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Harkin EF, Nasrallah G, Le François B, Albert PR. Transcriptional Regulation of the Human 5-HT1A Receptor Gene by Lithium: Role of Deaf1 and GSK3β. Int J Mol Sci 2023; 24:15620. [PMID: 37958600 PMCID: PMC10647674 DOI: 10.3390/ijms242115620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/11/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023] Open
Abstract
Serotonin 1A (5-HT1A) autoreceptors located on serotonin neurons inhibit their activity, and their upregulation has been implicated in depression, suicide and resistance to antidepressant treatment. Conversely, post-synaptic 5-HT1A heteroreceptors are important for antidepressant response. The transcription factor deformed epidermal autoregulatory factor 1 (Deaf1) acts as a presynaptic repressor and postsynaptic enhancer of 5-HT1A transcription, but the mechanism is unclear. Because Deaf1 interacts with and is phosphorylated by glycogen synthase kinase 3β (GSK3β)-a constitutively active protein kinase that is inhibited by the mood stabilizer lithium at therapeutic concentrations-we investigated the role of GSK3β in Deaf1 regulation of human 5-HT1A transcription. In 5-HT1A promoter-reporter assays, human HEK293 kidney and 5-HT1A-expressing SKN-SH neuroblastoma cells, transfection of Deaf1 reduced 5-HT1A promoter activity by ~45%. To identify potential GSK3β site(s) on Deaf1, point mutations of known and predicted phosphorylation sites on Deaf1 were tested. Deaf1 repressor function was not affected by any of the mutants tested except the Y300F mutant, which augmented Deaf1 repression. Both lithium and the selective GSK3 inhibitors CHIR-99021 and AR-014418 attenuated and reversed Deaf1 repression compared to vector. This inhibition was at concentrations that maximally inhibit GSK3β activity as detected by the GSK3β-sensitive TCF/LEF reporter construct. Our results support the hypothesis that GSK3β regulates the activity of Deaf1 to repress 5-HT1A transcription and provide a potential mechanism for actions of GSK3 inhibitors on behavior.
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Affiliation(s)
| | | | | | - Paul R. Albert
- Ottawa Hospital Research Institute (Neuroscience), University of Ottawa, 451 Smyth Road, Ottawa, ON K1H-8M5, Canada (B.L.F.)
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2
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McGee SR, Rajamanickam S, Adhikari S, Falayi OC, Wilson TA, Shayota BJ, Cooley Coleman JA, Skinner C, Caylor RC, Stevenson RE, Quaio CRDAC, Wilke BC, Bain JM, Anyane-Yeboa K, Brown K, Greally JM, Bijlsma EK, Ruivenkamp CAL, Politi K, Arbogast LA, Collard MW, Huggenvik JI, Elsea SH, Jensik PJ. Expansion and mechanistic insights into de novo DEAF1 variants in DEAF1-associated neurodevelopmental disorders. Hum Mol Genet 2023; 32:386-401. [PMID: 35981081 PMCID: PMC10310974 DOI: 10.1093/hmg/ddac200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/11/2022] [Accepted: 08/08/2022] [Indexed: 01/24/2023] Open
Abstract
De novo deleterious and heritable biallelic mutations in the DNA binding domain (DBD) of the transcription factor deformed epidermal autoregulatory factor 1 (DEAF1) result in a phenotypic spectrum of disorders termed DEAF1-associated neurodevelopmental disorders (DAND). RNA-sequencing using hippocampal RNA from mice with conditional deletion of Deaf1 in the central nervous system indicate that loss of Deaf1 activity results in the altered expression of genes involved in neuronal function, dendritic spine maintenance, development, and activity, with reduced dendritic spines in hippocampal regions. Since DEAF1 is not a dosage-sensitive gene, we assessed the dominant negative activity of previously identified de novo variants and a heritable recessive DEAF1 variant on selected DEAF1-regulated genes in 2 different cell models. While no altered gene expression was observed in cells over-expressing the recessive heritable variant, the gene expression profiles of cells over-expressing de novo variants resulted in similar gene expression changes as observed in CRISPR-Cas9-mediated DEAF1-deleted cells. Altered expression of DEAF1-regulated genes was rescued by exogenous expression of WT-DEAF1 but not by de novo variants in cells lacking endogenous DEAF1. De novo heterozygous variants within the DBD of DEAF1 were identified in 10 individuals with a phenotypic spectrum including autism spectrum disorder, developmental delays, sleep disturbance, high pain tolerance, and mild dysmorphic features. Functional assays demonstrate these variants alter DEAF1 transcriptional activity. Taken together, this study expands the clinical phenotypic spectrum of individuals with DAND, furthers our understanding of potential roles of DEAF1 on neuronal function, and demonstrates dominant negative activity of identified de novo variants.
