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Zhao J, Longo N, Lewis RG, Nicholas TJ, Boyden SE, Andrews A, Larson A, Bayrak-Toydemir P, Botto LD, Mao R. Novel molecular mechanism in Malan syndrome uncovered through genome sequencing reanalysis, exon-level Array, and RNA sequencing. Am J Med Genet A 2024; 194:e63516. [PMID: 38168088 PMCID: PMC11003828 DOI: 10.1002/ajmg.a.63516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/07/2023] [Accepted: 12/09/2023] [Indexed: 01/05/2024]
Abstract
The NFIX gene encodes a DNA-binding protein belonging to the nuclear factor one (NFI) family of transcription factors. Pathogenic variants of NFIX are associated with two autosomal dominant Mendelian disorders, Malan syndrome (MIM 614753) and Marshall-Smith syndrome (MIM 602535), which are clinically distinct due to different disease-causing mechanisms. NFIX variants associated with Malan syndrome are missense variants mostly located in exon 2 encoding the N-terminal DNA binding and dimerization domain or are protein-truncating variants that trigger nonsense-mediated mRNA decay (NMD) resulting in NFIX haploinsufficiency. NFIX variants associated with Marshall-Smith syndrome are protein-truncating and are clustered between exons 6 and 10, including a recurrent Alu-mediated deletion of exons 6 and 7, which can escape NMD. The more severe phenotype of Marshall-Smith syndrome is likely due to a dominant-negative effect of these protein-truncating variants that escape NMD. Here, we report a child with clinical features of Malan syndrome who has a de novo NFIX intragenic duplication. Using genome sequencing, exon-level microarray analysis, and RNA sequencing, we show that this duplication encompasses exons 6 and 7 and leads to NFIX haploinsufficiency. To our knowledge, this is the first reported case of Malan Syndrome caused by an intragenic NFIX duplication.
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Affiliation(s)
- Jian Zhao
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- ARUP Laboratories, Salt Lake City, UT, USA
| | - Nicola Longo
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- ARUP Laboratories, Salt Lake City, UT, USA
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Robert G Lewis
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- ARUP Laboratories, Salt Lake City, UT, USA
| | - Thomas J Nicholas
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Steven E Boyden
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Ashley Andrews
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Austin Larson
- Section of Genetics, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Pinar Bayrak-Toydemir
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- ARUP Laboratories, Salt Lake City, UT, USA
| | - Lorenzo D Botto
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Rong Mao
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
- ARUP Laboratories, Salt Lake City, UT, USA
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Ru Y, Ma M, Zhou X, Kriti D, Cohen N, D’Souza S, Schaniel C, Motch Perrine SM, Kuo S, Pinto D, Housman G, Wu M, Holmes G, Schadt E, van Bakel H, Zhang B, Jabs EW. Transcriptomic landscape of human induced pluripotent stem cell-derived osteogenic differentiation identifies a regulatory role of KLF16. bioRxiv 2024:2024.02.11.579844. [PMID: 38405902 PMCID: PMC10888757 DOI: 10.1101/2024.02.11.579844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Osteogenic differentiation is essential for bone development and metabolism, but the underlying gene regulatory networks have not been well investigated. We differentiated mesenchymal stem cells, derived from 20 human induced pluripotent stem cell lines, into preosteoblasts and osteoblasts, and performed systematic RNA-seq analyses of 60 samples for differential gene expression. We noted a highly significant correlation in expression patterns and genomic proximity among transcription factor (TF) and long noncoding RNA (lncRNA) genes. We identified TF-TF regulatory networks, regulatory roles of lncRNAs on their neighboring coding genes for TFs and splicing factors, and differential splicing of TF, lncRNA, and splicing factor genes. TF-TF regulatory and gene co-expression network analyses suggested an inhibitory role of TF KLF16 in osteogenic differentiation. We demonstrate that in vitro overexpression of human KLF16 inhibits osteogenic differentiation and mineralization, and in vivo Klf16+/- mice exhibit increased bone mineral density, trabecular number, and cortical bone area. Thus, our model system highlights the regulatory complexity of osteogenic differentiation and identifies novel osteogenic genes.
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Affiliation(s)
- Ying Ru
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Meng Ma
- Mount Sinai Genomics, Sema4, Stamford, CT, 06902, USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Divya Kriti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ninette Cohen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Present address: Division of Cytogenetics and Molecular Pathology, Zucker School of Medicine at Hofstra/Northwell, Northwell Health Laboratories, Lake Success, NY, 11030, USA
| | - Sunita D’Souza
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Present address: St Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Christoph Schaniel
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medicine, Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Susan M. Motch Perrine
- Department of Anthropology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Sharon Kuo
- Department of Anthropology, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
| | - Dalila Pinto
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Genevieve Housman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Meng Wu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, 55905
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905
| | - Greg Holmes
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, 55905
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905
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Lui JC, Baron J. Epigenetic Causes of Overgrowth Syndromes. J Clin Endocrinol Metab 2024; 109:312-320. [PMID: 37450557 PMCID: PMC11032252 DOI: 10.1210/clinem/dgad420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/21/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Human overgrowth disorders are characterized by excessive prenatal and/or postnatal growth of various tissues. These disorders often present with tall stature, macrocephaly, and/or abdominal organomegaly and are sometimes associated with additional phenotypic abnormalities such as intellectual disability and increased cancer risk. As the genetic etiology of these disorders have been elucidated, a surprising pattern has emerged. Multiple monogenic overgrowth syndromes result from variants in epigenetic regulators: variants in histone methyltransferases NSD1 and EZH2 cause Sotos syndrome and Weaver syndrome, respectively, variants in DNA methyltransferase DNMT3A cause Tatton-Brown-Rahman syndrome, and variants in chromatin remodeler CHD8 cause an autism spectrum disorder with overgrowth. In addition, very recently, a variant in histone reader protein SPIN4 was identified in a new X-linked overgrowth disorder. In this review, we discuss the genetics of these overgrowth disorders and explore possible common underlying mechanisms by which epigenetic pathways regulate human body size.
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Affiliation(s)
- Julian C Lui
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey Baron
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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Liu X, Chen C, Wan L, Zhu G, Zhao Y, Hu L, Liang Y, Gao J, Wang J, Yang G. A novel nonsense variant in NSD1 gene in a female child with Sotos syndrome: A case report and literature review. Brain Behav 2023; 13:e3290. [PMID: 37908045 PMCID: PMC10726859 DOI: 10.1002/brb3.3290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 09/13/2023] [Accepted: 10/10/2023] [Indexed: 11/02/2023] Open
Abstract
INTRODUCTION Sotos syndrome (SS) is an overgrowth disease characterized by distinctive facial features, advanced bone age, macrocephaly, and developmental delay is associated with alterations in the NSD1 gene. Here, we report a case of a 4-year-old female child with SS caused by NSD1 gene nonsense mutation. METHODS Whole-exome sequencing (WES) was applied for probands and her parents. Sanger sequencing was used to confirm the mutation. We performed the literature review using PubMed and found 12 articles and 14 patients who presented with SS. RESULTS The patient showed typical facial features of SS, hand deformities, and seizure. WES revealed de novo heterozygous variant: NSD1 (NM_022455.5), c.6095G > A, p.TRP2032*. We also reviewed the phenotype spectrum of 14 patients with SS, who exhibited a variety of clinical phenotypes, including developmental delay, seizures, scoliosis, hearing loss, cardiac and urinary system abnormalities, and so on. DISCUSSION The lack of correlation between mutation sites or types and phenotypes was summarized by literature reviewing. The NSD1 protein contains 14 functional domains and this nonsense mutation was located in SET domain. Early appearance of the termination codon leads to protein truncation. Haploinsufficiency of the NSD1 gene causes the overgrowth disorders.
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Affiliation(s)
- Xinting Liu
- Senior Department of Pediatricsthe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of Pediatrics, the First Medical CenterChinese PLA General HospitalBeijingChina
- Medical School of Chinese PLABeijingChina
| | - Chen Chen
- Senior Department of Pediatricsthe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of Pediatrics, the First Medical CenterChinese PLA General HospitalBeijingChina
| | - Lin Wan
- Senior Department of Pediatricsthe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of Pediatrics, the First Medical CenterChinese PLA General HospitalBeijingChina
- Medical School of Chinese PLABeijingChina
| | - Gang Zhu
- Senior Department of Pediatricsthe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of Pediatrics, the First Medical CenterChinese PLA General HospitalBeijingChina
- Medical School of Chinese PLABeijingChina
| | - Yan Zhao
- Senior Department of Pediatricsthe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of Pediatrics, the First Medical CenterChinese PLA General HospitalBeijingChina
| | - Lizhu Hu
- Senior Department of Pediatricsthe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of Pediatrics, the First Medical CenterChinese PLA General HospitalBeijingChina
- Medical School of Chinese PLABeijingChina
| | - Yan Liang
- Senior Department of Pediatricsthe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of Pediatrics, the First Medical CenterChinese PLA General HospitalBeijingChina
- Medical School of Chinese PLABeijingChina
| | - Jing Gao
- Senior Department of Pediatricsthe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of Pediatrics, the First Medical CenterChinese PLA General HospitalBeijingChina
| | - Jing Wang
- Senior Department of Pediatricsthe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of Pediatrics, the First Medical CenterChinese PLA General HospitalBeijingChina
| | - Guang Yang
- Senior Department of Pediatricsthe Seventh Medical Center of PLA General HospitalBeijingChina
- Department of Pediatrics, the First Medical CenterChinese PLA General HospitalBeijingChina
- The Second School of Clinical MedicineSouthern Medical UniversityGuangzhouChina
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Dini G, Verrotti A, Gorello P, Soliani L, Cordelli DM, Antona V, Mencarelli A, Colavito D, Prontera P. NFIA haploinsufficiency: case series and literature review. Front Pediatr 2023; 11:1292654. [PMID: 37915986 PMCID: PMC10616848 DOI: 10.3389/fped.2023.1292654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023] Open
Abstract
Background NFIA-related disorder (OMIM #613735) is an autosomal dominant neurodevelopmental disorder characterized by a variable degree of cognitive impairment and non-specific dysmorphic features. To date, fewer than thirty patients affected by this disorder have been described. Methods Our study included three children with NFIA haploinsufficiency recruited from three medical genetics centers. Clinical presentations were recorded on a standardized case report form. Results All patients presented a variable degree of intellectual disability. None of the individuals in our cohort had urinary tract malformations. Three novel mutations, c.344G>A, c.261T>G, and c.887_888del are reported here. Conclusion NFIA haploinsufficiency can be suspected through careful observation of specific dysmorphisms, including macrocephaly and craniofacial abnormalities. Instrumental tests such as MRI and renal ultrasound provide further diagnostic clues, while genetic testing can confirm the diagnosis.
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Affiliation(s)
- Gianluca Dini
- Department of Pediatrics, University of Perugia, Perugia, Italy
| | | | - Paolo Gorello
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Luca Soliani
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, UOC di Neuropsichiatria Dell'Età Pediatrica, Bologna, Italy
- Dipartimento di Scienze Mediche e Chirurgiche (DIMEC), Università di Bologna, Bologna, Italy
| | - Duccio Maria Cordelli
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, UOC di Neuropsichiatria Dell'Età Pediatrica, Bologna, Italy
- Dipartimento di Scienze Mediche e Chirurgiche (DIMEC), Università di Bologna, Bologna, Italy
| | - Vincenzo Antona
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D'Alessandro,” University of Palermo, Palermo, Italy
| | - Amedea Mencarelli
- Medical Genetics Unit, S. Maria della Misericordia Hospital, Perugia, Italy
| | | | - Paolo Prontera
- Medical Genetics Unit, S. Maria della Misericordia Hospital, Perugia, Italy
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Pan D, Zhong J, Zhang J, Dong H, Zhao D, Zhang H, Yao B. Function and regulation of nuclear factor 1 X-type on chondrocyte proliferation and differentiation. Gene 2023; 881:147620. [PMID: 37433356 DOI: 10.1016/j.gene.2023.147620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/26/2023] [Accepted: 07/05/2023] [Indexed: 07/13/2023]
Abstract
Nuclear factor 1 X-type (Nfix) is a transcription factor related to mental and physical development. However, very few studies have reported the effects of Nfix on cartilage. This study aims to reveal the influence of Nfix on the proliferation and differentiation of chondrocytes, and to explore its potential action mechanism. We isolated primary chondrocytes from the costal cartilage of newborn C57BL/6 mice and with Nfix overexpression or silencing treatment. We used Alcian blue staining and found that Nfix overexpression significantly promoted ECM synthesis in chondrocytes while silencing inhibited ECM synthesis. Using RNA-seq technology to study the expression pattern of Nfix in primary chondrocytes. We found that Nfix overexpression significantly up-regulated genes that are related to chondrocyte proliferation and extracellular matrix (ECM) synthesis and significantly down-regulated genes related to chondrocyte differentiation and ECM degradation. Nfix silencing, however, significantly up-regulated genes associated with cartilage catabolism and significantly down-regulated genes associated with cartilage growth promotion. Furthermore, Nfix exerted a positive regulatory effect on Sox9, and we propose that Nfix may promote chondrocyte proliferation and inhibit differentiation by stimulating Sox9 and its downstream genes. Our findings suggest that Nfix may be a potential target for the regulation of chondrocyte proliferation and differentiation.
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Affiliation(s)
- Daian Pan
- Research Center of Traditional Chinese Medicine, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun 130021, China; Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China; Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Jinghong Zhong
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Jingcheng Zhang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Haisi Dong
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Daqing Zhao
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - He Zhang
- Research Center of Traditional Chinese Medicine, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun 130021, China; Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Baojin Yao
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China.
