that KDM5B gene can have a pivotal role in the development of neurodevelopmental disorders through its demethylase activity.
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Affiliation(s)
- Gianmaria Miolo
- Medical Laboratory Department, Genetics Section, Pordenone Hospital, Italy; Medical and Preventive Oncology, IRCCS Aviano, National Cancer Institute, Italy.
| | - Maria Grazia Giuffrida
- Fondazione IRCCS Casa Sollievo Della Sofferenza, Cytogenetics Unit, San Giovanni Rotondo (FG), Italy
| | - Giuseppe Corona
- Immunopathology and Cancer Biomarkers Unit, IRCCS Aviano, National Cancer Institute, Italy
| | - Anna Capalbo
- Fondazione IRCCS Casa Sollievo Della Sofferenza, Cytogenetics Unit, San Giovanni Rotondo (FG), Italy
| | - Barbara Pivetta
- Medical Laboratory Department, Genetics Section, Pordenone Hospital, Italy
| | - Giovanni Tessitori
- Medical Laboratory Department, Genetics Section, Pordenone Hospital, Italy
| | - Laura Bernardini
- Fondazione IRCCS Casa Sollievo Della Sofferenza, Cytogenetics Unit, San Giovanni Rotondo (FG), Italy
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15
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Alarcon-Martinez T, Khan A, Myers KA. Torpedo Maculopathy Associated with NEXMIF Mutation. Mol Syndromol 2019; 10:229-233. [PMID: 31602197 DOI: 10.1159/000498835] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2019] [Indexed: 11/19/2022] Open
Abstract
Mutations in the neurite extension and migration factor (NEXMIF) gene are associated with X-linked intellectual disability. Thus far, all males reported with NEXMIF mutations have mild to profound intellectual disability with varying combinations of autistic features, poor or absent speech, epilepsy, facial dysmorphism, and strabismus. Affected females tend to have milder intellectual disability but severe, drug-resistant epilepsy. Here, we present a 32-month-old boy with a novel de novo frameshift NEXMIF pathogenic variant (p.Glu375ArgfsX21) who has mild motor delay, language delay, autistic features, and strabismus. In addition to these commonly described findings of NEXMIF mutations, his fundus exam revealed a very rare ophthalmologic abnormality, torpedo maculopathy. This finding has not previously been reported with NEXMIF mutation; however, on literature review, 7/15 males with NEXMIF mutations had other ophthalmologic abnormalities. This patient expands the phenotypic spectrum for males with NEXMIF mutations and suggests that NEXMIF may play an important role in ocular development.
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Affiliation(s)
- Tuğba Alarcon-Martinez
- Division of Child Neurology, Department of Pediatrics, Montreal Children's Hospital, McGill University Health Centre, McGill University, Montreal, QC, Canada
| | - Ayesha Khan
- Department of Ophthalmology, Montreal Children's Hospital, McGill University Health Centre, McGill University, Montreal, QC, Canada.,Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Kenneth A Myers
- Division of Child Neurology, Department of Pediatrics, Montreal Children's Hospital, McGill University Health Centre, McGill University, Montreal, QC, Canada.,Research Institute of the McGill University Health Centre, Montreal, QC, Canada
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16
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Collins BE, Greer CB, Coleman BC, Sweatt JD. Histone H3 lysine K4 methylation and its role in learning and memory. Epigenetics Chromatin 2019; 12:7. [PMID: 30616667 PMCID: PMC6322263 DOI: 10.1186/s13072-018-0251-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/19/2018] [Indexed: 01/09/2023] Open
Abstract
Epigenetic modifications such as histone methylation permit change in chromatin structure without accompanying change in the underlying genomic sequence. A number of studies in animal models have shown that dysregulation of various components of the epigenetic machinery causes cognitive deficits at the behavioral level, suggesting that proper epigenetic control is necessary for the fundamental processes of learning and memory. Histone H3 lysine K4 (H3K4) methylation comprises one component of such epigenetic control, and global levels of this mark are increased in the hippocampus during memory formation. Modifiers of H3K4 methylation are needed for memory formation, shown through animal studies, and many of the same modifiers are mutated in human cognitive diseases. Indeed, all of the known H3K4 methyltransferases and four of the known six H3K4 demethylases have been associated with impaired cognition in a neurologic or psychiatric disorder. Cognitive impairment in such patients often manifests as intellectual disability, consistent with a role for H3K4 methylation in learning and memory. As a modification quintessentially, but not exclusively, associated with transcriptional activity, H3K4 methylation provides unique insights into the regulatory complexity of writing, reading, and erasing chromatin marks within an activated neuron. The following review will discuss H3K4 methylation and connect it to transcriptional events required for learning and memory within the developed nervous system. This will include an initial discussion of the most recent advances in the developing methodology to analyze H3K4 methylation, namely mass spectrometry and deep sequencing, as well as how these methods can be applied to more deeply understand the biology of this mark in the brain. We will then introduce the core enzymatic machinery mediating addition and removal of H3K4 methylation marks and the resulting epigenetic signatures of these marks throughout the neuronal genome. We next foray into the brain, discussing changes in H3K4 methylation marks within the hippocampus during memory formation and retrieval, as well as the behavioral correlates of H3K4 methyltransferase deficiency in this region. Finally, we discuss the human cognitive diseases connected to each H3K4 methylation modulator and summarize advances in developing drugs to target them.