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Affiliation(s)
- Stacey R McGee
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | - Shivakumar Rajamanickam
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | - Sandeep Adhikari
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | | | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA
| | - Brian J Shayota
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA
- Department of Pediatrics, Division of Genetics, University of Utah, Salt Lake City, UT
| | | | | | | | | | - Caio Robledo D' Angioli Costa Quaio
- Instituto da Criança (Children’s Hospital), Hospital das Clínicas (HCFMUSP), Faculdade de Medicina (FMUSP), Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratório Clínico, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | | | - Jennifer M Bain
- Department of Neurology, Division of Child Neurology, Columbia University Irving Medical Center, New York, USA
| | - Kwame Anyane-Yeboa
- Department of Pediatrics, Division of Clinical Genetics, Columbia University Irving Medical Center, New York, USA
| | - Kaitlyn Brown
- Departments of Pediatrics and Genetics, Albert Einstein College of Medicine, Bronx, NY USA
| | - John M Greally
- Departments of Pediatrics and Genetics, Albert Einstein College of Medicine, Bronx, NY USA
- Departments of Genetics, Albert Einstein College of Medicine, Bronx, NY USA
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, PO box 9600, 2300 RC, Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Centre, PO box 9600, 2300 RC, Leiden, The Netherlands
| | | | - Lydia A Arbogast
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | - Michael W Collard
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | - Jodi I Huggenvik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA
| | - Philip J Jensik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL USA
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3
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Wu L, Huang J, Trivedi P, Sun X, Yu H, He Z, Zhang X. Zinc finger myeloid Nervy DEAF-1 type (ZMYND) domain containing proteins exert molecular interactions to implicate in carcinogenesis. Discov Oncol 2022; 13:139. [PMID: 36520265 PMCID: PMC9755447 DOI: 10.1007/s12672-022-00597-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Morphogenesis and organogenesis in the low organisms have been found to be modulated by a number of proteins, and one of such factor, deformed epidermal auto-regulatory factor-1 (DEAF-1) has been initially identified in Drosophila. The mammalian homologue of DEAF-1 and structurally related proteins have been identified, and they formed a family with over 20 members. The factors regulate gene expression through association with co-repressors, recognition of genomic marker, to exert histone modification by catalyze addition of some chemical groups to certain amino acid residues on histone and non-histone proteins, and degradation host proteins, so as to regulate cell cycle progression and execution of cell death. The formation of fused genes during chromosomal translocation, exemplified with myeloid transforming gene on chromosome 8 (MTG8)/eight-to-twenty one translocation (ETO) /ZMYND2, MTG receptor 1 (MTGR1)/ZMYND3, MTG on chromosome 16/MTGR2/ZMYND4 and BS69/ZMYND11 contributes to malignant transformation. Other anomaly like copy number variation (CNV) of BS69/ZMYND11 and promoter hyper methylation of BLU/ZMYND10 has been noted in malignancies. It has been reported that when fusing with Runt-related transcription factor 1 (RUNX1), the binding of MTG8/ZMYND2 with co-repressors is disturbed, and silencing of BLU/ZMYND10 abrogates its ability to inhibition of cell cycle and promotion of apoptotic death. Further characterization of the implication of ZMYND proteins in carcinogenesis would enhance understanding of the mechanisms of occurrence and early diagnosis of tumors, and effective antitumor efficacy.