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7
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Uzman CY, Gürsoy S, Hazan F. A rare cause of intellectual disability: Novel mutations of NFIX gene in two patients with clinical features of Marshall-Smith syndrome and Malan syndrome. Int J Dev Neurosci 2023. [PMID: 37336770 DOI: 10.1002/jdn.10280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/12/2023] [Accepted: 05/19/2023] [Indexed: 06/21/2023] Open
Abstract
Marshall-Smith syndrome (MSS) and Malan syndrome (MS) are both allelic disorders caused by mutations in the NFIX gene. MS is characterized by overgrowth, intellectual disability, distinctive facial features, and accelerated skeletal maturation. On the other hand, clinical features of MSS consist of advanced bone age, dysmorphic features, intellectual disability, and failure to thrive at birth. In this study, we presented the clinical and molecular findings of two different patients with MS and MSS as a rare cause of intellectual disability and reported two novel variants in the NFIX gene. NFIX gene sequencing revealed a novel heterozygous c.1287delC (p.G430Vfs*34) mutation in patient 1 whose clinical diagnosis was compatible with Marshall-Smith syndrome, and in the second patient, physical features consistent with Malan syndrome, was detected a heterozygous one nucleotide duplication, c.303dupC (pCys102LeufsTer17).
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Affiliation(s)
- Ceren Yılmaz Uzman
- Department of Pediatric Genetics, S.B.Ü. Dr. Behçet Uz Children's Education and Research Hospital, Izmir, Turkey
| | - Semra Gürsoy
- Department of Pediatric Genetics, S.B.Ü. Dr. Behçet Uz Children's Education and Research Hospital, Izmir, Turkey
| | - Filiz Hazan
- Department of Medical Genetics, S.B.Ü. Dr. Behçet Uz Children's Education and Research Hospital, Izmir, Turkey
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Kooblall KG, Stevenson M, Stewart M, Harris L, Zalucki O, Dewhurst H, Butterfield N, Leng H, Hough TA, Ma D, Siow B, Potter P, Cox RD, Brown SD, Horwood N, Wright B, Lockstone H, Buck D, Vincent TL, Hannan FM, Bassett JD, Williams GR, Lines KE, Piper M, Wells S, Teboul L, Hennekam RC, Thakker RV. A Mouse Model with a Frameshift Mutation in the Nuclear Factor I/X ( NFIX) Gene Has Phenotypic Features of Marshall-Smith Syndrome. JBMR Plus 2023; 7:e10739. [PMID: 37283649 PMCID: PMC10241085 DOI: 10.1002/jbm4.10739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
The nuclear factor I/X (NFIX) gene encodes a ubiquitously expressed transcription factor whose mutations lead to two allelic disorders characterized by developmental, skeletal, and neural abnormalities, namely, Malan syndrome (MAL) and Marshall-Smith syndrome (MSS). NFIX mutations associated with MAL mainly cluster in exon 2 and are cleared by nonsense-mediated decay (NMD) leading to NFIX haploinsufficiency, whereas NFIX mutations associated with MSS are clustered in exons 6-10 and escape NMD and result in the production of dominant-negative mutant NFIX proteins. Thus, different NFIX mutations have distinct consequences on NFIX expression. To elucidate the in vivo effects of MSS-associated NFIX exon 7 mutations, we used CRISPR-Cas9 to generate mouse models with exon 7 deletions that comprised: a frameshift deletion of two nucleotides (Nfix Del2); in-frame deletion of 24 nucleotides (Nfix Del24); and deletion of 140 nucleotides (Nfix Del140). Nfix +/Del2, Nfix +/Del24, Nfix +/Del140, Nfix Del24/Del24, and Nfix Del140/Del140 mice were viable, normal, and fertile, with no skeletal abnormalities, but Nfix Del2/Del2 mice had significantly reduced viability (p < 0.002) and died at 2-3 weeks of age. Nfix Del2 was not cleared by NMD, and NfixDel2/Del2 mice, when compared to Nfix +/+ and Nfix +/Del2 mice, had: growth retardation; short stature with kyphosis; reduced skull length; marked porosity of the vertebrae with decreased vertebral and femoral bone mineral content; and reduced caudal vertebrae height and femur length. Plasma biochemistry analysis revealed Nfix Del2/Del2 mice to have increased total alkaline phosphatase activity but decreased C-terminal telopeptide and procollagen-type-1-N-terminal propeptide concentrations compared to Nfix +/+ and Nfix +/Del2 mice. Nfix Del2/Del2 mice were also found to have enlarged cerebral cortices and ventricular areas but smaller dentate gyrus compared to Nfix +/+ mice. Thus, Nfix Del2/Del2 mice provide a model for studying the in vivo effects of NFIX mutants that escape NMD and result in developmental abnormalities of the skeletal and neural tissues that are associated with MSS. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Kreepa G. Kooblall
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
| | - Mark Stevenson
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
| | - Michelle Stewart
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | | | - Oressia Zalucki
- The School of Biomedical Sciences and The Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
| | - Hannah Dewhurst
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Natalie Butterfield
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Houfu Leng
- Centre for OA Pathogenesis Versus Arthritis, The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)Medical Sciences Division University of OxfordOxfordUK
| | - Tertius A. Hough
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Da Ma
- Department of Internal MedicineWake Forest University School of MedicineWinston‐SalemNCUSA
| | | | - Paul Potter
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Roger D. Cox
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Stephen D.M. Brown
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Nicole Horwood
- Centre for OA Pathogenesis Versus Arthritis, The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)Medical Sciences Division University of OxfordOxfordUK
| | - Benjamin Wright
- Oxford Genomics Centre, The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Helen Lockstone
- Oxford Genomics Centre, The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - David Buck
- Oxford Genomics Centre, The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Tonia L. Vincent
- Centre for OA Pathogenesis Versus Arthritis, The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)Medical Sciences Division University of OxfordOxfordUK
| | - Fadil M. Hannan
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
- Nuffield Department of Women's and Reproductive HealthUniversity of OxfordOxfordUK
| | - J.H. Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Graham R. Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Kate E. Lines
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
| | - Michael Piper
- The School of Biomedical Sciences and The Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
| | - Sara Wells
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Lydia Teboul
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Raoul C. Hennekam
- Department of Pediatrics, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Rajesh V. Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
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9
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Marinella G, Conti E, Buchignani B, Sgherri G, Pasquariello R, Giordano F, Cristofani P, Battini R, Battaglia A. Further characterization of NFIB-associated phenotypes: Report of two new individuals. Am J Med Genet A 2023; 191:540-545. [PMID: 36321570 PMCID: PMC10091694 DOI: 10.1002/ajmg.a.63018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/13/2022] [Accepted: 10/07/2022] [Indexed: 01/11/2023]
Abstract
Nuclear Factor I B (NFIB) haploinsufficiency has recently been identified as a cause of intellectual disability (ID) and macrocephaly. Here we report on two new individuals carrying a microdeletion in the chromosomal region 9p23-p22.3 containing NFIB. The first is a 7-year 9-month old boy with developmental delays, ID, definite facial anomalies, and brain and spinal cord magnetic resonance imaging findings including periventricular nodular heterotopia, hypoplasia of the corpus callosum, arachnoid cyst in the left middle cranial fossa, syringomyelia in the thoracic spinal cord and distal tract of the conus medullaris, and a stretched appearance of the filum terminale. The second is a 32-year-old lady (the proband' mother) with dysmorphic features, and a history of learning disability, hypothyroidism, poor growth, left inguinal hernia, and panic attacks. Her brain magnetic resonance imaging findings include a dysmorphic corpus callosum, and a small cyst in the left choroidal fissure that marks the hippocampal head. Array-based comparative genomic hybridization identified, in both, a 232 Kb interstitial deletion at 9p23p22.3 including several exons of NFIB and no other known genes. Our two individuals add to the knowledge of this rare disorder through the addition of new brain and spinal cord MRI findings and dysmorphic features. We propose that NFIB haploinsufficiency causes a clinically recognizable malformation-ID syndrome.
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Affiliation(s)
- Gemma Marinella
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, Pisa, Italy
| | - Eugenia Conti
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, Pisa, Italy
| | - Bianca Buchignani
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, Pisa, Italy.,Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Pisa, Italy
| | - Giada Sgherri
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, Pisa, Italy
| | - Rosa Pasquariello
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, Pisa, Italy
| | - Flavio Giordano
- Department of Neurosurgery, Children's Hospital A. Meyer-University of Florence, Firenze, Florence, Italy
| | - Paola Cristofani
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, Pisa, Italy
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, Pisa, Italy.,Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Pisa, Italy
| | - Agatino Battaglia
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, Pisa, Italy
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10
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Timberlake AT, Kiziltug E, Jin SC, Nelson-Williams C, Loring E, Allocco A, Marlier A, Banka S, Stuart H, Passos-Buenos MR, Rosa R, Rogatto SR, Tonne E, Stiegler AL, Boggon TJ, Alperovich M, Steinbacher D, Staffenberg DA, Flores RL, Persing JA, Kahle KT, Lifton RP. De novo mutations in the BMP signaling pathway in lambdoid craniosynostosis. Hum Genet 2023; 142:21-32. [PMID: 35997807 DOI: 10.1007/s00439-022-02477-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/08/2022] [Indexed: 01/18/2023]
Abstract
Lambdoid craniosynostosis (CS) is a congenital anomaly resulting from premature fusion of the cranial suture between the parietal and occipital bones. Predominantly sporadic, it is the rarest form of CS and its genetic etiology is largely unexplored. Exome sequencing of 25 kindreds, including 18 parent-offspring trios with sporadic lambdoid CS, revealed a marked excess of damaging (predominantly missense) de novo mutations that account for ~ 40% of sporadic cases. These mutations clustered in the BMP signaling cascade (P = 1.6 × 10-7), including mutations in genes encoding BMP receptors (ACVRL1 and ACVR2A), transcription factors (SOX11, FOXO1) and a transcriptional co-repressor (IFRD1), none of which have been implicated in other forms of CS. These missense mutations are at residues critical for substrate or target sequence recognition and many are inferred to cause genetic gain-of-function. Additionally, mutations in transcription factor NFIX were implicated in syndromic craniosynostosis affecting diverse sutures. Single cell RNA sequencing analysis of the mouse lambdoid suture identified enrichment of mutations in osteoblast precursors (P = 1.6 × 10-6), implicating perturbations in the balance between proliferation and differentiation of osteoprogenitor cells in lambdoid CS. The results contribute to the growing knowledge of the genetics of CS, have implications for genetic counseling, and further elucidate the molecular etiology of premature suture fusion.
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Affiliation(s)
- Andrew T Timberlake
- Hansjörg Wyss Department of Plastic Surgery, New York University Langone Medical Center, New York, NY, USA.
| | - Emre Kiziltug
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | | | - Erin Loring
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | | | - August Allocco
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Arnaud Marlier
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9WL, UK.,Manchester Centre for Genomic Medicine, Health Innovation Manchester, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Helen Stuart
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9WL, UK.,Manchester Centre for Genomic Medicine, Health Innovation Manchester, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | | | - Rafael Rosa
- Clinical Genetics, UFCSPA and Irmandade da Santa Casa de Misericórdia de Porto Alegre (ISCMPA), Porto Alegre, RS, Brazil
| | - Silvia R Rogatto
- Neogene Laboratory, Research Center (CIPE), AC Camargo Cancer Center, São Paulo, SP, Brazil
| | - Elin Tonne
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Amy L Stiegler
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Michael Alperovich
- Section of Plastic and Reconstructive Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Derek Steinbacher
- Section of Plastic and Reconstructive Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - David A Staffenberg
- Hansjörg Wyss Department of Plastic Surgery, New York University Langone Medical Center, New York, NY, USA
| | - Roberto L Flores
- Hansjörg Wyss Department of Plastic Surgery, New York University Langone Medical Center, New York, NY, USA
| | - John A Persing
- Section of Plastic and Reconstructive Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, MA, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA. .,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA.
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11
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Romero VI, Arias-Almeida B, Aguiar SA. NSD1 gene evolves under episodic selection within primates and mutations of specific exons in humans cause Sotos syndrome. BMC Genomics 2022; 23:849. [PMID: 36550402 PMCID: PMC9783842 DOI: 10.1186/s12864-022-09071-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Modern human brains and skull shapes differ from other hominids. Brain growth disorders as micro- (ASPM, MCPH1) and macrocephaly (NFIX, GLI3) have been highlighted as relevant for the evolution in humans due to the impact in early brain development. Genes associated with macrocephaly have been reported to cause this change, for example NSD1 which causes Sotos syndrome. RESULTS In this study we performed a systematic literature review, located the reported variants associated to Sotos syndrome along the gene domains, compared the sequences with close primates, calculated their similarity, Ka/Ks ratios, nucleotide diversity and selection, and analyzed the sequence and structural conservation with distant primates. We aimed to understand if NSD1 in humans differs from other primates since the evolution of NSD1 has not been analyzed in primates, nor if the localization of the mutations is limited to humans. Our study found that most variations causing Sotos syndrome are in exon 19, 22 and 10. In the primate comparison we did not detect Ka/Ks ratios > 1, but a high nucleotide diversity with non-synonymous variations in exons 10, 5, 9, 11 and 23, and sites under episodic selection in exon 5 and 23, and human, macaque/colobus/tarsier/galago and tarsier/lemur/colobus. Most of the domains are conserved in distant primates with a particular progressive development from a simple PWWP1 in O. garnetti to a complex structure in Human. CONCLUSION NSD1 is a chromatin modifier that suggests that the selection could influence brain development during modern human evolution and is not present in other primates; however, nowadays the nucleotide diversity is associated with Sotos syndrome.