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Affiliation(s)
- Bridget E Collins
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA
| | - Celeste B Greer
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA
| | - Benjamin C Coleman
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA
| | - J David Sweatt
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA.
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17
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Lebrun N, Mehler-Jacob C, Poirier K, Zordan C, Lacombe D, Carion N, Billuart P, Bienvenu T. Novel KDM5B splice variants identified in patients with developmental disorders: Functional consequences. Gene 2018; 679:305-313. [PMID: 30217758 DOI: 10.1016/j.gene.2018.09.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/28/2018] [Accepted: 09/10/2018] [Indexed: 12/11/2022]
Abstract
Histone lysine methylation influences processes such as gene expression and DNA repair. Thirty Jumonji C (JmjC) domain-containing proteins have been identified and phylogenetically clustered into seven subfamilies. Most JmjC domain-containing proteins have been shown to possess histone demethylase activity toward specific histone methylation marks. One of these subfamilies, the KDM5 family, is characterized by five conserved domains and includes four members. Interestingly, de novo loss-of-function and missense variants in KDM5B were identified in patients with intellectual disability (ID) and autism spectrum disorder (ASD) but also in unaffected individuals. Here, we report two novel de novo splice variants in the KDM5B gene in three patients with ID and ASD. The c.808 + 1G > A variant was identified in a boy with mild ID and autism traits and is associated with a significant reduced KDM5B mRNA expression without alteration of its H3K4me3 pattern. In contrast, the c.576 + 2T > C variant was found in twins with global delay in developmental milestones, poor language and ASD. This variant causes the production of an abnormal transcript which may produce an altered protein with the loss of the ARID1B domain with an increase in global gene H3K4me3. Our data reinforces the recent observation that the KDM5B haploinsufficiency is not a mechanism involved in intellectual disability and that KDM5B disorder associated with LOF variants is a recessive disorder. However, some variants may also cause gain of function, and need to be interpreted with caution, and functional studies should be performed to identify the molecular consequences of these different rare variants.
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Affiliation(s)
- Nicolas Lebrun
- Inserm, U1016, Institut Cochin, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; CNRS, UMR8104, Paris, France; Institut de Psychiatrie et de Neurosciences de Paris, 102 rue de la santé, 75014 Paris, France
| | - Claire Mehler-Jacob
- Service de Neuropédiatrie, HU-Paris Sud site Bicêtre AP-HP, 78 rue du Général Leclerc, 94270 Le Kremlin-Bicêtre, France
| | - Karine Poirier
- Inserm, U1016, Institut Cochin, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; CNRS, UMR8104, Paris, France
| | - Cecile Zordan
- Service de Génétique Médicale, Hôpital Pellegrin, Place Amélie Raba-Léon, CHU de Bordeaux, 33076 Bordeaux Cedex, France
| | - Didier Lacombe
- Service de Génétique Médicale, Hôpital Pellegrin, Place Amélie Raba-Léon, CHU de Bordeaux, 33076 Bordeaux Cedex, France
| | - Nathalie Carion
- Laboratoire de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, AP-HP, Paris, France
| | - Pierre Billuart
- Inserm, U1016, Institut Cochin, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; CNRS, UMR8104, Paris, France; Institut de Psychiatrie et de Neurosciences de Paris, 102 rue de la santé, 75014 Paris, France
| | - Thierry Bienvenu
- Inserm, U1016, Institut Cochin, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; CNRS, UMR8104, Paris, France; Institut de Psychiatrie et de Neurosciences de Paris, 102 rue de la santé, 75014 Paris, France; Laboratoire de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, AP-HP, Paris, France.