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Affiliation(s)
- Longji Wu
- Department of Pathophysiology, School of Basic Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Songshan Lake Scientific and Industrial Park, Dongguan, 523808, Guangdong, People's Republic of China
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
- Institute of Modern Biology, Nanjing University, Nanjing, Jiangsu, China
| | - Jing Huang
- Department of Pathophysiology, School of Basic Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Songshan Lake Scientific and Industrial Park, Dongguan, 523808, Guangdong, People's Republic of China
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
| | - Pankaj Trivedi
- Department of Experimental Medicine, La Sapienza University, Rome, Italy
| | - Xuerong Sun
- Institute of Aging, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
| | - Hongbing Yu
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
| | - Zhiwei He
- Department of Pathophysiology, School of Basic Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Songshan Lake Scientific and Industrial Park, Dongguan, 523808, Guangdong, People's Republic of China
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China
| | - Xiangning Zhang
- Department of Pathophysiology, School of Basic Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Songshan Lake Scientific and Industrial Park, Dongguan, 523808, Guangdong, People's Republic of China.
- Chinese-American Tumor Institute, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, People's Republic of China.
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Abbasi S, Schild-Poulter C. Identification of Ku70 Domain-Specific Interactors Using BioID2. Cells 2021; 10:cells10030646. [PMID: 33799447 PMCID: PMC8001828 DOI: 10.3390/cells10030646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 11/23/2022] Open
Abstract
Since its inception, proximity-dependent biotin identification (BioID), an in vivo biochemical screening method to identify proximal protein interactors, has seen extensive developments. Improvements and variants of the original BioID technique are being reported regularly, each expanding upon the existing potential of the original technique. While this is advancing our capabilities to study protein interactions under different contexts, we have yet to explore the full potential of the existing BioID variants already at our disposal. Here, we used BioID2 in an innovative manner to identify and map domain-specific protein interactions for the human Ku70 protein. Four HEK293 cell lines were created, each stably expressing various BioID2-tagged Ku70 segments designed to collectively identify factors that interact with different regions of Ku70. Historically, although many interactions have been mapped to the C-terminus of the Ku70 protein, few have been mapped to the N-terminal von Willebrand A-like domain, a canonical protein-binding domain ideally situated as a site for protein interaction. Using this segmented approach, we were able to identify domain-specific interactors as well as evaluate advantages and drawbacks of the BioID2 technique. Our study identifies several potential new Ku70 interactors and validates RNF113A and Spindly as proteins that contact or co-localize with Ku in a Ku70 vWA domain-specific manner.
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5
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Exome sequencing identifies de novo splicing variant in XRCC6 in sporadic case of autism. J Hum Genet 2019; 65:287-296. [PMID: 31827253 DOI: 10.1038/s10038-019-0707-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/27/2019] [Accepted: 12/01/2019] [Indexed: 02/06/2023]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with heterogeneity in presentation, genetic etiology, and clinical outcome. Although numerous ASD susceptibility genes have been described, they only account for a small fraction of the estimated heritability, supporting the need to identify more risk variants. This study reports the whole exome sequencing for 24 simplex families with sporadic cases of ASD. These families were selected following a rigorous family history study designed to exclude families with any history of neurodevelopmental or psychiatric disease. Fifteen rare, de novo variants, including fourteen missense variants and one splicing variant, in thirteen families were identified. We describe a splicing variant in XRCC6 which was predicted to destroy the 5' splice site in intron 9 and introduce a premature stop codon. We observed intron 9 retention in XRCC6 transcripts and reduced XRCC6 expression in the proband. Reduced XRCC6 activity and function may be relevant to ASD etiology due to XRCC6's role in nonhomologous DNA repair and interactions of the C-terminal SAP domain with DEAF1, a nuclear transcriptional regulator that is important during embryonic development.