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Affiliation(s)
- Vanessa I. Romero
- School of Medicine, Universidad San Francisco de Quito, Quito, Ecuador
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12
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Seed L, G N, Prentice S, Chandershekar P. Early diagnosis of Malan syndrome in an infant presenting with macrocephaly. BMJ Case Rep 2022; 15:e249391. [PMID: 36379624 PMCID: PMC9668004 DOI: 10.1136/bcr-2022-249391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We present an infant with persistent macrocephaly and developmental delay. There is a wide range of differential diagnoses for this presentation, including many rare genetic conditions. Here, a diagnosis of Malan syndrome was made-a rare overgrowth syndrome caused by haploinsufficiency of NFIX and features affecting the neurological and musculoskeletal systems. Improvements in genomic medicine technologies and clinical services have revolutionised the way clinicians diagnose rare diseases. We highlight the importance of early genetic testing, particularly if there are red flag features such as developmental delay, and the need for a coordinated strategy to improve the management of rare diseases like Malan syndrome.
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Affiliation(s)
- Lydia Seed
- University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Natasha G
- Department of Neonatology, Lister Hospital, East and North Hertfordshire NHS Trust, Stevenage, UK
| | - Sarah Prentice
- Department of Neonatology, Lister Hospital, East and North Hertfordshire NHS Trust, Stevenage, UK
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Prathiba Chandershekar
- Department of Neonatology, Lister Hospital, East and North Hertfordshire NHS Trust, Stevenage, UK
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13
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Langley E, Farach LS, Mowrey K. Case Report: Novel pathogenic variant in NFIX in two sisters with Malan syndrome due to germline mosaicism. Front Genet 2022; 13:1044660. [DOI: 10.3389/fgene.2022.1044660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
Abstract
Malan syndrome is an autosomal dominant disorder caused by pathogenic variants in NFIX with less than 100 cases reported thus far. NFIX is important for stem cell proliferation, quiescence, and differentiation during development and its protein plays a role in replication, signal transduction, and transcription. As a result of pathogenic variants, symptoms of Malan syndrome include overgrowth, intellectual disability, speech delay, and dysmorphic features. Currently, the recurrence risk for this disorder is indicated at less than 1%, standard for de novo autosomal dominant disorders. Herein, we report an additional set of sisters with the same novel pathogenic variant in NFIX and clinical features consistent with Malan syndrome providing evidence of germline mosaicism. Considering the rarity of this condition in conjunction with three previous reports of germline mosaicism, it is worthwhile to investigate and re-evaluate the proper recurrence risk for this condition. This discovery would be paramount for family planning and genetic counseling practices in families with affected individuals.
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14
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Alfieri P, Macchiaiolo M, Collotta M, Montanaro FAM, Caciolo C, Cumbo F, Galassi P, Panfili FM, Cortellessa F, Zollino M, Accadia M, Seri M, Tartaglia M, Bartuli A, Mammì C, Vicari S, Priolo M. Characterization of Cognitive, Language and Adaptive Profiles of Children and Adolescents with Malan Syndrome. J Clin Med 2022; 11:jcm11144078. [PMID: 35887841 PMCID: PMC9316998 DOI: 10.3390/jcm11144078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/16/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022] Open
Abstract
Malan Syndrome (MS) is an ultra-rare overgrowth genetic syndrome due to heterozygous variants or deletions in the Nuclear Factor I X (NFIX) gene. It is characterized by an unusual facial phenotype, generalized overgrowth, intellectual disability (ID) and behavioral problems. Even though limitations in cognitive and adaptive functioning have been previously described, systematic studies on MS cohorts are still lacking. Here, we aim to define the cognitive and adaptive behavior profile of MS children and adolescents, providing quantitative data from standardized evaluations. Subjects included in this study were evaluated from October 2020 to January 2022 and the study is based on a retrospective data archive: fifteen MS individuals were recruited and underwent evaluation with Wechsler Intelligence Scales, Leiter International Performance Scales and Griffith Mental Development Scales for cognitive profiles and with Vineland Adaptive Behavior Scales-II Edition (VABS-II) for adaptive functioning. Language skills and visuomotor integration abilities were assessed too. Comparisons and correlations between scales and subtests were performed. All the assessed MS individuals showed both low cognitive and adaptive functioning. One subject presented with mild ID, five had moderate ID and eight showed severe ID. One female toddler received a diagnosis of psychomotor delay. Linguistic skills were impaired in all individuals, with language comprehension relatively more preserved. Results revealed significant differences between VABS-II subdomains and a strong relationship between cognitive and adaptive functioning. All subjects exhibited mild to moderate ID and adaptive behavior lower than normal, with communication skills being the most affected. Regarding the daily living skills domain, personal and community subscale scores were dramatically lower than for the domestic subdomain, highlighting the importance of considering behavior within developmental and environmental contexts. Our cognitive and adaptive MS characterization provides a more accurate quantitative MS profiling, which is expected to help clinicians to better understand the complexity of this rare disorder.
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Affiliation(s)
- Paolo Alfieri
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.C.); (F.A.M.M.); (C.C.); (F.C.); (P.G.); (S.V.)
- Correspondence: ; Tel.: +39-668-594-721
| | - Marina Macchiaiolo
- Rare Diseases and Medical Genetics Unit, University-Hospital Pediatric Department (DPUO), Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.M.); (F.C.); (A.B.)
| | - Martina Collotta
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.C.); (F.A.M.M.); (C.C.); (F.C.); (P.G.); (S.V.)
| | - Federica Alice Maria Montanaro
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.C.); (F.A.M.M.); (C.C.); (F.C.); (P.G.); (S.V.)
| | - Cristina Caciolo
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.C.); (F.A.M.M.); (C.C.); (F.C.); (P.G.); (S.V.)
| | - Francesca Cumbo
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.C.); (F.A.M.M.); (C.C.); (F.C.); (P.G.); (S.V.)
| | - Paolo Galassi
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.C.); (F.A.M.M.); (C.C.); (F.C.); (P.G.); (S.V.)
| | - Filippo Maria Panfili
- Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy;
| | - Fabiana Cortellessa
- Rare Diseases and Medical Genetics Unit, University-Hospital Pediatric Department (DPUO), Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.M.); (F.C.); (A.B.)
| | - Marcella Zollino
- Genetica Medica, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168 Rome, Italy;
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore Facoltà di Medicina e Chirurgia, 00168 Roma, Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital “Cardinale G. Panico”, 73039 Tricase, Italy;
| | - Marco Seri
- Unit of Medical Genetics, Azienda Ospedaliero Universitaria di Bologna, IRCCS, 40126 Bologna, Italy;
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy;
| | - Andrea Bartuli
- Rare Diseases and Medical Genetics Unit, University-Hospital Pediatric Department (DPUO), Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.M.); (F.C.); (A.B.)
| | - Corrado Mammì
- Operative Unit of Medical Genetics Bianchi-Melacrino-Morelli Great Metropolitan Hospital, 89133 Reggio Calabria, Italy; (C.M.); (M.P.)
| | - Stefano Vicari
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.C.); (F.A.M.M.); (C.C.); (F.C.); (P.G.); (S.V.)
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Manuela Priolo
- Operative Unit of Medical Genetics Bianchi-Melacrino-Morelli Great Metropolitan Hospital, 89133 Reggio Calabria, Italy; (C.M.); (M.P.)
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15
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Brennan K, Zheng H, Fahrner JA, Shin JH, Gentles AJ, Schaefer B, Sunwoo JB, Bernstein JA, Gevaert O. NSD1 mutations deregulate transcription and DNA methylation of bivalent developmental genes in Sotos syndrome. Hum Mol Genet 2022; 31:2164-2184. [PMID: 35094088 PMCID: PMC9262396 DOI: 10.1093/hmg/ddac026] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/04/2022] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Sotos syndrome (SS), the most common overgrowth with intellectual disability (OGID) disorder, is caused by inactivating germline mutations of NSD1, which encodes a histone H3 lysine 36 methyltransferase. To understand how NSD1 inactivation deregulates transcription and DNA methylation (DNAm), and to explore how these abnormalities affect human development, we profiled transcription and DNAm in SS patients and healthy control individuals. We identified a transcriptional signature that distinguishes individuals with SS from controls and was also deregulated in NSD1-mutated cancers. Most abnormally expressed genes displayed reduced expression in SS; these downregulated genes consisted mostly of bivalent genes and were enriched for regulators of development and neural synapse function. DNA hypomethylation was strongly enriched within promoters of transcriptionally deregulated genes: overexpressed genes displayed hypomethylation at their transcription start sites while underexpressed genes featured hypomethylation at polycomb binding sites within their promoter CpG island shores. SS patients featured accelerated molecular aging at the levels of both transcription and DNAm. Overall, these findings indicate that NSD1-deposited H3K36 methylation regulates transcription by directing promoter DNA methylation, partially by repressing polycomb repressive complex 2 (PRC2) activity. These findings could explain the phenotypic similarity of SS to OGID disorders that are caused by mutations in PRC2 complex-encoding genes.
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Affiliation(s)
- Kevin Brennan
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Hong Zheng
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - June Ho Shin
- Department of Otolaryngology – Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Andrew J Gentles
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Bradley Schaefer
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - John B Sunwoo
- Department of Otolaryngology – Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
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16
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Macchiaiolo M, Panfili FM, Vecchio D, Gonfiantini MV, Cortellessa F, Caciolo C, Zollino M, Accadia M, Seri M, Chinali M, Mammì C, Tartaglia M, Bartuli A, Alfieri P, Priolo M. A deep phenotyping experience: up to date in management and diagnosis of Malan syndrome in a single center surveillance report. Orphanet J Rare Dis 2022; 17:235. [PMID: 35717370 PMCID: PMC9206304 DOI: 10.1186/s13023-022-02384-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/06/2022] [Indexed: 12/14/2022] Open
Abstract
Background Malan syndrome (MALNS) is a recently described ultrarare syndrome lacking guidelines for diagnosis, management and monitoring of evolutive complications. Less than 90 patients are reported in the literature and limited clinical information are available to assure a proper health surveillance.
Results A multidisciplinary team with high expertise in MALNS has been launched at the “Ospedale Pediatrico Bambino Gesù”, Rome, Italy. Sixteen Italian MALNS individuals with molecular confirmed clinical diagnosis of MALNS were enrolled in the program. For all patients, 1-year surveillance in a dedicated outpatient Clinic was attained. The expert panel group enrolled 16 patients and performed a deep phenotyping analysis directed to clinically profiling the disorder and performing critical revision of previously reported individuals. Some evolutive complications were also assessed. Previously unappreciated features (e.g., high risk of bone fractures in childhood, neurological/neurovegetative symptoms, noise sensitivity and Chiari malformation type 1) requiring active surveillance were identified. A second case of neoplasm was recorded. No major cardiovascular anomalies were noticed. An accurate clinical description of 9 new MALNS cases was provided. Conclusions Deep phenotyping has provided a more accurate characterization of the main clinical features of MALNS and allows broadening the spectrum of disease. A minimal dataset of clinical evaluations and follow-up timeline has been proposed for proper management of patients affected by this ultrarare disorder. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02384-9.
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Affiliation(s)
- Marina Macchiaiolo
- Rare Diseases and Medical Genetics Unit, University-Hospital Pediatric Department (DPUO), Bambino Gesù Children's Hospital, IRCSS, Piazza di Sant'Onofrio, 4, 00165, Rome, Italy.
| | - Filippo M Panfili
- University of Rome Tor Vergata, Rome, Italy.,Academic Department of Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Davide Vecchio
- Rare Diseases and Medical Genetics Unit, University-Hospital Pediatric Department (DPUO), Bambino Gesù Children's Hospital, IRCSS, Piazza di Sant'Onofrio, 4, 00165, Rome, Italy
| | - Michaela V Gonfiantini
- Rare Diseases and Medical Genetics Unit, University-Hospital Pediatric Department (DPUO), Bambino Gesù Children's Hospital, IRCSS, Piazza di Sant'Onofrio, 4, 00165, Rome, Italy
| | - Fabiana Cortellessa
- Rare Diseases and Medical Genetics Unit, University-Hospital Pediatric Department (DPUO), Bambino Gesù Children's Hospital, IRCSS, Piazza di Sant'Onofrio, 4, 00165, Rome, Italy
| | - Cristina Caciolo
- Child and Adolescent Psychiatric Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marcella Zollino
- Genetica Medica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore Facoltà di Medicina e Chirurgia, Rome, Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital "Cardinale G. Panico", Tricase, Lecce, Italy
| | - Marco Seri
- Unit of Medical Genetics, IRCCS Azienda Ospedaliero Universitaria di Bologna, Bologna, Italy
| | - Marcello Chinali
- Department of Pediatric Cardiology and Cardiac Surgery, Bambino Gesù Children's Hospital IRCSS, Rome, Italy
| | - Corrado Mammì
- Operative Unit of Medical Genetics, Bianchi-Melacrino-Morelli Hospital, V. Melacrino, 89100, Reggio Calabria, Italy
| | - Marco Tartaglia
- Genetics and Rare Disease Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Bartuli
- Rare Diseases and Medical Genetics Unit, University-Hospital Pediatric Department (DPUO), Bambino Gesù Children's Hospital, IRCSS, Piazza di Sant'Onofrio, 4, 00165, Rome, Italy
| | - Paolo Alfieri
- Child and Adolescent Psychiatric Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Manuela Priolo
- Operative Unit of Medical Genetics, Bianchi-Melacrino-Morelli Hospital, V. Melacrino, 89100, Reggio Calabria, Italy.