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18
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Zabaneh D, Krapohl E, Gaspar HA, Curtis C, Lee SH, Patel H, Newhouse S, Wu HM, Simpson MA, Putallaz M, Lubinski D, Plomin R, Breen G. A genome-wide association study for extremely high intelligence. Mol Psychiatry 2018; 23:1226-1232. [PMID: 29731509 PMCID: PMC5987166 DOI: 10.1038/mp.2017.121] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 03/20/2017] [Accepted: 04/11/2017] [Indexed: 12/16/2022]
Abstract
We used a case-control genome-wide association (GWA) design with cases consisting of 1238 individuals from the top 0.0003 (~170 mean IQ) of the population distribution of intelligence and 8172 unselected population-based controls. The single-nucleotide polymorphism heritability for the extreme IQ trait was 0.33 (0.02), which is the highest so far for a cognitive phenotype, and significant genome-wide genetic correlations of 0.78 were observed with educational attainment and 0.86 with population IQ. Three variants in locus ADAM12 achieved genome-wide significance, although they did not replicate with published GWA analyses of normal-range IQ or educational attainment. A genome-wide polygenic score constructed from the GWA results accounted for 1.6% of the variance of intelligence in the normal range in an unselected sample of 3414 individuals, which is comparable to the variance explained by GWA studies of intelligence with substantially larger sample sizes. The gene family plexins, members of which are mutated in several monogenic neurodevelopmental disorders, was significantly enriched for associations with high IQ. This study shows the utility of extreme trait selection for genetic study of intelligence and suggests that extremely high intelligence is continuous genetically with normal-range intelligence in the population.
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Affiliation(s)
- D Zabaneh
- King’s College London, MRC Social,
Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology
and Neuroscience, London, UK
| | - E Krapohl
- King’s College London, MRC Social,
Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology
and Neuroscience, London, UK
| | - H A Gaspar
- King’s College London, MRC Social,
Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology
and Neuroscience, London, UK,NIHR Biomedical Research Centre for
Mental Health, South London and Maudsley NHS Trust, London,
UK
| | - C Curtis
- King’s College London, MRC Social,
Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology
and Neuroscience, London, UK,NIHR Biomedical Research Centre for
Mental Health, South London and Maudsley NHS Trust, London,
UK
| | - S H Lee
- King’s College London, MRC Social,
Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology
and Neuroscience, London, UK,NIHR Biomedical Research Centre for
Mental Health, South London and Maudsley NHS Trust, London,
UK
| | - H Patel
- King’s College London, MRC Social,
Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology
and Neuroscience, London, UK,NIHR Biomedical Research Centre for
Mental Health, South London and Maudsley NHS Trust, London,
UK
| | - S Newhouse
- King’s College London, MRC Social,
Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology
and Neuroscience, London, UK,NIHR Biomedical Research Centre for
Mental Health, South London and Maudsley NHS Trust, London,
UK
| | - H M Wu
- King’s College London, MRC Social,
Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology
and Neuroscience, London, UK
| | - M A Simpson
- Department of Medical and Molecular
Genetics, Division of Genetics and Molecular Medicine, Guy’s Hospital,
London, UK
| | - M Putallaz
- Duke University Talent Identification
Program, Duke University, Durham, NC, USA
| | - D Lubinski
- Department of Psychology and Human
Development, Vanderbilt University, Nashville, TN,
USA
| | - R Plomin
- King’s College London, MRC Social,
Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology
and Neuroscience, London, UK
| | - G Breen
- King’s College London, MRC Social,
Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology
and Neuroscience, London, UK,NIHR Biomedical Research Centre for
Mental Health, South London and Maudsley NHS Trust, London,
UK,King's College London, MRC Social Genetic and
Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and
Neuroscience, 16 De Crespigny Park, London
SE5 8AF, UK. E-mail:
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19
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Lambert N, Dauve C, Ranza E, Makrythanasis P, Santoni F, Sloan-Béna F, Gimelli S, Blouin JL, Guipponi M, Bottani A, Antonarakis SE, Kosel MM, Fluss J, Paoloni-Giacobino A. Novel NEXMIF pathogenic variant in a boy with severe autistic features, intellectual disability, and epilepsy, and his mildly affected mother. J Hum Genet 2018; 63:847-850. [DOI: 10.1038/s10038-018-0459-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/27/2018] [Accepted: 03/27/2018] [Indexed: 01/27/2023]
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20
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Lorenzo M, Stolte-Dijkstra I, van Rheenen P, Smith RG, Scheers T, Walia JS. Clinical spectrum of KIAA2022 pathogenic variants in males: Case report of two boys with KIAA2022 pathogenic variants and review of the literature. Am J Med Genet A 2018; 176:1455-1462. [PMID: 29693785 DOI: 10.1002/ajmg.a.38667] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 02/08/2018] [Accepted: 02/16/2018] [Indexed: 11/06/2022]
Abstract
KIAA2022 is an X-linked intellectual disability (XLID) syndrome affecting males more severely than females. Few males with KIAA2022 variants and XLID have been reported. We present a clinical report of two unrelated males, with two nonsense KIAA2022 pathogenic variants, with profound intellectual disabilities, limited language development, strikingly similar autistic behavior, delay in motor milestones, and postnatal growth restriction. Patient 1, 19-years-old, has long ears, deeply set eyes with keratoconus, strabismus, a narrow forehead, anteverted nares, café-au-lait spots, macroglossia, thick vermilion of the upper and lower lips, and prognathism. He has gastroesophageal reflux, constipation with delayed rectosigmoid colonic transit time, difficulty regulating temperature, several musculoskeletal issues, and a history of one grand mal seizure. Patient 2, 10-years-old, has mild dysmorphic features, therapy resistant vomiting with diminished motility of the stomach, mild constipation, cortical visual impairment with intermittent strabismus, axial hypotonia, difficulty regulating temperature, and cutaneous mastocytosis. Genetic testing identified KIAA2022 variant c.652C > T(p.Arg218*) in Patient 1, and a novel nonsense de novo variant c.2707G > T(p.Glu903*) in Patient 2. We also summarized features of all reported males with KIAA2022 variants to date. This report not only adds knowledge of a novel pathogenic variant to the KIAA2022 variant database, but also likely extends the spectrum by describing novel dysmorphic features and medical conditions including macroglossia, café-au-lait spots, keratoconus, severe cutaneous mastocytosis, and motility problems of the GI tract, which may help physicians involved in the care of patients with this syndrome. Lastly, we describe the power of social media in bringing families with rare medical conditions together.