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6
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Nabais Sá MJ, Jensik PJ, McGee SR, Parker MJ, Lahiri N, McNeil EP, Kroes HY, Hagerman RJ, Harrison RE, Montgomery T, Splitt M, Palmer EE, Sachdev RK, Mefford HC, Scott AA, Martinez-Agosto JA, Lorenz R, Orenstein N, Berg JN, Amiel J, Heron D, Keren B, Cobben JM, Menke LA, Marco EJ, Graham JM, Pierson TM, Karimiani EG, Maroofian R, Manzini MC, Cauley ES, Colombo R, Odent S, Dubourg C, Phornphutkul C, de Brouwer APM, de Vries BBA, Vulto-vanSilfhout AT. De novo and biallelic DEAF1 variants cause a phenotypic spectrum. Genet Med 2019; 21:2059-2069. [PMID: 30923367 DOI: 10.1038/s41436-019-0473-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/15/2019] [Indexed: 01/24/2023] Open
Abstract
PURPOSE To investigate the effect of different DEAF1 variants on the phenotype of patients with autosomal dominant and recessive inheritance patterns and on DEAF1 activity in vitro. METHODS We assembled a cohort of 23 patients with de novo and biallelic DEAF1 variants, described the genotype-phenotype correlation, and investigated the differential effect of de novo and recessive variants on transcription assays using DEAF1 and Eif4g3 promoter luciferase constructs. RESULTS The proportion of the most prevalent phenotypic features, including intellectual disability, speech delay, motor delay, autism, sleep disturbances, and a high pain threshold, were not significantly different in patients with biallelic and pathogenic de novo DEAF1 variants. However, microcephaly was exclusively observed in patients with recessive variants (p < 0.0001). CONCLUSION We propose that different variants in the DEAF1 gene result in a phenotypic spectrum centered around neurodevelopmental delay. While a pathogenic de novo dominant variant would also incapacitate the product of the wild-type allele and result in a dominant-negative effect, a combination of two recessive variants would result in a partial loss of function. Because the clinical picture can be nonspecific, detailed phenotype information, segregation, and functional analysis are fundamental to determine the pathogenicity of novel variants and to improve the care of these patients.
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Affiliation(s)
- Maria J Nabais Sá
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Philip J Jensik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Stacey R McGee
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Michael J Parker
- Sheffield Clinical Genetics Service, OPD2 Northern General Hospital, Sheffield, UK
| | - Nayana Lahiri
- Department of Clinical Genetics, St George's University Hospitals NHS Foundation Trust & St George's, University of London, London, UK
| | - Evan P McNeil
- Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Hester Y Kroes
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Randi J Hagerman
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis School of Medicine, Sacramento, Sacramento, CA, USA.,Department of Pediatrics, University of California Davis Medical Center, Sacramento, Sacramento, CA, USA
| | - Rachel E Harrison
- Department of Clinical Genetics, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Tara Montgomery
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Miranda Splitt
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Elizabeth E Palmer
- Sydney Children's Hospital, Randwick, NSW, Australia.,School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, Sydney, NSW, Australia
| | - Rani K Sachdev
- Sydney Children's Hospital, Randwick, NSW, Australia.,School of Women's and Children's Health, UNSW Medicine, The University of New South Wales, Sydney, NSW, Australia
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington-Seattle, Seattle, WA, USA
| | - Abbey A Scott
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | | | - Naama Orenstein
- Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jonathan N Berg
- Department of Clinical Genetics, Ninewells Hospital and Medical School, Dundee, Angus, UK.,Clinical Genetics, University of Dundee, Dundee, Angus, UK
| | - Jeanne Amiel
- Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique, INSERM UMR 1163, Institut Imagine, Paris, France
| | - Delphine Heron
- Département de Génétique, Hôpital Pitié-Salpêtrière, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Boris Keren
- Département de Génétique, Hôpital Pitié-Salpêtrière, Assistance publique-Hôpitaux de Paris, Paris, France
| | - Jan-Maarten Cobben
- Department of Pediatrics, Amsterdam University Medical Centers, Amsterdam, The Netherlands.,North West Thames Genetics NHS, Northwick Park Hospital, London, UK
| | - Leonie A Menke
- Department of Pediatrics, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Elysa J Marco
- Department of Child Neurology, Cortica Healthcare, San Rafael, CA, USA
| | - John M Graham
- Division of Clinical Genetics and Dysmorphology, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tyler Mark Pierson
- Department of Pediatrics, Department of Neurology, and the Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ehsan Ghayoor Karimiani
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's, University of London, London, UK
| | - Reza Maroofian
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's, University of London, London, UK
| | - M Chiara Manzini
- GW Institute for Neuroscience, Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Edmund S Cauley