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Partyka LM. Anesthetic Considerations in an Infant With Malan Syndrome: A Case Report. A A Pract 2022; 16:e01600. [DOI: 10.1213/xaa.0000000000001600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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18
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Song M, Yu J, Li B, Dong J, Gao J, Shang L, Zhou X, Bai Y. Identification of functionally important miRNA targeted genes associated with child obesity trait in genome-wide association studies. BMC Genomics 2022; 23:360. [PMID: 35546387 PMCID: PMC9092671 DOI: 10.1186/s12864-022-08576-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have uncovered thousands of genetic variants that are associated with complex human traits and diseases. miRNAs are single-stranded non-coding RNAs. In particular, genetic variants located in the 3'UTR region of mRNAs may play an important role in gene regulation through their interaction with miRNAs. Existing studies have not been thoroughly conducted to elucidate 3'UTR variants discovered through GWAS. The goal of this study is to analyze patterns of GWAS functional variants located in 3'UTRs about their relevance in the network between hosting genes and targeting miRNAs, and elucidate the association between the genes harboring these variants and genetic traits. METHODS We employed MIGWAS, ANNOVAR, MEME, and DAVID software packages to annotate the variants obtained from GWAS for 31 traits and elucidate the association between their harboring genes and their related traits. We identified variants that occurred in the motif regions that may be functionally important in affecting miRNA binding. We also conducted pathway analysis and functional annotation on miRNA targeted genes harboring 3'UTR variants for a trait with the highest percentage of 3'UTR variants occurring. RESULTS The Child Obesity trait has the highest percentage of 3'UTR variants (75%). Of the 16 genes related to the Child Obesity trait, 5 genes (ETV7, GMEB1, NFIX, ZNF566, ZBTB40) had a significant association with the term DNA-Binding (p < 0.05). EQTL analysis revealed 2 relevant tissues and 10 targeted genes associated with the Child Obesity trait. In addition, Red Blood Cells (RBC), Hemoglobin (HB), and Package Cell Volume (PCV) have overlapping variants. In particular, the PIM1 variant occurred inside the HB Motif region 37,174,641-37,174,660, and LUC7L3 variant occurred inside RBC Motif region 50,753,918-50,753,937. CONCLUSION Variants located in 3'UTR can alter the binding affinity of miRNA and impact gene regulation, thus warranting further annotation and analysis. We have developed a bioinformatics bash pipeline to automatically annotate variants, determine the number of variants in different categories for each given trait, and check common variants across different traits. This is a valuable tool to annotate a large number of GWAS result files.
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Affiliation(s)
- Melinda Song
- University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Jiaqi Yu
- College Preparatory School, 6100 Broadway, Oakland, CA 94618 USA
| | - Binze Li
- Bellaire High School, 5100 Maple St, Bellaire, TX 77401 USA
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Julian Dong
- Northville High School, 45700 Six Mile Road, Northville, MI 48168 USA
- College of Engineering, University of Michigan, Ann Arbor, MI 48109 USA
| | - Jeslyn Gao
- Simsbury High School, 34 Farms Village Rd, Simsbury, CT 06070 USA
| | - Lulu Shang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109 USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Yongsheng Bai
- Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197 USA
- Next-Gen Intelligent Science Training, Ann Arbor, MI 48105 USA
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Zhang Z, Yang W, Zhu T, Wang L, Zhao X, Zhao G, Qu L, Jia Y. Genetic Parameter Estimation and Whole Sequencing Analysis of the Genetic Architecture of Chicken Keel Bending. Front Genet 2022; 13:833132. [PMID: 35401685 PMCID: PMC8984200 DOI: 10.3389/fgene.2022.833132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/24/2022] [Indexed: 11/18/2022] Open
Abstract
Bone health is particularly important for high-yielding commercial layer chickens. The keel of poultry is an extension of the abdomen side of the sternum along the sagittal plane and is one of the most important bones. In this study, the keel phenotype of White Leghorns laying hen flocks showed significant individual differences. To clarify its genetic mechanism, we first estimated the heritability of keel bend (KB) in White Leghorn, recorded the production performance of the chicken flock, examined the blood biochemical indexes and bone quality in KB and keel normal (KN) chickens, and performed whole-genome pooled sequencing in KB and KN chickens. We then performed selection elimination analysis to determine the genomic regions that may affect the keel phenotypes. The results show that KB is a medium heritability trait. We found that cage height had a significant effect on the KB (p < 0.01). At 48 weeks, there were significant differences in the number of eggs, the number of normal eggs, and eggshell strength (p < 0.05). The content of parathyroid hormone was lower (p < 0.01) and that of calcitonin was higher (p < 0.01) in KB chickens than in KN chickens. The differences in bone mineral density, bone strength, and bone cortical thickness of the humerus and femur were extremely significant (p < 0.01), with all being lower in KB chickens than in KN chickens. In addition, the bones of KB chickens contained more fat organization. A total of 128 genes were identified in selective sweep regions. We identified 10 important candidate genes: ACP5, WNT1, NFIX, CNN1, CALR, FKBP11, TRAPPC5, MAP2K7, RELA, and ENSGALG00000047166. Among the significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways found, we identifed two bone-related pathways, one involving “osteoclast differentiation” and the other the “MAPK signaling pathway.” These results may help us better understand the molecular mechanism of bone traits in chickens and other birds and provide new insights for the genetic breeding of chickens.
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Affiliation(s)
- Zhihao Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Science, Beijing, China
| | - Weifang Yang
- Beijing General Station of Animal Husbandry, Beijing, China
| | - Tao Zhu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Liang Wang
- Beijing General Station of Animal Husbandry, Beijing, China
| | - Xiaoyu Zhao
- Hebei Dawu Poultry Breeding Co., Ltd., Hebei, China
| | | | - Lujiang Qu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Lujiang Qu, ; Yaxiong Jia,
| | - Yaxiong Jia
- Institute of Animal Sciences, Chinese Academy of Agricultural Science, Beijing, China
- *Correspondence: Lujiang Qu, ; Yaxiong Jia,
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20
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Uluca B, Lektemur Esen C, Saritas Erdogan S, Kumbasar A. NFI transcriptionally represses CDON and is required for SH-SY5Y cell survival. Biochim Biophys Acta Gene Regul Mech 2022; 1865:194798. [PMID: 35151899 DOI: 10.1016/j.bbagrm.2022.194798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/14/2022] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Nuclear Factor One (NFI) family of transcription factors regulate proliferation and multiple aspects of differentiation, playing analogous roles in embryonic development and various types of cancer. While all NFI family members are expressed in the developing brain and are involved in progression of brain cancers, their role in neuroblastoma has not been studied. Here we show that NFIB is required for the survival and proliferation of SH-SY5Y neuroblastoma cells, assessed by viability and colony formation assays. Cdon, an Ig superfamily member, is a SHH dependence receptor that acts as a tumor suppressor in neuroblastoma. In the absence of NFI, Cdon is upregulated in the developing mouse brain, however the mechanisms by which its transcription is regulated remains unknown. We report CDON as a downstream target of NFIs in SH-SY5Y cells. There are three putative NFI binding sites within the one kb CDON promoter, two of which are occupied by NFIs in SH-SY5Y cells and human neural stem cells. In dual-luciferase assays, Nfib directly represses CDON proximal promoter activity. Moreover, silencing NFIB leads to upregulation of CDON in SH-SY5Y cells, however, decreased cell proliferation in NFIB silenced cells could not be rescued by concomitantly silencing CDON, suggesting other molecular players are involved. For instance, p21, an NFI target in glioblastoma and breast cancer cells, is also upregulated upon NFIB knock-down. We propose that NFIB is indispensable for SH-SY5Y cells which may involve regulation of apoptosis inducer proteins CDON and p21.
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Affiliation(s)
- Betül Uluca
- Department of Molecular Biology and Genetics, Istanbul Technical University, Maslak, Istanbul 34469, Turkey; Department of Molecular Biotechnology, Turkish-German University, Beykoz, Istanbul 34820, Turkey
| | - Cemre Lektemur Esen
- Department of Molecular Biology and Genetics, Istanbul Technical University, Maslak, Istanbul 34469, Turkey
| | - Sinem Saritas Erdogan
- Department of Molecular Biology and Genetics, Istanbul Technical University, Maslak, Istanbul 34469, Turkey
| | - Asli Kumbasar
- Department of Molecular Biology and Genetics, Istanbul Technical University, Maslak, Istanbul 34469, Turkey.
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21
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Xiang J, Ding Y, Yang F, Gao A, Zhang W, Tang H, Mao J, He Q, Zhang Q, Wang T. Genetic Analysis of Children With Unexplained Developmental Delay and/or Intellectual Disability by Whole-Exome Sequencing. Front Genet 2021; 12:738561. [PMID: 34858471 PMCID: PMC8631448 DOI: 10.3389/fgene.2021.738561] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/07/2021] [Indexed: 11/25/2022] Open
Abstract
Background: Whole-exome sequencing (WES) has been recommended as a first-tier clinical diagnostic test for individuals with neurodevelopmental disorders (NDDs). We aimed to identify the genetic causes of 17 children with developmental delay (DD) and/or intellectual disability (ID). Methods: WES and exome-based copy number variation (CNV) analysis were performed for 17 patients with unexplained DD/ID. Results: Single-nucleotide variant (SNV)/small insertion or deletion (Indel) analysis and exome-based CNV calling yielded an overall diagnostic rate of 58.8% (10/17), of which diagnostic SNVs/Indels accounted for 41.2% (7/17) and diagnostic CNVs accounted for 17.6% (3/17). Conclusion: Our findings expand the known mutation spectrum of genes related to DD/ID and indicate that exome-based CNV analysis could improve the diagnostic yield of patients with DD/ID.
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Affiliation(s)
- Jingjing Xiang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Yang Ding
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Fei Yang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Ang Gao
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Wei Zhang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Hui Tang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Jun Mao
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Quanze He
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Qin Zhang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Ting Wang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.,Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
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22
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Kataoka H, Yoshida R, Iwasa N, Sato M, Manabe S, Kawachi K, Makabe S, Akihisa T, Ushio Y, Teraoka A, Tsuchiya K, Nitta K, Mochizuki T. Germline Mutations for Kidney Volume in ADPKD. Kidney Int Rep 2021. [PMID: 35257066 PMCID: PMC8897295 DOI: 10.1016/j.ekir.2021.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/06/2021] [Indexed: 12/22/2022] Open
Abstract
Introduction Valid prediction models or predictors of disease progression in children and young patients with autosomal dominant polycystic kidney disease (ADPKD) are lacking. Although total kidney volume (TKV) and Mayo imaging classification are generally used to predict disease progression in patients with ADPKD, it remains unclear whether germline mutation types are associated with these factors. We therefore investigated the association between mutation type and TKV and Mayo imaging classification among patients with ADPKD. Methods A total of 129 patients with ADPKD who underwent genetic analyses were enrolled in the study. The associations between the severity of PKD (TKV ≥ 1000 ml and Mayo classes 1C–1E) and the PKD1 mutation types (nonsense mutation, frameshift or splicing mutation, and substitution) were evaluated. Results Among the mutation types, only PKD1 splicing/frameshift mutation had significant associations with TKV ≥ 1000 ml in sex-adjusted and multivariable logistic analyses. Similarly, only the PKD1 splicing/frameshift mutation was significantly associated with Mayo 1C–1E in sex-adjusted and multivariable logistic analyses. PKD1 nonsense mutation, PKD1 substitution, or PKD1 mutation position had no significant association with TKV ≥ 1000 ml or Mayo 1C–1E. Conclusion Kidney cyst severity differs according to the mutation types in PKD1. Patients with PKD1 splicing mutations or PKD1 frameshift mutations are associated with TKV ≥ 1000 ml or Mayo 1C–1E. Detailed assessment of mutation types may be useful for predicting renal prognosis in patients with ADPKD and may especially contribute to the care of a high-risk group of children with ADPKD.
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23
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Beyens A, Pottie L, Sips P, Callewaert B. Clinical and Molecular Delineation of Cutis Laxa Syndromes: Paradigms for Homeostasis. Adv Exp Med Biol 2021; 1348:273-309. [PMID: 34807425 DOI: 10.1007/978-3-030-80614-9_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Cutis laxa (CL) syndromes are a large and heterogeneous group of rare connective tissue disorders that share loose redundant skin as a hallmark clinical feature, which reflects dermal elastic fiber fragmentation. Both acquired and congenital-Mendelian- forms exist. Acquired forms are progressive and often preceded by inflammatory triggers in the skin, but may show systemic elastolysis. Mendelian forms are often pleiotropic in nature and classified upon systemic manifestations and mode of inheritance. Though impaired elastogenesis is a common denominator in all Mendelian forms of CL, the underlying gene defects are diverse and affect structural components of the elastic fiber or impair metabolic pathways interfering with cellular trafficking, proline synthesis, or mitochondrial functioning. In this chapter we provide a detailed overview of the clinical and molecular characteristics of the different cutis laxa types and review the latest insights on elastic fiber assembly and homeostasis from both human and animal studies.
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Affiliation(s)
- Aude Beyens
- Center for Medical Genetics Ghent, Department of Dermatology, Department of Biomolecular Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Lore Pottie
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Patrick Sips
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium.
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24
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Abstract
Scoliosis is a complex disease with undetermined pathogenesis and has a strong relationship with genetics. Models of scoliosis in animals have been established for better comprehending its pathogenesis and treatment. In this review, we searched all the genetic animal models with body curvature in databases, and reviewed the related genes and scoliosis types. Meanwhile, we also summarized the pathogenesis of scoliosis reported so far. Summarizing the positive phenotypic animal models contributes to a better understanding on the pathogenesis of scoliosis and facilitates the selection of experimental models when a possible pathogenic factor is concerned.
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Affiliation(s)
- Xin Lv
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Jinghong Xu
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Jiajiong Jiang
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Pengfei Wu
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Renchun Tan
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Bing Wang
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China.