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Affiliation(s)
- Melissa Lorenzo
- Faculty of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Irene Stolte-Dijkstra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Patrick van Rheenen
- Department of Pediatric Gastroenterology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Tom Scheers
- Department of Child and Adolescent Psychiatry, University of Groningen, Groningen, The Netherlands
| | - Jagdeep S Walia
- Department of Pediatrics, Queen's University, Kingston, Ontario, Canada
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21
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Whole exome sequencing reveals inherited and de novo variants in autism spectrum disorder: a trio study from Saudi families. Sci Rep 2017; 7:5679. [PMID: 28720891 PMCID: PMC5515956 DOI: 10.1038/s41598-017-06033-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/06/2017] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with genetic and clinical heterogeneity. The interplay of de novo and inherited rare variants has been suspected in the development of ASD. Here, we applied whole exome sequencing (WES) on 19 trios from singleton Saudi families with ASD. We developed an analysis pipeline that allows capturing both de novo and inherited rare variants predicted to be deleterious. A total of 47 unique rare variants were detected in 17 trios including 38 which are newly discovered. The majority were either autosomal recessive or X-linked. Our pipeline uncovered variants in 15 ASD-candidate genes, including 5 (GLT8D1, HTATSF1, OR6C65, ITIH6 and DDX26B) that have not been reported in any human condition. The remaining variants occurred in genes formerly associated with ASD or other neurological disorders. Examples include SUMF1, KDM5B and MXRA5 (Known-ASD genes), PRODH2 and KCTD21 (implicated in schizophrenia), as well as USP9X and SMS (implicated in intellectual disability). Consistent with expectation and previous studies, most of the genes implicated herein are enriched for biological processes pertaining to neuronal function. Our findings underscore the private and heterogeneous nature of the genetic architecture of ASD even in a population with high consanguinity rates.
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22
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Lu HC, Tan Q, Rousseaux MWC, Wang W, Kim JY, Richman R, Wan YW, Yeh SY, Patel JM, Liu X, Lin T, Lee Y, Fryer JD, Han J, Chahrour M, Finnell RH, Lei Y, Zurita-Jimenez ME, Ahimaz P, Anyane-Yeboa K, Van Maldergem L, Lehalle D, Jean-Marcais N, Mosca-Boidron AL, Thevenon J, Cousin MA, Bro DE, Lanpher BC, Klee EW, Alexander N, Bainbridge MN, Orr HT, Sillitoe RV, Ljungberg MC, Liu Z, Schaaf CP, Zoghbi HY. Disruption of the ATXN1-CIC complex causes a spectrum of neurobehavioral phenotypes in mice and humans. Nat Genet 2017; 49:527-536. [PMID: 28288114 DOI: 10.1038/ng.3808] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 02/10/2017] [Indexed: 12/18/2022]
Abstract
Gain-of-function mutations in some genes underlie neurodegenerative conditions, whereas loss-of-function mutations in the same genes have distinct phenotypes. This appears to be the case with the protein ataxin 1 (ATXN1), which forms a transcriptional repressor complex with capicua (CIC). Gain of function of the complex leads to neurodegeneration, but ATXN1-CIC is also essential for survival. We set out to understand the functions of the ATXN1-CIC complex in the developing forebrain and found that losing this complex results in hyperactivity, impaired learning and memory, and abnormal maturation and maintenance of upper-layer cortical neurons. We also found that CIC activity in the hypothalamus and medial amygdala modulates social interactions. Informed by these neurobehavioral features in mouse mutants, we identified five individuals with de novo heterozygous truncating mutations in CIC who share similar clinical features, including intellectual disability, attention deficit/hyperactivity disorder (ADHD), and autism spectrum disorder. Our study demonstrates that loss of ATXN1-CIC complexes causes a spectrum of neurobehavioral phenotypes.