- GW Institute for Neuroscience, Department of Pharmacology and Physiology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Roberto Colombo
- Faculty of Medicine"Agostino Gemelli"Catholic University of the Sacred Heart, Rome, Italy.,Center for the Study of Rare Inherited Diseases (CeSMER), Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy
| | - Sylvie Odent
- Service de Génétique Clinique, CLAD-Ouest CHU Rennes, Univ Rennes, CNRS 6290 Institut de Génétique et Développement de Rennes (IGDR), Rennes, France
| | | | - Chanika Phornphutkul
- Division of Human Genetics, Department of Pediatrics, Hasbro Children's Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
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Chen L, Jensik PJ, Alaimo JT, Walkiewicz M, Berger S, Roeder E, Faqeih EA, Bernstein JA, Smith ACM, Mullegama SV, Saffen DW, Elsea SH. Functional analysis of novel DEAF1 variants identified through clinical exome sequencing expands DEAF1-associated neurodevelopmental disorder (DAND) phenotype. Hum Mutat 2017; 38:1774-1785. [PMID: 28940898 PMCID: PMC5679464 DOI: 10.1002/humu.23339] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 08/30/2017] [Accepted: 09/05/2017] [Indexed: 11/06/2022]
Abstract
Deformed epidermal autoregulatory factor-1 (DEAF1), a transcription factor essential for central nervous system and early embryonic development, has recently been implicated in a series of intellectual disability-related neurodevelopmental anomalies termed, in this study, as DEAF1-associated neurodevelopmental disorder (DAND). We identified six potentially deleterious DEAF1 variants in a cohort of individuals with DAND via clinical exome sequencing (CES) and in silico analysis, including two novel de novo variants: missense variant c.634G > A p.Gly212Ser in the SAND domain and deletion variant c.913_915del p.Lys305del in the NLS domain, as well as c.676C > T p.Arg226Trp, c.700T > A p.Trp234Arg, c.737G > C p.Arg246Thr, and c.791A > C p.Gln264Pro. Luciferase reporter, immunofluorescence staining, and electrophoretic mobility shift assays revealed that these variants had decreased transcriptional repression activity at the DEAF1 promoter and reduced affinity to consensus DEAF1 DNA binding sequences. In addition, c.913_915del p.K305del localized primarily to the cytoplasm and interacted with wild-type DEAF1. Our results demonstrate that variants located within the SAND or NLS domains significantly reduce DEAF1 transcriptional regulatory activities and are thus, likely to contribute to the underlying clinical concerns in DAND patients. These findings illustrate the importance of experimental characterization of variants with uncertain significance identified by CES to assess their potential clinical significance and possible use in diagnosis.
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Affiliation(s)
- Li Chen
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Philip J. Jensik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Joseph T. Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
| | - Seth Berger
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Departments of Pediatrics, Baylor College of Medicine, San Antonio, TX, USA
| | - Eissa A. Faqeih
- Department of Pediatrics Subspecialty, Children’s Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | - Ann C. M. Smith
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sureni V. Mullegama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - David W. Saffen
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Institutes of Brain Science, Fudan University, Shanghai, China
- State Key Laboratory for Medical Neurobiology, Fudan University, Shanghai, China
| | - Sarah H. Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
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8
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Morris G, Walder K, Carvalho AF, Tye SJ, Lucas K, Berk M, Maes M. The role of hypernitrosylation in the pathogenesis and pathophysiology of neuroprogressive diseases. Neurosci Biobehav Rev 2017; 84:453-469. [PMID: 28789902 DOI: 10.1016/j.neubiorev.2017.07.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 07/02/2017] [Accepted: 07/31/2017] [Indexed: 12/12/2022]
Abstract
There is a wealth of data indicating that de novo protein S-nitrosylation in general and protein transnitrosylation in particular mediates the bulk of nitric oxide signalling. These processes enable redox sensing and facilitate homeostatic regulation of redox dependent protein signalling, function, stability and trafficking. Increased S-nitrosylation in an environment of increasing oxidative and nitrosative stress (O&NS) is initially a protective mechanism aimed at maintaining protein structure and function. When O&NS becomes severe, mechanisms governing denitrosylation and transnitrosylation break down leading to the pathological state referred to as hypernitrosylation (HN). Such a state has been implicated in the pathogenesis and pathophysiology of several neuropsychiatric and neurodegenerative diseases and we investigate its potential role in the development and maintenance of neuroprogressive disorders. In this paper, we propose a model whereby the hypernitrosylation of a range of functional proteins and enzymes lead to changes in activity which conspire to produce at least some of the core abnormalities contributing to the development and maintenance of pathology in these illnesses.