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25
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Rots D, Chater-Diehl E, Dingemans AJM, Goodman SJ, Siu MT, Cytrynbaum C, Choufani S, Hoang N, Walker S, Awamleh Z, Charkow J, Meyn S, Pfundt R, Rinne T, Gardeitchik T, de Vries BBA, Deden AC, Leenders E, Kwint M, Stumpel CTRM, Stevens SJC, Vermeulen JR, van Harssel JVT, Bosch DGM, van Gassen KLI, van Binsbergen E, de Geus CM, Brackel H, Hempel M, Lessel D, Denecke J, Slavotinek A, Strober J, Crunk A, Folk L, Wentzensen IM, Yang H, Zou F, Millan F, Person R, Xie Y, Liu S, Ousager LB, Larsen M, Schultz-Rogers L, Morava E, Klee EW, Berry IR, Campbell J, Lindstrom K, Pruniski B, Neumeyer AM, Radley JA, Phornphutkul C, Schmidt B, Wilson WG, Õunap K, Reinson K, Pajusalu S, van Haeringen A, Ruivenkamp C, Cuperus R, Santos-Simarro F, Palomares-Bralo M, Pacio-Míguez M, Ritter A, Bhoj E, Tønne E, Tveten K, Cappuccio G, Brunetti-Pierri N, Rowe L, Bunn J, Saenz M, Platzer K, Mertens M, Caluseriu O, Nowaczyk MJM, Cohn RD, Kannu P, Alkhunaizi E, Chitayat D, Scherer SW, Brunner HG, Vissers LELM, Kleefstra T, Koolen DA, Weksberg R. Truncating SRCAP variants outside the Floating-Harbor syndrome locus cause a distinct neurodevelopmental disorder with a specific DNA methylation signature. Am J Hum Genet 2021; 108:1053-68. [PMID: 33909990 DOI: 10.1016/j.ajhg.2021.04.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/31/2021] [Indexed: 02/08/2023] Open
Abstract
Truncating variants in exons 33 and 34 of the SNF2-related CREBBP activator protein (SRCAP) gene cause the neurodevelopmental disorder (NDD) Floating-Harbor syndrome (FLHS), characterized by short stature, speech delay, and facial dysmorphism. Here, we present a cohort of 33 individuals with clinical features distinct from FLHS and truncating (mostly de novo) SRCAP variants either proximal (n = 28) or distal (n = 5) to the FLHS locus. Detailed clinical characterization of the proximal SRCAP individuals identified shared characteristics: developmental delay with or without intellectual disability, behavioral and psychiatric problems, non-specific facial features, musculoskeletal issues, and hypotonia. Because FLHS is known to be associated with a unique set of DNA methylation (DNAm) changes in blood, a DNAm signature, we investigated whether there was a distinct signature associated with our affected individuals. A machine-learning model, based on the FLHS DNAm signature, negatively classified all our tested subjects. Comparing proximal variants with typically developing controls, we identified a DNAm signature distinct from the FLHS signature. Based on the DNAm and clinical data, we refer to the condition as “non-FLHS SRCAP-related NDD.” All five distal variants classified negatively using the FLHS DNAm model while two classified positively using the proximal model. This suggests divergent pathogenicity of these variants, though clinically the distal group presented with NDD, similar to the proximal SRCAP group. In summary, for SRCAP, there is a clear relationship between variant location, DNAm profile, and clinical phenotype. These results highlight the power of combined epigenetic, molecular, and clinical studies to identify and characterize genotype-epigenotype-phenotype correlations.
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26
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Moirangthem A, Mandal K, Saxena D, Srivastava P, Gambhir PS, Agrawal N, Shambhavi A, Nampoothiri S, Phadke SR. Genetic heterogeneity of disorders with overgrowth and intellectual disability: Experience from a center in North India. Am J Med Genet A 2021; 185:2345-2355. [PMID: 33942996 DOI: 10.1002/ajmg.a.62241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/25/2021] [Accepted: 04/10/2021] [Indexed: 12/24/2022]
Abstract
Overgrowth, defined as height and/or OFC ≥ +2SD, characterizes a subset of patients with syndromic intellectual disability (ID). Many of the disorders with overgrowth and ID (OGID) are rare and the full phenotypic and genotypic spectra have not been unraveled. This study was undertaken to characterize the phenotypic and genotypic profile of patients with OGID. Patients with OGID were ascertained from the cohort of patients who underwent cytogenetic microarray (CMA) and/or exome sequencing (ES) at our center over a period of 6 years. Thirty-one subjects (six females) formed the study group with ages between 3.5 months and 13 years. CMA identified pathogenic deletions in two patients. In another 11 patients, a disease causing variant was detected by ES. The spectrum of disorders encompassed aberrations in genes involved in the two main pathways associated with OGID. These were genes involved in epigenetic regulation like NSD1, NFIX, FOXP1, and those in the PI3K-AKT pathway like PTEN, AKT3, TSC2, PPP2R5D. Five novel pathogenic variants were added by this study. NSD1-related Sotos syndrome was the most common disorder, seen in five patients. A causative variant was identified in 61.5% of patients who underwent only ES compared to the low yield of 11.1% in the CMA group. The molecular etiology could be confirmed in 13 subjects with OGID giving a diagnostic yield of 42%. The major burden was formed by autosomal dominant monogenic disorders. Hence, ES maybe a better first-tier genomic test rather than CMA in OGID.
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Affiliation(s)
- Amita Moirangthem
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Deepti Saxena
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Priyanka Srivastava
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Poonam Singh Gambhir
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Neha Agrawal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Arya Shambhavi
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, AIMS, Cochin, Kerala, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
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27
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Fortin O, Vincelette C, Khan AQ, Berrahmoune S, Dassi C, Karimi M, Scheffer IE, Lu J, Davis K, Myers KA. Seizures in Sotos syndrome: Phenotyping in 49 patients. Epilepsia Open 2021; 6:425-430. [PMID: 34033256 PMCID: PMC8166795 DOI: 10.1002/epi4.12484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/15/2021] [Accepted: 03/24/2021] [Indexed: 01/29/2023] Open
Abstract
We aimed to describe the phenotypic spectrum of seizures in Sotos syndrome, a genetic condition involving overgrowth, macrocephaly, dysmorphic features, and learning disability, in which 60%‐90% have NSD1 pathogenic variants. Patients were recruited from clinics and referral from support groups. Those with seizures and a clinical diagnosis of Sotos syndrome were included. Phenotyping data were collected via structured clinical interview and chart review. Forty‐nine patients were included. Twenty had NSD1 testing results available; of these, 15 (75%) had NSD1 pathogenic variants. Seizure onset age ranged from 3 months to 12 years. Staring spells (absence or focal impaired awareness seizure) were the most frequently reported semiology (33/49; 67%), followed by febrile seizures (25/49; 51%) and afebrile bilateral tonic‐clonic seizures (25/49; 51%). Most patients (33/49; 67%) had multiple seizure types. The majority (33/49; 67%) had seizures controlled on a single antiseizure medication or no medication. Nine (18%) had drug‐resistant epilepsy. Epilepsy syndromes included febrile seizures plus, Lennox‐Gastaut syndrome, childhood absence epilepsy, and generalized tonic‐clonic seizures alone. The seizure phenotype in Sotos syndrome most commonly involves staring spells, afebrile tonic‐clonic seizures or febrile convulsions; however, other seizure types may occur. Seizures are typically well‐controlled with medication, but drug‐resistant epilepsy occurs in a minority.
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Affiliation(s)
- Olivier Fortin
- Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, Quebec, Canada
| | - Christian Vincelette
- School of Nursing, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Quebec, Canada
| | - Afsheen Q Khan
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Saoussen Berrahmoune
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Christelle Dassi
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Mitra Karimi
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, Victoria, Australia.,Department of Paediatrics, Royal Children's Hospital, The University of Melbourne, Flemington, Victoria, Australia.,The Florey Institute of Neuroscience and Mental Health, Heidelberg, Victoria, Australia
| | - Jun Lu
- Department of Pediatrics, Haikou People's Hospital, Haikou, China
| | - Kellie Davis
- Division of Medical Genetics, Department of Pediatrics, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Kenneth A Myers
- Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, Quebec, Canada.,Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,Department of Neurology & Neurosurgery, Montreal Children's Hospital, McGill University, Montreal, Quebec, Canada
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Deconte D, dos Santos CBL, de Morais CO, Yonamine TM, Nogueira LT, Ferreira MAT, Franceschi VB, Longhi ALS, Villacis RAR, Rogatto SR, Ligabue-Braun R, Zen PRG, Rosa RFM, Fiegenbaum M. Unusual features in a child with Marshall-Smith syndrome due to a novel NFIX variant: Evidence for an abnormal protein function. Gene Reports 2021. [DOI: 10.1016/j.genrep.2020.100991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Knie B, Morota N, Ihara S, Tamada I. Fronto-orbital advancement in a patient with Marshall-Smith syndrome: a case report and review of the literature. Childs Nerv Syst 2021; 37:677-682. [PMID: 32617711 DOI: 10.1007/s00381-020-04741-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 06/11/2020] [Indexed: 10/23/2022]
Abstract
OBJECTIVE The present report aimed to document the clinical features of a case of Marshall-Smith syndrome (MSS), an extremely rare embryonic developmental disorder with associated craniosynostosis. PATIENT AND METHOD We presented herein a case of a 2-year-old female patient with MSS who underwent fronto-orbital advancement for multisuture craniosynostosis. RESULTS The patient's proptosis improved after surgery, and no further surgical intervention was required for corneal exposure. A second FOA followed by revision tarsorrhaphy further improved eye closure. CONCLUSION Surgical procedures to correct dysplastic features and limit neurological impairment are a worthwhile supportive treatment for improving the quality of life and general condition of patients with MSS.
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Affiliation(s)
- Bettina Knie
- Department of Neurosurgery, Vivantes Klinikum im Friedrichshain, Berlin, Germany.
- Division of Neurosurgery, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan.
| | - Nobuhito Morota
- Division of Neurosurgery, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
- Division of Pediatric Neurosurgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Satoshi Ihara
- Division of Neurosurgery, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Ikkei Tamada
- Department of Plastic and Reconstructive Surgery, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
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30
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Mulder PA, van Balkom IDC, Landlust AM, Priolo M, Menke LA, Acero IH, Alkuraya FS, Arias P, Bernardini L, Bijlsma EK, Cole T, Coubes C, Dapia I, Davies S, Di Donato N, Elcioglu NH, Fahrner JA, Foster A, González NG, Huber I, Iascone M, Kaiser AS, Kamath A, Kooblall K, Lapunzina P, Liebelt J, Lynch SA, Maas SM, Mammì C, Mathijssen IB, McKee S, Mirzaa GM, Montgomery T, Neubauer D, Neumann TE, Pintomalli L, Pisanti MA, Plomp AS, Price S, Salter C, Santos-Simarro F, Sarda P, Schanze D, Segovia M, Shaw-Smith C, Smithson S, Suri M, Tatton-Brown K, Tenorio J, Thakker RV, Valdez RM, Van Haeringen A, Van Hagen JM, Zenker M, Zollino M, Dunn WW, Piening S, Hennekam RC. Development, behaviour and sensory processing in Marshall-Smith syndrome and Malan syndrome: phenotype comparison in two related syndromes. J Intellect Disabil Res 2020; 64:956-969. [PMID: 33034087 PMCID: PMC8957705 DOI: 10.1111/jir.12787] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 08/19/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Ultrarare Marshall-Smith and Malan syndromes, caused by changes of the gene nuclear factor I X (NFIX), are characterised by intellectual disability (ID) and behavioural problems, although questions remain. Here, development and behaviour are studied and compared in a cross-sectional study, and results are presented with genetic findings. METHODS Behavioural phenotypes are compared of eight individuals with Marshall-Smith syndrome (three male individuals) and seven with Malan syndrome (four male individuals). Long-term follow-up assessment of cognition and adaptive behaviour was possible in three individuals with Marshall-Smith syndrome. RESULTS Marshall-Smith syndrome individuals have more severe ID, less adaptive behaviour, more impaired speech and less reciprocal interaction compared with individuals with Malan syndrome. Sensory processing difficulties occur in both syndromes. Follow-up measurement of cognition and adaptive behaviour in Marshall-Smith syndrome shows different individual learning curves over time. CONCLUSIONS Results show significant between and within syndrome variability. Different NFIX variants underlie distinct clinical phenotypes leading to separate entities. Cognitive, adaptive and sensory impairments are common in both syndromes and increase the risk of challenging behaviour. This study highlights the value of considering behaviour within developmental and environmental context. To improve quality of life, adaptations to environment and treatment are suggested to create a better person-environment fit.