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Affiliation(s)
- Hsiang-Chih Lu
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA
| | - Qiumin Tan
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Maxime W C Rousseaux
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Wei Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ji-Yoen Kim
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ronald Richman
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, USA
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Szu-Ying Yeh
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA
| | - Jay M Patel
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Xiuyun Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, USA
| | - Tao Lin
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Yoontae Lee
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - John D Fryer
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jing Han
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Maria Chahrour
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Richard H Finnell
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, Texas, USA
| | - Yunping Lei
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, Texas, USA
| | - Maria E Zurita-Jimenez
- Department of Pediatrics, Dell Pediatric Research Institute, University of Texas at Austin Dell Medical School, Austin, Texas, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Kwame Anyane-Yeboa
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | | | - Daphne Lehalle
- University Hospital Federation, Translational Medicine for Congenital Anomalies (TRANSLAD), Dijon University Hospital, Dijon, France.,Genetic Center and Reference Center for Congenital Anomalies of the East of France, Dijon University Hospital, Dijon, France.,Research Unit 4271, Genetics for Congenital Anomalies, Burgundy University, Dijon, France
| | - Nolwenn Jean-Marcais
- University Hospital Federation, Translational Medicine for Congenital Anomalies (TRANSLAD), Dijon University Hospital, Dijon, France.,Genetic Center and Reference Center for Congenital Anomalies of the East of France, Dijon University Hospital, Dijon, France
| | - Anne-Laure Mosca-Boidron
- University Hospital Federation, Translational Medicine for Congenital Anomalies (TRANSLAD), Dijon University Hospital, Dijon, France.,Genetic Center and Reference Center for Congenital Anomalies of the East of France, Dijon University Hospital, Dijon, France.,Research Unit 4271, Genetics for Congenital Anomalies, Burgundy University, Dijon, France.,Chromosomal and Molecular Genetics Laboratory, Biological Center, Dijon University Hospital, Dijon, France
| | - Julien Thevenon
- University Hospital Federation, Translational Medicine for Congenital Anomalies (TRANSLAD), Dijon University Hospital, Dijon, France.,Genetic Center and Reference Center for Congenital Anomalies of the East of France, Dijon University Hospital, Dijon, France.,Research Unit 4271, Genetics for Congenital Anomalies, Burgundy University, Dijon, France
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Della E Bro
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Matthew N Bainbridge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.,Codified Genomics, LLC, Houston, Texas, USA
| | - Harry T Orr
- Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota, USA.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Roy V Sillitoe
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - M Cecilia Ljungberg
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Christian P Schaaf
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Huda Y Zoghbi
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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23
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Webster R, Cho MT, Retterer K, Millan F, Nowak C, Douglas J, Ahmad A, Raymond GV, Johnson MR, Pujol A, Begtrup A, McKnight D, Devinsky O, Chung WK. De novo loss of function mutations in KIAA2022 are associated with epilepsy and neurodevelopmental delay in females. Clin Genet 2016; 91:756-763. [PMID: 27568816 DOI: 10.1111/cge.12854] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 01/31/2023]
Abstract
Intellectual disability (ID) affects about 3% of the population and has a male gender bias. Of at least 700 genes currently linked to ID, more than 100 have been identified on the X chromosome, including KIAA2022. KIAA2022 is located on Xq13.3 and is expressed in the developing brain. The protein product of KIAA2022, X‐linked Intellectual Disability Protein Related to Neurite Extension (XPN), is developmentally regulated and is involved in neuronal migration and cell adhesion. The clinical manifestations of loss‐of‐function KIAA2022 mutations have been described previously in 15 males, born from unaffected carrier mothers, but few females. Using whole‐exome sequencing, we identified a cohort of five unrelated female patients with de novo probably gene damaging variants in KIAA2022 and core phenotypic features of ID, developmental delay, epilepsy refractory to treatment, and impaired language, of similar severity as reported for male counterparts. This study supports KIAA2022 as a novel cause of X‐linked dominant ID, and broadens the phenotype for KIAA2022 mutations.