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Affiliation(s)
- Gerwyn Morris
- Tir Na Nog, Bryn Road seaside 87, Llanelli, SA152LW, Wales, United Kingdom
| | - Ken Walder
- Deakin University, The Centre for Molecular and Medical Research, School of Medicine, P.O. Box 291, Geelong, 3220, Australia
| | - André F Carvalho
- Department of Clinical Medicine and Translational Psychiatry Research Group, Faculty of Medicine, Federal University of Ceará, 60430-040, Fortaleza, CE, Brazil
| | - Susannah J Tye
- Deakin University, The Centre for Molecular and Medical Research, School of Medicine, P.O. Box 291, Geelong, 3220, Australia; Department of Clinical Medicine and Translational Psychiatry Research Group, Faculty of Medicine, Federal University of Ceará, 60430-040, Fortaleza, CE, Brazil; Deakin University, IMPACT Strategic Research Centre, School of Medicine, P.O. Box 281, Geelong, 3220, Australia; Orygen Youth Health Research Centre and the Centre of Youth Mental Health, The Florey Institute for Neuroscience and Mental Health and the Department of Psychiatry, University of Melbourne, Parkville, 3052, Australia
| | - Kurt Lucas
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, 55128 Mainz, Germany
| | - Michael Berk
- Deakin University, IMPACT Strategic Research Centre, School of Medicine, P.O. Box 281, Geelong, 3220, Australia; Orygen Youth Health Research Centre and the Centre of Youth Mental Health, The Florey Institute for Neuroscience and Mental Health and the Department of Psychiatry, University of Melbourne, Parkville, 3052, Australia.
| | - Michael Maes
- Deakin University, IMPACT Strategic Research Centre, School of Medicine, P.O. Box 281, Geelong, 3220, Australia; Department of Psychiatry, Chulalongkorn University, Faculty of Medicine, Bangkok, Thailand; Department of Psychiatry, Medical University of Plovdiv, Plovdiv, Bulgaria
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9
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Mullegama SV, Jensik P, Li C, Dorrani N, Kantarci S, Blumberg B, Grody WW, Strom SP. Coupling clinical exome sequencing with functional characterization studies to diagnose a patient with familial Mediterranean fever and MED13L haploinsufficiency syndromes. Clin Case Rep 2017; 5:833-840. [PMID: 28588821 PMCID: PMC5458005 DOI: 10.1002/ccr3.904] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/28/2017] [Accepted: 02/11/2017] [Indexed: 02/06/2023] Open
Abstract
Clinicians should consider that clinical exome sequencing provides the unique potential to disentangle complex phenotypes into multiple genetic etiologies. Further, functional studies on variants of uncertain significance are necessary to arrive at an accurate diagnosis for the patient.