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Affiliation(s)
- P A Mulder
- Autism Team Northern-Netherlands, Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
| | - I D C van Balkom
- Autism Team Northern-Netherlands, Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
- Rob Giel Research Centre, Department of Psychiatry, University Medical Center Groningen, Groningen, Netherlands
| | - A M Landlust
- Autism Team Northern-Netherlands, Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
| | - M Priolo
- Unità Operativa di Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, Reggio Calabria, Italy
| | - L A Menke
- Department of Paediatrics, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - I H Acero
- Genetics Unit, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - F S Alkuraya
- Saudi Human Genome Project, King Abdulaziz City for Science and Technology, and Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - P Arias
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - L Bernardini
- Cytogenetics Unit, Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - E K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, Netherlands
| | - T Cole
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - C Coubes
- Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, CHRU Montpellier, Montpellier, France
| | - I Dapia
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - S Davies
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - N Di Donato
- Institute for Clinical Genetics, TU Dresden, Dresden, Germany
| | - N H Elcioglu
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul and Eastern Mediterranean University, Mersin, Turkey
| | - J A Fahrner
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - A Foster
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - N G González
- Unit Hospital Universitario Central de Asturias, Oviedo, Spain
| | - I Huber
- Sørland Hospital, Kristiansand, Norway
| | - M Iascone
- Medical Genetics Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - A-S Kaiser
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - A Kamath
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - K Kooblall
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - P Lapunzina
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - J Liebelt
- South Australian Clinical Genetics Services, Women's and Children's Hospital, North Adelaide, Australia
| | - S A Lynch
- UCD Academic Centre on Rare Diseases, School of Medicine and Medical Sciences, University College Dublin, and Clinical Genetics, Temple Street Children's University Hospital, Dublin, Ireland
| | - S M Maas
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, Netherlands
| | - C Mammì
- Unità Operativa di Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, Reggio Calabria, Italy
| | - I B Mathijssen
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, Netherlands
| | - S McKee
- Northern Ireland Regional Genetics Service, Belfast Health and Social Care Trust, Belfast, UK
| | - G M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, and Division of Genetic Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - T Montgomery
- Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK
| | - D Neubauer
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - T E Neumann
- Mitteldeutscher Praxisverbund Humangenetik, Halle, Germany
| | - L Pintomalli
- Unità Operativa di Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, Reggio Calabria, Italy
| | - M A Pisanti
- Medical Genetic and Laboratory Unit, "Antonio Cardarelli" Hospital, Naples, Italy
| | - A S Plomp
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, Netherlands
| | - S Price
- Department of Clinical Genetics, Northampton General Hospital NHS Trust, Northampton, UK
| | - C Salter
- Wessex Clinical Genetics Service, Princess Ann Hospital, Southampton, UK
| | - F Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - P Sarda
- Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, CHRU Montpellier, Montpellier, France
| | - D Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - M Segovia
- CENAGEM, Centro Nacional de Genética, Buenos Aires, Argentina
| | - C Shaw-Smith
- Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - S Smithson
- University Hospitals Bristol NHS Trust, Bristol, UK
| | - M Suri
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - K Tatton-Brown
- Division of Genetics and Epidemiology, Institute of Cancer Research, London and South West Thames Regional Genetics Service, St. George's University Hospitals NHS Foundation Trust, London, UK
| | - J Tenorio
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - R V Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - R M Valdez
- Genetics Unit, Hospital Militar Central "Cirujano Mayor Dr. Cosme Argerich", Buenos Aires, Argentina
| | - A Van Haeringen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, Netherlands
| | - J M Van Hagen
- Department of Clinical Genetics, VU University Medical Centre, Amsterdam, Netherlands
| | - M Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - M Zollino
- Department of Laboratory Medicine, Institute of Medical Genetics, Catholic University, Rome, Italy
| | - W W Dunn
- Department of Occupational Therapy Education, School of Health Professions, University of Missouri, Columbia, MO, USA
| | - S Piening
- Autism Team Northern-Netherlands, Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
- Rob Giel Research Centre, Department of Psychiatry, University Medical Center Groningen, Groningen, Netherlands
| | - R C Hennekam
- Autism Team Northern-Netherlands, Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
- Department of Paediatrics, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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Sihombing NRB, Winarni TI, van Bokhoven H, van der Burgt I, de Leeuw N, Faradz SMH. Pathogenic variant in NFIX gene affecting three sisters due to paternal mosaicism. Am J Med Genet A 2020; 182:2731-2736. [PMID: 32945093 DOI: 10.1002/ajmg.a.61835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 06/14/2020] [Accepted: 06/25/2020] [Indexed: 12/26/2022]
Abstract
We present a family with three girls presenting similar dysmorphic features, including overgrowth, intellectual disability, macrocephaly, prominent forehead, midface retrusion, strabismus, and scoliosis. Both parents were unaffected, suggesting the presence of an autosomal recessive syndrome. Following exome sequencing, a heterozygous nonsense variant was identified in the NFIX gene in all three siblings. The father appeared to have a low-grade (7%) mosaicism for this variant in his blood. Previously, de novo pathogenic variants in NFIX have been identified in Marshall-Smith syndrome and Malan syndrome, which share distinctive phenotypic features shared with the patients of the present family. This case emphasizes the importance of further molecular analysis especially in familial cases, to exclude the possibility of parental mosaicism.
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Affiliation(s)
- Nydia Rena Benita Sihombing
- Doctoral Program of Medical and Health Sciences, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Tri Indah Winarni
- Division of Human Genetics, Center for Biomedical Research (CEBIOR), Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ineke van der Burgt
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sultana M H Faradz
- Division of Human Genetics, Center for Biomedical Research (CEBIOR), Faculty of Medicine, Diponegoro University, Semarang, Indonesia
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33
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Tabata K, Iida A, Takeshita E, Nakagawa E, Sato N, Sasaki M, Inoue K, Goto YI. A novel pathogenic NFIX variant in a Malan syndrome patient associated with hindbrain overcrowding. J Neurol Sci 2020; 412:116758. [PMID: 32193017 DOI: 10.1016/j.jns.2020.116758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Kenshiro Tabata
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo 187-8551, Japan
| | - Aritoshi Iida
- Department of Clinical Genome Analysis, Medical Genome Center, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo 187-8551, Japan
| | - Eri Takeshita
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo 187-8551, Japan
| | - Eiji Nakagawa
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo 187-8551, Japan
| | - Noriko Sato
- Department of Radiology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo 187-8551, Japan
| | - Masayuki Sasaki
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo 187-8551, Japan
| | - Ken Inoue
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo 187-8551, Japan
| | - Yu-Ichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo 187-8551, Japan; Medical Genome Center, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo 187-8551, Japan.
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34
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Gokhman D, Nissim-Rafinia M, Agranat-Tamir L, Housman G, García-Pérez R, Lizano E, Cheronet O, Mallick S, Nieves-Colón MA, Li H, Alpaslan-Roodenberg S, Novak M, Gu H, Osinski JM, Ferrando-Bernal M, Gelabert P, Lipende I, Mjungu D, Kondova I, Bontrop R, Kullmer O, Weber G, Shahar T, Dvir-Ginzberg M, Faerman M, Quillen EE, Meissner A, Lahav Y, Kandel L, Liebergall M, Prada ME, Vidal JM, Gronostajski RM, Stone AC, Yakir B, Lalueza-Fox C, Pinhasi R, Reich D, Marques-Bonet T, Meshorer E, Carmel L. Differential DNA methylation of vocal and facial anatomy genes in modern humans. Nat Commun 2020; 11:1189. [PMID: 32132541 PMCID: PMC7055320 DOI: 10.1038/s41467-020-15020-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 02/13/2020] [Indexed: 12/11/2022] Open
Abstract
Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that likely emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes associated with face and vocal tract anatomy went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-associated genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.
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Affiliation(s)
- David Gokhman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
| | - Malka Nissim-Rafinia
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Lily Agranat-Tamir
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
- Department of Statistics, The Hebrew University of Jerusalem, 91905, Jerusalem, Israel
| | - Genevieve Housman
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | | | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - Swapan Mallick
- Broad Institute, Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Maria A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Heng Li
- Broad Institute, Cambridge, MA, 02138, USA
| | | | - Mario Novak
- Institute for Anthropological Research, 10000, Zagreb, Croatia
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | | | - Jason M Osinski
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
| | | | - Pere Gelabert
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
| | - Iddi Lipende
- Gombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania
| | - Deus Mjungu
- Gombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania
| | - Ivanela Kondova
- Biomedical Primate Research Centre (BPRC), Rijswijk, Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Centre (BPRC), Rijswijk, Netherlands
| | - Ottmar Kullmer
- Department of Palaeoanthropology and Messel Research, Senckenberg Center of Human Evolution and Paleoecology, Frankfurt am Main, Germany
| | - Gerhard Weber
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - Tal Shahar
- Department of Neurosurgery, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Mona Dvir-Ginzberg
- Laboratory of Cartilage Biology, Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University of Jerusalem, 91120, Jerusalem, Israel
| | - Marina Faerman
- Laboratory of Bioanthropology and Ancient DNA, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, 91120, Jerusalem, Israel
| | - Ellen E Quillen
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 85287, USA
| | - Alexander Meissner
- Broad Institute, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Yonatan Lahav
- Otolaryngology - Head & Neck Surgery Department, Laryngeal Surgery Unit, Kaplan Medical Center, Rehovot, Israel
- The Hebrew University Medical School, Jerusalem, Israel
| | - Leonid Kandel
- Orthopaedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Meir Liebergall
- Orthopaedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - María E Prada
- I.E.S.O. 'Los Salados'. Junta de Castilla y León, León, Spain
| | - Julio M Vidal
- Junta de Castilla y León, Servicio de Cultura de León, León, Spain
| | - Richard M Gronostajski
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
- Genetics, Genomics and Bioinformatics Program, New York State Center of Excellence in Bioinformatics and Life Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ, 85287, USA
| | - Benjamin Yakir
- Department of Statistics, The Hebrew University of Jerusalem, 91905, Jerusalem, Israel
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - David Reich
- Broad Institute, Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Barcelona, Spain
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
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Oishi S, Zalucki O, Vega MS, Harkins D, Harvey TJ, Kasherman M, Davila RA, Hale L, White M, Piltz S, Thomas P, Burne THJ, Harris L, Piper M. Investigating cortical features of Sotos syndrome using mice heterozygous for Nsd1. Genes Brain Behav 2020; 19:e12637. [PMID: 31909872 DOI: 10.1111/gbb.12637] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/03/2020] [Accepted: 01/04/2020] [Indexed: 12/18/2022]
Abstract
Sotos syndrome is a developmental disorder characterized by a suite of clinical features. In children, the three cardinal features of Sotos syndrome are a characteristic facial appearance, learning disability and overgrowth (height and/or head circumference > 2 SDs above average). These features are also evident in adults with this syndrome. Over 90% of Sotos syndrome patients are haploinsufficient for the gene encoding nuclear receptor-binding Su(var)3-9, Enhancer-of-zesteand Trithorax domain-containing protein 1 (NSD1). NSD1 is a histone methyltransferase that catalyzes the methylation of lysine residue 36 on histone H3. However, although the symptomology of Sotos syndrome is well established, many aspects of NSD1 biology remain unknown. Here, we assessed the expression of Nsd1 within the mouse brain, and showed a predominantly neuronal pattern of expression for this histone-modifying factor. We also generated a mouse strain lacking one allele of Nsd1 and analyzed morphological and behavioral characteristics in these mice, showing behavioral characteristics reminiscent of some of the deficits seen in Sotos syndrome patients.
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Affiliation(s)
- Sabrina Oishi
- The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Oressia Zalucki
- The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Michelle S Vega
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Danyon Harkins
- The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Tracey J Harvey
- The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Maria Kasherman
- The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Raul A Davila
- The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Lauren Hale
- The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Melissa White
- School of Biological Sciences and South Australia Genome Editing Facility, University of Adelaide, Adelaide, South Australia, Australia
| | - Sandra Piltz
- School of Biological Sciences and South Australia Genome Editing Facility, University of Adelaide, Adelaide, South Australia, Australia
| | - Paul Thomas
- School of Biological Sciences and South Australia Genome Editing Facility, University of Adelaide, Adelaide, South Australia, Australia
| | - Thomas H J Burne
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, Queensland, Australia
| | - Lachlan Harris
- The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
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Zenker M, Bunt J, Schanze I, Schanze D, Piper M, Priolo M, Gerkes EH, Gronostajski RM, Richards LJ, Vogt J, Wessels MW, Hennekam RC. Variants in nuclear factor I genes influence growth and development. Am J Med Genet 2019; 181:611-626. [DOI: 10.1002/ajmg.c.31747] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/26/2019] [Accepted: 10/09/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Martin Zenker
- Institute of Human GeneticsUniversity Hospital, Otto‐von‐Guericke‐University Magdeburg Germany
| | - Jens Bunt
- Queensland Brain InstituteThe University of Queensland Brisbane Queensland Australia
| | - Ina Schanze
- Institute of Human GeneticsUniversity Hospital, Otto‐von‐Guericke‐University Magdeburg Germany
| | - Denny Schanze
- Institute of Human GeneticsUniversity Hospital, Otto‐von‐Guericke‐University Magdeburg Germany
| | - Michael Piper
- Queensland Brain InstituteThe University of Queensland Brisbane Queensland Australia
- School of Biomedical SciencesThe University of Queensland Brisbane Queensland Australia
| | - Manuela Priolo
- Operative Unit of Medical GeneticsGreat Metropolitan Hospital Bianchi‐Melacrino‐Morelli Reggio Calabria Italy
| | - Erica H. Gerkes
- Department of Genetics, University of GroningenUniversity Medical Center Groningen Groningen the Netherlands
| | - Richard M. Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life SciencesState University of New York Buffalo NY
| | - Linda J. Richards
- Queensland Brain InstituteThe University of Queensland Brisbane Queensland Australia
- School of Biomedical SciencesThe University of Queensland Brisbane Queensland Australia
| | - Julie Vogt
- West Midlands Regional Clinical Genetics Service and Birmingham Health PartnersWomen's and Children's Hospitals NHS Foundation Trust Birmingham UK
| | - Marja W. Wessels
- Department of Clinical Genetics, Erasmus MCUniversity Medical Center Rotterdam Rotterdam The Netherlands
| | - Raoul C. Hennekam
- Department of PediatricsUniversity of Amsterdam Amsterdam The Netherlands
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37
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Bellucco FT, de Mello CB, Meloni VA, Melaragno MI. Malan syndrome in a patient with 19p13.2p13.12 deletion encompassing NFIX and CACNA1A genes: Case report and review of the literature. Mol Genet Genomic Med 2019; 7:e997. [PMID: 31574590 PMCID: PMC6900369 DOI: 10.1002/mgg3.997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/16/2019] [Indexed: 11/16/2022] Open
Abstract
Background Malan syndrome is a recently introduced overgrowth disorder described in a limited number of individuals. Haploinsufficiency and also point mutations of NFIX gene have been proposed as its leading causative mechanism, however, due to the limited number of cases and different deletion sizes, genotype/phenotype correlations are still limited. Methods Here, we report the first Brazilian case of Malan syndrome caused by a 990 kb deletion in 19p13.2p13.12, focusing on clinical and behavioral aspects of the syndrome. Results The patient presented with macrocephaly, facial dysmorphisms, hypotonia, developmental delay, moderate thoracolumbar scoliosis, and seizures. The intellectual and behavioral assessments showed severe cognitive, language, and adaptive functions impairments. The 19p deleted region of our patient encompasses NFIX, CACNA1A, which seems to be related to a higher frequency of seizures among individuals with microdeletions in 19p13.2, and 15 other coding genes, including CC2D1A and NACC1, both known to be involved in neurobiological process and pathways. Conclusion Deletions involving NFIX gene should be considered in patients with overgrowth during childhood, macrocephaly, developmental delay, and seizures, as well as severe intellectual disability.