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Affiliation(s)
- R Webster
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - M T Cho
- GeneDx, Gaithersburg, MD, USA
| | | | | | - C Nowak
- Boston Children's Hospital, Boston, MA, USA
| | - J Douglas
- Boston Children's Hospital, Boston, MA, USA
| | - A Ahmad
- University of Michigan, Ann Arbor, MI, USA
| | - G V Raymond
- Department of Neurology and Pediatrics, University of Minnesota Medical Center, Minneapolis, MN, USA
| | - M R Johnson
- Department of Neurology and Pediatrics, University of Minnesota Medical Center, Minneapolis, MN, USA
| | - A Pujol
- Neurometabolic Diseases Laboratory, ICREA/IDIBELL and CIBERER U759, Barcelona, Spain
| | | | | | - O Devinsky
- New York University School of Medicine, New York, NY, USA
| | - W K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
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24
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Fattahi Z, Kalhor Z, Fadaee M, Vazehan R, Parsimehr E, Abolhassani A, Beheshtian M, Zamani G, Nafissi S, Nilipour Y, Akbari M, Kahrizi K, Kariminejad A, Najmabadi H. Improved diagnostic yield of neuromuscular disorders applying clinical exome sequencing in patients arising from a consanguineous population. Clin Genet 2016; 91:386-402. [DOI: 10.1111/cge.12810] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 04/28/2016] [Accepted: 05/25/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Z. Fattahi
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - Z. Kalhor
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
| | - M. Fadaee
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - R. Vazehan
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - E. Parsimehr
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - A. Abolhassani
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - M. Beheshtian
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - G. Zamani
- Department of NeurologyTehran University of Medical Sciences Tehran Iran
| | - S. Nafissi
- Department of Pediatric Neurology, Pediatrics Center of Excellence, Children's Medical CenterTehran University of Medical Sciences Tehran Iran
| | - Y. Nilipour
- Pediatric Pathology Research Center, Mofid Children HospitalShahid Beheshti University of Medical Sciences Tehran Iran
| | - M.R. Akbari
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Women's College Research InstituteWomen's College Hospital Toronto Canada
- Dalla Lana School of Public HealthUniversity of Toronto Toronto Canada
| | - K. Kahrizi
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
| | - A. Kariminejad
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - H. Najmabadi
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
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25
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de Lange IM, Helbig KL, Weckhuysen S, Møller RS, Velinov M, Dolzhanskaya N, Marsh E, Helbig I, Devinsky O, Tang S, Mefford HC, Myers CT, van Paesschen W, Striano P, van Gassen K, van Kempen M, de Kovel CGF, Piard J, Minassian BA, Nezarati MM, Pessoa A, Jacquette A, Maher B, Balestrini S, Sisodiya S, Warde MTA, De St Martin A, Chelly J, van 't Slot R, Van Maldergem L, Brilstra EH, Koeleman BPC. De novo mutations of KIAA2022 in females cause intellectual disability and intractable epilepsy. J Med Genet 2016; 53:850-858. [PMID: 27358180 PMCID: PMC5264224 DOI: 10.1136/jmedgenet-2016-103909] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/02/2016] [Accepted: 05/27/2016] [Indexed: 12/13/2022]
Abstract
Background Mutations in the KIAA2022 gene have been reported in male patients with X-linked intellectual disability, and related female carriers were unaffected. Here, we report 14 female patients who carry a heterozygous de novo KIAA2022 mutation and share a phenotype characterised by intellectual disability and epilepsy. Methods Reported females were selected for genetic testing because of substantial developmental problems and/or epilepsy. X-inactivation and expression studies were performed when possible. Results All mutations were predicted to result in a frameshift or premature stop. 12 out of 14 patients had intractable epilepsy with myoclonic and/or absence seizures, and generalised in 11. Thirteen patients had mild to severe intellectual disability. This female phenotype partially overlaps with the reported male phenotype which consists of more severe intellectual disability, microcephaly, growth retardation, facial dysmorphisms and, less frequently, epilepsy. One female patient showed completely skewed X-inactivation, complete absence of RNA expression in blood and a phenotype similar to male patients. In the six other tested patients, X-inactivation was random, confirmed by a non-significant twofold to threefold decrease of RNA expression in blood, consistent with the expected mosaicism between cells expressing mutant or normal KIAA2022 alleles. Conclusions Heterozygous loss of KIAA2022 expression is a cause of intellectual disability in females. Compared with its hemizygous male counterpart, the heterozygous female disease has less severe intellectual disability, but is more often associated with a severe and intractable myoclonic epilepsy.