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Affiliation(s)
- Fernanda T Bellucco
- Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Claudia B de Mello
- Department of Psychobiology, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Vera A Meloni
- Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
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38
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Hancarova M, Havlovicova M, Putzova M, Vseticka J, Prchalova D, Stranecky V, Sedlacek Z. Parental gonadal but not somatic mosaicism leading to de novo
NFIX
variants shared by two brothers with Malan syndrome. Am J Med Genet A 2019; 179:2119-2123. [DOI: 10.1002/ajmg.a.61302] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/02/2019] [Accepted: 07/09/2019] [Indexed: 11/12/2022]
Affiliation(s)
- Miroslava Hancarova
- Department of Biology and Medical GeneticsCharles University 2nd Faculty of Medicine and University Hospital Motol Prague Czech Republic
| | - Marketa Havlovicova
- Department of Biology and Medical GeneticsCharles University 2nd Faculty of Medicine and University Hospital Motol Prague Czech Republic
| | | | | | - Darina Prchalova
- Department of Biology and Medical GeneticsCharles University 2nd Faculty of Medicine and University Hospital Motol Prague Czech Republic
| | - Viktor Stranecky
- Department of Pediatrics and Adolescent MedicineCharles University 1st Faculty of Medicine and General University Hospital Prague Czech Republic
| | - Zdenek Sedlacek
- Department of Biology and Medical GeneticsCharles University 2nd Faculty of Medicine and University Hospital Motol Prague Czech Republic
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39
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Wilkerson BA, Chitsazan AD, VandenBosch LS, Wilken MS, Reh TA, Bermingham-McDonogh O. Open chromatin dynamics in prosensory cells of the embryonic mouse cochlea. Sci Rep 2019; 9:9060. [PMID: 31227770 DOI: 10.1038/s41598-019-45515-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 06/10/2019] [Indexed: 12/13/2022] Open
Abstract
Hearing loss is often due to the absence or the degeneration of hair cells in the cochlea. Understanding the mechanisms regulating the generation of hair cells may therefore lead to better treatments for hearing disorders. To elucidate the transcriptional control mechanisms specifying the progenitor cells (i.e. prosensory cells) that generate the hair cells and support cells critical for hearing function, we compared chromatin accessibility using ATAC-seq in sorted prosensory cells (Sox2-EGFP+) and surrounding cells (Sox2-EGFP−) from E12, E14.5 and E16 cochlear ducts. In Sox2-EGFP+, we find greater accessibility in and near genes restricted in expression to the prosensory region of the cochlear duct including Sox2, Isl1, Eya1 and Pou4f3. Furthermore, we find significant enrichment for the consensus binding sites of Sox2, Six1 and Gata3—transcription factors required for prosensory development—in the open chromatin regions. Over 2,200 regions displayed differential accessibility with developmental time in Sox2-EGFP+ cells, with most changes in the E12-14.5 window. Open chromatin regions detected in Sox2-EGFP+ cells map to over 48,000 orthologous regions in the human genome that include regions in genes linked to deafness. Our results reveal a dynamic landscape of open chromatin in prosensory cells with potential implications for cochlear development and disease.
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Abstract
Overgrowth syndromes are a heterogeneous group of rare disorders characterized by generalized or segmental excessive growth commonly associated with additional features, such as visceromegaly, macrocephaly and a large range of various symptoms. These syndromes are caused by either genetic or epigenetic anomalies affecting factors involved in cell proliferation and/or the regulation of epigenetic markers. Some of these conditions are associated with neurological anomalies, such as cognitive impairment or autism. Overgrowth syndromes are frequently associated with an increased risk of cancer (embryonic tumours during infancy or carcinomas during adulthood), but with a highly variable prevalence. Given this risk, syndrome-specific tumour screening protocols have recently been established for some of these conditions. Certain specific clinical traits make it possible to discriminate between different syndromes and orient molecular explorations to determine which molecular tests to conduct, despite the syndromes having overlapping clinical features. Recent advances in molecular techniques using next-generation sequencing approaches have increased the number of patients with an identified molecular defect (especially patients with segmental overgrowth). This Review discusses the clinical and molecular diagnosis, tumour risk and recommendations for tumour screening for the most prevalent generalized and segmental overgrowth syndromes.
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Affiliation(s)
- Frédéric Brioude
- Sorbonne Université, INSERM UMR_S938, Centre de Recherche Saint Antoine, AP-HP Hôpital Trousseau, Paris, France.
| | - Annick Toutain
- CHU de Tours, Hôpital Bretonneau, Service de Génétique, INSERM UMR1253, iBrain, Université de Tours, Faculté de Médecine, Tours, France
| | - Eloise Giabicani
- Sorbonne Université, INSERM UMR_S938, Centre de Recherche Saint Antoine, AP-HP Hôpital Trousseau, Paris, France
| | - Edouard Cottereau
- CHU de Tours, Hôpital Bretonneau, Service de Génétique, Tours, France
| | - Valérie Cormier-Daire
- Service de génétique clinique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut Imagine, Hôpital Necker-Enfants Malades, Paris, France
| | - Irene Netchine
- Sorbonne Université, INSERM UMR_S938, Centre de Recherche Saint Antoine, AP-HP Hôpital Trousseau, Paris, France
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41
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Oishi S, Harkins D, Kurniawan ND, Kasherman M, Harris L, Zalucki O, Gronostajski RM, Burne THJ, Piper M. Heterozygosity for Nuclear Factor One X in mice models features of Malan syndrome. EBioMedicine 2019; 39:388-400. [PMID: 30503862 PMCID: PMC6354567 DOI: 10.1016/j.ebiom.2018.11.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/16/2018] [Accepted: 11/20/2018] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Nuclear Factor One X (NFIX) haploinsufficiency in humans results in Malan syndrome, a disorder characterized by overgrowth, macrocephaly and intellectual disability. Although clinical assessments have determined the underlying symptomology of Malan syndrome, the fundamental mechanisms contributing to the enlarged head circumference and intellectual disability in these patients remains undefined. METHODS Here, we used Nfix heterozygous mice as a model to investigate these aspects of Malan syndrome. Volumetric magnetic resonance imaging (MRI) was used to calculate the volumes of 20 brain sub regions. Diffusion tensor MRI was used to perform tractography-based analyses of the corpus callosum, hippocampal commissure, and anterior commissure, as well as structural connectome mapping of the whole brain. Immunohistochemistry examined the neocortical cellular populations. Two behavioral assays were performed, including the active place avoidance task to assess spatial navigation and learning and memory function, and the 3-chambered sociability task to examine social behaviour. FINDINGS Adult Nfix+/- mice exhibit significantly increased brain volume (megalencephaly) compared to wildtypes, with the cerebral cortex showing the highest increase. Moreover, all three forebrain commissures, in particular the anterior commissure, revealed significantly reduced fractional anisotropy, axial and radial diffusivity, and tract density intensity. Structural connectome analyses revealed aberrant connectivity between many crucial brain regions. Finally, Nfix+/- mice exhibit behavioral deficits that model intellectual disability. INTERPRETATION Collectively, these data provide a significant conceptual advance in our understanding of Malan syndrome by suggesting that megalencephaly underlies the enlarged head size of these patients, and that disrupted cortical connectivity may contribute to the intellectual disability these patients exhibit. FUND: Australian Research Council (ARC) Discovery Project Grants, ARC Fellowship, NYSTEM and Australian Postgraduate Fellowships.
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Affiliation(s)
- Sabrina Oishi
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Danyon Harkins
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Nyoman D Kurniawan
- The Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Maria Kasherman
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Lachlan Harris
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; The Francis Crick Institute, 1 Midland Road, King's Cross, London, United Kingdom
| | - Oressia Zalucki
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Thomas H J Burne
- The Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, Brisbane, QLD 4076, Australia
| | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; The Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
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Abstract
Individuals with acromegaloid physical appearance or tall stature may be referred to endocrinologists to exclude growth hormone (GH) excess. While some of these subjects could be healthy individuals with normal variants of growth or physical traits, others will have acromegaly or pituitary gigantism, which are, in general, straightforward diagnoses upon assessment of the GH/IGF-1 axis. However, some patients with physical features resembling acromegaly - usually affecting the face and extremities -, or gigantism - accelerated growth/tall stature - will have no abnormalities in the GH axis. This scenario is termed pseudoacromegaly, and its correct diagnosis can be challenging due to the rarity and variability of these conditions, as well as due to significant overlap in their characteristics. In this review we aim to provide a comprehensive overview of pseudoacromegaly conditions, highlighting their similarities and differences with acromegaly and pituitary gigantism, to aid physicians with the diagnosis of patients with pseudoacromegaly.
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Affiliation(s)
- Pedro Marques
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Márta Korbonits
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
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43
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Rai A, Narayanan DL, Phadke SR. Malan syndrome: Extension of genotype and phenotype spectrum. Am J Med Genet A 2018; 176:2896-2900. [PMID: 30548146 DOI: 10.1002/ajmg.a.40663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 07/09/2018] [Accepted: 09/18/2018] [Indexed: 01/02/2023]
Abstract
Malan syndrome and Marshall-Smith syndrome (MSS) are allelic disorders caused by mutation in NFIX gene. We report a 3-year- 6 months- old female with clinical features suggestive of Malan syndrome with mutation in exon 2 of NFIX gene. NFIX gene, where most of the mutations in Malan syndrome are located. She did not have advanced bone age. The radiographs of long bones showed metaphyseal changes which were not reported previously. This study reports the first mutation proven case from India and highlights the overlap between MSS and Malan syndrome.
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Affiliation(s)
- Archana Rai
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
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44
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Priolo M. Nuclear Factor One X Mice model for Malan syndrome: the less the better. EBioMedicine 2018; 39:15-16. [PMID: 30529069 PMCID: PMC6355653 DOI: 10.1016/j.ebiom.2018.11.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 11/29/2022] Open
Affiliation(s)
- Manuela Priolo
- Operative Unite of Medical Genetics, Great Metropolitan Hospital Bianchi-Melacrino-Morelli, Reggio Calabria, Italy.
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45
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Fraser J, Essebier A, Brown AS, Davila RA, Sengar AS, Tu Y, Ensbey KS, Day BW, Scott MP, Gronostajski RM, Wainwright BJ, Boden M, Harvey TJ, Piper M. Granule neuron precursor cell proliferation is regulated by NFIX and intersectin 1 during postnatal cerebellar development. Brain Struct Funct 2018; 224:811-827. [PMID: 30511336 DOI: 10.1007/s00429-018-1801-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 11/24/2018] [Indexed: 01/06/2023]
Abstract
Cerebellar granule neurons are the most numerous neuronal subtype in the central nervous system. Within the developing cerebellum, these neurons are derived from a population of progenitor cells found within the external granule layer of the cerebellar anlage, namely the cerebellar granule neuron precursors (GNPs). The timely proliferation and differentiation of these precursor cells, which, in rodents occurs predominantly in the postnatal period, is tightly controlled to ensure the normal morphogenesis of the cerebellum. Despite this, our understanding of the factors mediating how GNP differentiation is controlled remains limited. Here, we reveal that the transcription factor nuclear factor I X (NFIX) plays an important role in this process. Mice lacking Nfix exhibit reduced numbers of GNPs during early postnatal development, but elevated numbers of these cells at postnatal day 15. Moreover, Nfix-/- GNPs exhibit increased proliferation when cultured in vitro, suggestive of a role for NFIX in promoting GNP differentiation. At a mechanistic level, profiling analyses using both ChIP-seq and RNA-seq identified the actin-associated factor intersectin 1 as a downstream target of NFIX during cerebellar development. In support of this, mice lacking intersectin 1 also displayed delayed GNP differentiation. Collectively, these findings highlight a key role for NFIX and intersectin 1 in the regulation of cerebellar development.
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Affiliation(s)
- James Fraser
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Alexandra Essebier
- The School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Alexander S Brown
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Raul Ayala Davila
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Ameet S Sengar
- Program in Neurosciences & Mental Health, The Hospital for Sick Children, Toronto, M5G 0A8, Canada
| | - YuShan Tu
- Program in Neurosciences & Mental Health, The Hospital for Sick Children, Toronto, M5G 0A8, Canada
| | - Kathleen S Ensbey
- Cell and Molecular Biology Department, Translational Brain Cancer Research Laboratory, QIMR Berghofer MRI, Brisbane, QLD, 4006, Australia
| | - Bryan W Day
- Cell and Molecular Biology Department, Translational Brain Cancer Research Laboratory, QIMR Berghofer MRI, Brisbane, QLD, 4006, Australia
| | - Matthew P Scott
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Brandon J Wainwright
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Mikael Boden
- The School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Tracey J Harvey
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia.
| | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia. .,Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia.