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Affiliation(s)
- Iris M de Lange
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Katherine L Helbig
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Sarah Weckhuysen
- Epilepsy Unit, Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpital de la Pitié Salpêtrière, Centre de reference épilepsies rares, Paris, France.,Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Rikke S Møller
- Danish Epilepsy Centre, Dianalund, Denmark.,Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Milen Velinov
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, USA.,Albert Einstein College of Medicine, Bronx, New York, USA
| | - Natalia Dolzhanskaya
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, USA.,Albert Einstein College of Medicine, Bronx, New York, USA
| | - Eric Marsh
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ingo Helbig
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Orrin Devinsky
- NYU Comprehensive Epilepsy Center, New York University Langone Medical Center, New York, New York, USA
| | - Sha Tang
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, Washington, USA
| | - Candace T Myers
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, Washington, USA
| | | | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, G. Gaslini Institute, University of Genoa, Genova, Italy
| | - Koen van Gassen
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marjan van Kempen
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Carolien G F de Kovel
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Juliette Piard
- Centre de génétique humaine, Université de Franche-Comté, Besançon, France
| | - Berge A Minassian
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Marjan M Nezarati
- Genetics Program, North York General Hospital and Prenatal Diagnosis & Medical Genetics, Mt. Sinai Hospital, Toronto, Canada
| | | | - Aurelia Jacquette
- Service de génétique, GHU Pitié-Salpêtrière, Université Pierre et Marie Curie, Paris, France
| | - Bridget Maher
- UCL Institute of Neurology, London, UK.,Epilepsy Society, Bucks, UK
| | | | - Sanjay Sisodiya
- UCL Institute of Neurology, London, UK.,Epilepsy Society, Bucks, UK
| | - Marie Therese Abi Warde
- Service de Pédiatrie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
| | - Anne De St Martin
- Service de Pédiatrie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
| | - Jamel Chelly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France.,Service de Diagnostic Génétique, Hôpital Civil de Strasbourg, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | | | - Ruben van 't Slot
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Eva H Brilstra
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bobby P C Koeleman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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26
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Vanderver A, Simons C, Helman G, Crawford J, Wolf NI, Bernard G, Pizzino A, Schmidt JL, Takanohashi A, Miller D, Khouzam A, Rajan V, Ramos E, Chowdhury S, Hambuch T, Ru K, Baillie GJ, Grimmond SM, Caldovic L, Devaney J, Bloom M, Evans SH, Murphy JLP, McNeill N, Fogel BL, Schiffmann R, van der Knaap MS, Taft RJ. Whole exome sequencing in patients with white matter abnormalities. Ann Neurol 2016; 79:1031-1037. [PMID: 27159321 DOI: 10.1002/ana.24650] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 03/27/2016] [Accepted: 03/28/2016] [Indexed: 01/25/2023]
Abstract
Here we report whole exome sequencing (WES) on a cohort of 71 patients with persistently unresolved white matter abnormalities with a suspected diagnosis of leukodystrophy or genetic leukoencephalopathy. WES analyses were performed on trio, or greater, family groups. Diagnostic pathogenic variants were identified in 35% (25 of 71) of patients. Potentially pathogenic variants were identified in clinically relevant genes in a further 7% (5 of 71) of cases, giving a total yield of clinical diagnoses in 42% of individuals. These findings provide evidence that WES can substantially decrease the number of unresolved white matter cases. Ann Neurol 2016;79:1031-1037.
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Affiliation(s)
- Adeline Vanderver
- Department of Neurology, Children's National Medical Center, Washington, DC.,Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC.,School of Medicine and Health Sciences, George Washington University, Washington, DC
| | - Cas Simons
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Guy Helman
- Department of Neurology, Children's National Medical Center, Washington, DC.,Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC
| | - Joanna Crawford
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Nicole I Wolf
- Department of Child Neurology, VU University Medical Center and Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | - Geneviève Bernard
- Departments of Pediatrics, Neurology, and Neurosurgery, Montreal Children's Hospital, McGill University Health Center, Montreal, Quebec, Canada
| | - Amy Pizzino
- Department of Neurology, Children's National Medical Center, Washington, DC
| | - Johanna L Schmidt
- Department of Neurology, Children's National Medical Center, Washington, DC.,Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC
| | - Asako Takanohashi
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC
| | - David Miller
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia.,University of Melbourne Centre for Cancer Research, University of Melbourne, Parkville, Victoria, Australia
| | | | | | | | | | | | - Kelin Ru
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Gregory J Baillie
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Sean M Grimmond
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia.,University of Melbourne Centre for Cancer Research, University of Melbourne, Parkville, Victoria, Australia
| | - Ljubica Caldovic
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC
| | - Joseph Devaney
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC
| | - Miriam Bloom
- Department of Pediatrics, Children's National Medical Center, Washington, DC
| | - Sarah H Evans
- Department of Physical Medicine and Rehabilitation, Children's National Medical Center, Washington, DC
| | | | - Nathan McNeill
- Institute for Metabolic Disease, Baylor Research Institute, Dallas, TX
| | - Brent L Fogel
- Department of Neurology, Program in Neurogenetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | | | | | - Marjo S van der Knaap
- Department of Child Neurology, VU University Medical Center and Neuroscience Campus Amsterdam, Amsterdam, the Netherlands.,Department of Functional Genomics, VU University, Amsterdam, the Netherlands
| | - Ryan J Taft
- School of Medicine and Health Sciences, George Washington University, Washington, DC.,Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia.,Illumina Inc, San Diego, CA
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27
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Mariani L, Lussi YC, Vandamme J, Riveiro A, Salcini AE. The H3K4me3/2 histone demethylase RBR-2 controls axon guidance by repressing the actin-remodeling gene wsp-1. Development 2016; 143:851-63. [PMID: 26811384 DOI: 10.1242/dev.132985] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/16/2016] [Indexed: 12/25/2022]
Abstract
The dynamic regulation of histone modifications is important for modulating transcriptional programs during development. Aberrant H3K4 methylation is associated with neurological disorders, but how the levels and the recognition of this modification affect specific neuronal processes is unclear. Here, we show that RBR-2, the sole homolog of the KDM5 family of H3K4me3/2 demethylases in Caenorhabditis elegans, ensures correct axon guidance by controlling the expression of the actin regulator wsp-1. Loss of rbr-2 results in increased levels of H3K4me3 at the transcriptional start site of wsp-1, with concomitant higher wsp-1 expression responsible for defective axon guidance. In agreement, overexpression of WSP-1 mimics rbr-2 loss, and its depletion restores normal axon guidance in rbr-2 mutants. NURF-1, an H3K4me3-binding protein and member of the chromatin-remodeling complex NURF, is required for promoting aberrant wsp-1 transcription in rbr-2 mutants and its ablation restores wild-type expression of wsp-1 and axon guidance. Thus, our results establish a precise role for epigenetic regulation in neuronal development by demonstrating a functional link between RBR-2 activity, H3K4me3 levels, the NURF complex and the expression of WSP-1.