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46
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Schanze I, Bunt J, Lim JWC, Schanze D, Dean RJ, Alders M, Blanchet P, Attié-Bitach T, Berland S, Boogert S, Boppudi S, Bridges CJ, Cho MT, Dobyns WB, Donnai D, Douglas J, Earl DL, Edwards TJ, Faivre L, Fregeau B, Genevieve D, Gérard M, Gatinois V, Holder-Espinasse M, Huth SF, Izumi K, Kerr B, Lacaze E, Lakeman P, Mahida S, Mirzaa GM, Morgan SM, Nowak C, Peeters H, Petit F, Pilz DT, Puechberty J, Reinstein E, Rivière JB, Santani AB, Schneider A, Sherr EH, Smith-Hicks C, Wieland I, Zackai E, Zhao X, Gronostajski RM, Zenker M, Richards LJ. NFIB Haploinsufficiency Is Associated with Intellectual Disability and Macrocephaly. Am J Hum Genet 2018; 103:752-768. [PMID: 30388402 PMCID: PMC6218805 DOI: 10.1016/j.ajhg.2018.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/03/2018] [Indexed: 12/19/2022] Open
Abstract
The nuclear factor I (NFI) family of transcription factors play an important role in normal development of multiple organs. Three NFI family members are highly expressed in the brain, and deletions or sequence variants in two of these, NFIA and NFIX, have been associated with intellectual disability (ID) and brain malformations. NFIB, however, has not previously been implicated in human disease. Here, we present a cohort of 18 individuals with mild ID and behavioral issues who are haploinsufficient for NFIB. Ten individuals harbored overlapping microdeletions of the chromosomal 9p23-p22.2 region, ranging in size from 225 kb to 4.3 Mb. Five additional subjects had point sequence variations creating a premature termination codon, and three subjects harbored single-nucleotide variations resulting in an inactive protein as determined using an in vitro reporter assay. All individuals presented with additional variable neurodevelopmental phenotypes, including muscular hypotonia, motor and speech delay, attention deficit disorder, autism spectrum disorder, and behavioral abnormalities. While structural brain anomalies, including dysgenesis of corpus callosum, were variable, individuals most frequently presented with macrocephaly. To determine whether macrocephaly could be a functional consequence of NFIB disruption, we analyzed a cortex-specific Nfib conditional knockout mouse model, which is postnatally viable. Utilizing magnetic resonance imaging and histology, we demonstrate that Nfib conditional knockout mice have enlargement of the cerebral cortex but preservation of overall brain structure and interhemispheric connectivity. Based on our findings, we propose that haploinsufficiency of NFIB causes ID with macrocephaly.
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Affiliation(s)
- Ina Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, Magdeburg 39120, Germany
| | - Jens Bunt
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Jonathan W C Lim
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, Magdeburg 39120, Germany
| | - Ryan J Dean
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Marielle Alders
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Patricia Blanchet
- INSERM U1183, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Université Montpellier, Centre de référence anomalies du développement SORO, Montpellier 34295, France
| | - Tania Attié-Bitach
- INSERM U1163, Laboratory of Embryology and Genetics of Congenital Malformations, Paris Descartes University, Sorbonne Paris Cité and Imagine Institute, Paris 75015, France
| | - Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, Bergen 5021, Norway
| | - Steven Boogert
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, Magdeburg 39120, Germany
| | - Sangamitra Boppudi
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, Magdeburg 39120, Germany
| | - Caitlin J Bridges
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, Magdeburg 39120, Germany
| | | | - William B Dobyns
- Department of Pediatrics (Genetics), University of Washington and Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Dian Donnai
- Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Central Manchester University Hospitals NHS Foundation Trust; Division of Evolution and Genomic Sciences School of Biological Sciences, and University of Manchester, Manchester M13 9WL, UK
| | - Jessica Douglas
- Boston Children's Hospital - The Feingold Center, Waltham, MA 02115, USA
| | - Dawn L Earl
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Timothy J Edwards
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia; The Faculty of Medicine Brisbane, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Laurence Faivre
- UMR1231, Génétique des Anomalies du Développement, Université de Bourgogne, Dijon 21079, France; Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire Dijon, Dijon 21079, France
| | - Brieana Fregeau
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David Genevieve
- INSERM U1183, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Université Montpellier, Centre de référence anomalies du développement SORO, Montpellier 34295, France
| | - Marion Gérard
- Service de Génétique, CHU de Caen - Hôpital Clémenceau, Caen Cedex 14000, France
| | - Vincent Gatinois
- INSERM U1183, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Université Montpellier, Centre de référence anomalies du développement SORO, Montpellier 34295, France
| | - Muriel Holder-Espinasse
- Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, Lille 59000, France; Department of Clinical Genetics, Guy's Hospital, London SE1 9RT, UK
| | - Samuel F Huth
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kosuke Izumi
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bronwyn Kerr
- Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Central Manchester University Hospitals NHS Foundation Trust; Division of Evolution and Genomic Sciences School of Biological Sciences, and University of Manchester, Manchester M13 9WL, UK
| | - Elodie Lacaze
- Department of genetics, Le Havre Hospital, 76600 Le Havre, France
| | - Phillis Lakeman
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Sonal Mahida
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Ghayda M Mirzaa
- Department of Pediatrics (Genetics), University of Washington and Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Sian M Morgan
- All Wales Genetics Laboratory, Institute of Medical Genetics, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Catherine Nowak
- Boston Children's Hospital - The Feingold Center, Waltham, MA 02115, USA
| | - Hilde Peeters
- Center for Human Genetics, University Hospital Leuven, KU Leuven, Leuven 3000, Belgium
| | - Florence Petit
- Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, Lille 59000, France
| | - Daniela T Pilz
- West of Scotland Genetics Service, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - Jacques Puechberty
- INSERM U1183, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Université Montpellier, Centre de référence anomalies du développement SORO, Montpellier 34295, France
| | - Eyal Reinstein
- Medical Genetics Institute, Meir Medical Center, Kfar-Saba 4428164, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Jean-Baptiste Rivière
- UMR1231, Génétique des Anomalies du Développement, Université de Bourgogne, Dijon 21079, France; Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire Dijon, Dijon 21079, France; Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Avni B Santani
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anouck Schneider
- INSERM U1183, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Université Montpellier, Centre de référence anomalies du développement SORO, Montpellier 34295, France
| | - Elliott H Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Ilse Wieland
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, Magdeburg 39120, Germany
| | - Elaine Zackai
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiaonan Zhao
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, Magdeburg 39120, Germany.
| | - Linda J Richards
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The Faculty of Medicine Brisbane, The University of Queensland, Brisbane, QLD 4072, Australia
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Kurosaka H. Choanal atresia and stenosis: Development and diseases of the nasal cavity. Wiley Interdiscip Rev Dev Biol 2018; 8:e336. [PMID: 30320458 DOI: 10.1002/wdev.336] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 09/10/2018] [Accepted: 09/19/2018] [Indexed: 12/16/2022]
Abstract
Proper craniofacial development in vertebrates depends on growth and fusion of the facial processes during embryogenesis. Failure of any step in this process could lead to craniofacial anomalies such as facial clefting, which has been well studied with regard to its molecular etiology and cellular pathogenesis. Nasal cavity invagination is also a critical event in proper craniofacial development, and is required for the formation of a functional nasal cavity and airway. The nasal cavity must connect the nasopharynx with the primitive choanae to complete an airway from the nostril to the nasopharynx. In contrast to orofacial clefts, defects in nasal cavity and airway formation, such as choanal atresia (CA), in which the connection between the nasal airway and nasopharynx is physically blocked, have largely been understudied. This is also true for a narrowed connection between the nasal cavity and the nasopharynx, which is known as choanal stenosis (CS). CA occurs in approximately 1 in 5,000 live births, and can present in isolation but typically arises as part of a syndrome. Despite the fact that CA and CS usually require immediate intervention, and substantially affect the quality of life of affected individuals, the etiology and pathogenesis of CA and CS have remained elusive. In this review I focus on the process of nasal cavity development with respect to forming a functional airway and discuss the cellular behavior and molecular networks governing this process. Additionally, the etiology of human CA is discussed using examples of disorders which involve CA or CS. This article is categorized under: Signaling Pathways > Cell Fate Signaling Comparative Development and Evolution > Model Systems Birth Defects > Craniofacial and Nervous System Anomalies.
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Affiliation(s)
- Hiroshi Kurosaka
- Department of Orthodontics and Dentofacial Orthopedics, Graduate School of Dentistry, Osaka University, Osaka, Japan
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Zalucki O, Harris L, Harvey TJ, Harkins D, Widagdo J, Oishi S, Matuzelski E, Yong XLH, Schmidt H, Anggono V, Burne THJ, Gronostajski RM, Piper M. NFIX-Mediated Inhibition of Neuroblast Branching Regulates Migration Within the Adult Mouse Ventricular–Subventricular Zone. Cereb Cortex 2018; 29:3590-3604. [DOI: 10.1093/cercor/bhy233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 08/26/2018] [Accepted: 08/29/2018] [Indexed: 12/13/2022] Open
Abstract
Abstract
Understanding the migration of newborn neurons within the brain presents a major challenge in contemporary biology. Neuronal migration is widespread within the developing brain but is also important within the adult brain. For instance, stem cells within the ventricular–subventricular zone (V-SVZ) and the subgranular zone of dentate gyrus of the adult rodent brain produce neuroblasts that migrate to the olfactory bulb and granule cell layer of the dentate gyrus, respectively, where they regulate key brain functions including innate olfactory responses, learning, and memory. Critically, our understanding of the factors mediating neuroblast migration remains limited. The transcription factor nuclear factor I X (NFIX) has previously been implicated in embryonic cortical development. Here, we employed conditional ablation of Nfix from the adult mouse brain and demonstrated that the removal of this gene from either neural stem and progenitor cells, or neuroblasts, within the V-SVZ culminated in neuroblast migration defects. Mechanistically, we identified aberrant neuroblast branching, due in part to increased expression of the guanylyl cyclase natriuretic peptide receptor 2 (Npr2), as a factor contributing to abnormal migration in Nfix-deficient adult mice. Collectively, these data provide new insights into how neuroblast migration is regulated at a transcriptional level within the adult brain.
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Affiliation(s)
- Oressia Zalucki
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lachlan Harris
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Tracey J Harvey
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Danyon Harkins
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jocelyn Widagdo
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD, Australia
| | - Sabrina Oishi
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Elise Matuzelski
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Xuan Ling Hilary Yong
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD, Australia
| | - Hannes Schmidt
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Victor Anggono
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD, Australia
| | - Thomas H J Burne
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD, Australia
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
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Piper M, Gronostajski R, Messina G. Nuclear Factor One X in Development and Disease. Trends Cell Biol 2018; 29:20-30. [PMID: 30287093 DOI: 10.1016/j.tcb.2018.09.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/03/2018] [Accepted: 09/06/2018] [Indexed: 02/06/2023]
Abstract
The past decade has seen incredible advances in the field of stem cell biology that have greatly improved our understanding of development and provided important insights into pathological processes. Transcription factors (TFs) play a central role in mediating stem cell proliferation, quiescence, and differentiation. One TF that contributes to these processes is Nuclear Factor One X (NFIX). Recently, NFIX activity has been shown to be essential in multiple organ systems and to have important translational impacts for human health. Here, we describe recent studies showing the contribution of NFIX to muscle development and muscular dystrophies, hematopoiesis, cancer, and neural stem cell biology, highlighting the importance of this knowledge in the development of therapeutic targets.
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Affiliation(s)
- Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Richard Gronostajski
- Department of Biochemistry, Genetics, Genomics & Bioinformatics Graduate Program, New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Graziella Messina
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy.
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50
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Jeannot E, Harlé A, Holmes A, Sastre-Garau X. Nuclear factor I X is a recurrent target for HPV16 insertions in anal carcinomas. Genes Chromosomes Cancer 2018; 57:638-644. [PMID: 30264502 DOI: 10.1002/gcc.22675] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 12/25/2022] Open
Abstract
Anal carcinomas (AC) are associated with human papillomavirus (HPV) DNA sequences, but little is known about the physical state of the viral genome in carcinoma cells. To define the integration status and gene(s) targeted by viral insertions in AC, tumor DNAs extracted from 35 tumor specimen samples in patients with HPV16-associated invasive carcinoma were analyzed using the detection of integrated papillomavirus sequences-PCR approach. The genomic status at integration sites was assessed using comparative genomic hybridization-array assay and gene expression using reverse transcription quantitative PCR (RT-qPCR). HPV16 DNA was found integrated in 25/35 (71%) cases and the integration locus could be determined at the molecular level in 19 cases (29 total integration loci). HPV DNA was inserted on different chromosomes, but 5 cases harbored viral sequences at 19p13.2, within the nuclear factor I X (NFIX) locus. Viral DNA mapped between the most distal and the two proximal alternatively expressed exons of this gene in three cases (CA21, CA04, and CA35) and upstream of this gene (663 kb and 2.3 Mb) in the others. CGH arrays showed genomic gains/amplifications at the NFIX region, associated with HPV within the gene and RT-qPCR, revealed NFIX mRNA overexpression. Other genes targeted by integration were IL20RB, RPS6KA2, MSRA1, PIP5K1B, SLX4IP, CECR1, BCAR3, ATF6, CSNK1G1, APBA2, AGK, ILF3, PVT1, TRMT1, RAD51B, FASN, CCDC57, DSG3, and ZNF563. We identified recurrent targeting of NFIX by HPV16 insertion in anal carcinomas, supporting a role for this gene in oncogenesis, as reported for non-HPV tumors.
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Affiliation(s)
- Emmanuelle Jeannot
- Department of Theranostic and Diagnostic Medicine, Institut Curie, PSL Research University, Paris, Saint-Cloud, France
| | - Alexandre Harlé
- Université de Lorraine, Nancy, France.,CNRS UMR 7039 CRAN, Vandoeuvre-Lès-Nancy, France.,Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre-Lès-Nancy, France
| | - Allyson Holmes
- Centre National de la Recherche Scientifique UMR3244, Sorbonne Universités, Institut Curie, PSL Research University, Paris, France
| | - Xavier Sastre-Garau
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre-Lès-Nancy, France
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