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Affiliation(s)
- Luca Mariani
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Yvonne C Lussi
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Julien Vandamme
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Alba Riveiro
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anna Elisabetta Salcini
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
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28
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Vallianatos CN, Iwase S. Disrupted intricacy of histone H3K4 methylation in neurodevelopmental disorders. Epigenomics 2015; 7:503-19. [PMID: 26077434 DOI: 10.2217/epi.15.1] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Methylation of histone H3 lysine 4 (H3K4me) is an intricately regulated posttranslational modification, which is broadly associated with enhancers and promoters of actively transcribed genomic loci. Recent advances in next-generation sequencing have identified a number of H3K4me regulators mutated in neurodevelopmental disorders including intellectual disabilities, autism spectrum disorders, and schizophrenia. Here, we aim to summarize the molecular function of H3K4me-regulating enzymes in brain development and function. We describe four H3K4me methyltransferases (KMT2A, KMT2C, KMT2D, KMT2F), four demethylases (KDM1A, KDM5A, KDM5B, KDM5C), and two reader proteins (PHF21A, PHF8) mutated in neurodevelopmental disorders. Understanding the role of these chromatin regulators in the development and maintenance of neural connections will advance therapeutic opportunities for prevention and treatment of these lifelong neurodevelopmental disorders.
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Affiliation(s)
- Christina N Vallianatos
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA.,Predoctoral Training Program in Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
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29
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Affected kindred analysis of human X chromosome exomes to identify novel X-linked intellectual disability genes. PLoS One 2015; 10:e0116454. [PMID: 25679214 PMCID: PMC4332666 DOI: 10.1371/journal.pone.0116454] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 12/08/2014] [Indexed: 12/30/2022] Open
Abstract
X-linked Intellectual Disability (XLID) is a group of genetically heterogeneous disorders caused by mutations in genes on the X chromosome. Deleterious mutations in ~10% of X chromosome genes are implicated in causing XLID disorders in ~50% of known and suspected XLID families. The remaining XLID genes are expected to be rare and even private to individual families. To systematically identify these XLID genes, we sequenced the X chromosome exome (X-exome) in 56 well-established XLID families (a single affected male from 30 families and two affected males from 26 families) using an Agilent SureSelect X-exome kit and the Illumina HiSeq 2000 platform. To enrich for disease-causing mutations, we first utilized variant filters based on dbSNP, the male-restricted portions of the 1000 Genomes Project, or the Exome Variant Server datasets. However, these databases present limitations as automatic filters for enrichment of XLID genes. We therefore developed and optimized a strategy that uses a cohort of affected male kindred pairs and an additional small cohort of affected unrelated males to enrich for potentially pathological variants and to remove neutral variants. This strategy, which we refer to as Affected Kindred/Cross-Cohort Analysis, achieves a substantial enrichment for potentially pathological variants in known XLID genes compared to variant filters from public reference databases, and it has identified novel XLID candidate genes. We conclude that Affected Kindred/Cross-Cohort Analysis can effectively enrich for disease-causing genes in rare, Mendelian disorders, and that public reference databases can be used effectively, but cautiously, as automatic filters for X-linked disorders.
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30
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Charzewska A, Rzońca S, Janeczko M, Nawara M, Smyk M, Bal J, Hoffman-Zacharska D. A duplication of the whole KIAA2022 gene validates the gene role in the pathogenesis of intellectual disability and autism. Clin Genet 2014; 88:297-9. [PMID: 25394356 DOI: 10.1111/cge.12528] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 10/15/2014] [Accepted: 10/15/2014] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - M Janeczko
- Genetic Counseling, University Children's Hospital of Cracow, Cracow, Poland
| | - M Nawara
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - M Smyk
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - J Bal
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - D Hoffman-Zacharska
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
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