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Affiliation(s)
- Sureni V Mullegama
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California
| | - Phillip Jensik
- Department of Physiology Southern Illinois University School of Medicine Carbondale Illinois
| | - Chen Li
- Department of Cellular and Genetic Medicine School of Basic Medical Sciences Fudan University Shanghai China
| | - Naghmeh Dorrani
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,Department of Human Genetics David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,Department of Pediatrics David Geffen School of Medicine University of California, Los Angeles Los Angeles California
| | | | - Sibel Kantarci
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California
| | | | - Wayne W Grody
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,Department of Human Genetics David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,Department of Pediatrics David Geffen School of Medicine University of California, Los Angeles Los Angeles California
| | - Samuel P Strom
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California
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10
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Jensik PJ, Vargas JD, Reardon SN, Rajamanickam S, Huggenvik JI, Collard MW. DEAF1 binds unmethylated and variably spaced CpG dinucleotide motifs. PLoS One 2014; 9:e115908. [PMID: 25531106 PMCID: PMC4274154 DOI: 10.1371/journal.pone.0115908] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/28/2014] [Indexed: 11/19/2022] Open
Abstract
DEAF1 is a transcriptional regulator associated with autoimmune and neurological disorders and is known to bind TTCG motifs. To further ascertain preferred DEAF1 DNA ligands, we screened a random oligonucleotide library containing an "anchored" CpG motif. We identified a binding consensus that generally conformed to a repeated TTCGGG motif, with the two invariant CpG dinucleotides separated by 6-11 nucleotides. Alteration of the consensus surrounding the dual CpG dinucleotides, or cytosine methylation of a single CpG half-site, eliminated DEAF1 binding. A sequence within the Htr1a promoter that resembles the binding consensus but contains a single CpG motif was confirmed to have low affinity binding with DEAF1. A DEAF1 binding consensus was identified in the EIF4G3 promoter and ChIP assay showed endogenous DEAF1 was bound to the region. We conclude that DEAF1 preferentially binds variably spaced and unmethylated CpG-containing half-sites when they occur within an appropriate consensus.
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Affiliation(s)
- Philip J. Jensik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
- * E-mail:
| | - Jesse D. Vargas
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
| | - Sara N. Reardon
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
| | - Shivakumar Rajamanickam
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
| | - Jodi I. Huggenvik
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
| | - Michael W. Collard
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois, United States of America
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11
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Vulto-van Silfhout AT, Rajamanickam S, Jensik PJ, Vergult S, de Rocker N, Newhall KJ, Raghavan R, Reardon SN, Jarrett K, McIntyre T, Bulinski J, Ownby SL, Huggenvik JI, McKnight GS, Rose GM, Cai X, Willaert A, Zweier C, Endele S, de Ligt J, van Bon BWM, Lugtenberg D, de Vries PF, Veltman JA, van Bokhoven H, Brunner HG, Rauch A, de Brouwer APM, Carvill GL, Hoischen A, Mefford HC, Eichler EE, Vissers LELM, Menten B, Collard MW, de Vries BBA. Mutations affecting the SAND domain of DEAF1 cause intellectual disability with severe speech impairment and behavioral problems. Am J Hum Genet 2014; 94:649-61. [PMID: 24726472 DOI: 10.1016/j.ajhg.2014.03.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/18/2014] [Indexed: 11/29/2022] Open
Abstract
Recently, we identified in two individuals with intellectual disability (ID) different de novo mutations in DEAF1, which encodes a transcription factor with an important role in embryonic development. To ascertain whether these mutations in DEAF1 are causative for the ID phenotype, we performed targeted resequencing of DEAF1 in an additional cohort of over 2,300 individuals with unexplained ID and identified two additional individuals with de novo mutations in this gene. All four individuals had severe ID with severely affected speech development, and three showed severe behavioral problems. DEAF1 is highly expressed in the CNS, especially during early embryonic development. All four mutations were missense mutations affecting the SAND domain of DEAF1. Altered DEAF1 harboring any of the four amino acid changes showed impaired transcriptional regulation of the DEAF1 promoter. Moreover, behavioral studies in mice with a conditional knockout of Deaf1 in the brain showed memory deficits and increased anxiety-like behavior. Our results demonstrate that mutations in DEAF1 cause ID and behavioral problems, most likely as a result of impaired transcriptional regulation by DEAF1.
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Affiliation(s)
| | - Shivakumar Rajamanickam
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Philip J Jensik
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University, Ghent 9000, Belgium
| | - Nina de Rocker
- Center for Medical Genetics, Ghent University, Ghent 9000, Belgium
| | - Kathryn J Newhall
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Ramya Raghavan
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Sara N Reardon
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Kelsey Jarrett
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Tara McIntyre
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Joseph Bulinski
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Stacy L Ownby
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Jodi I Huggenvik
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - G Stanley McKnight
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Gregory M Rose
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA; Department of Anatomy, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Xiang Cai
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Andy Willaert
- Center for Medical Genetics, Ghent University, Ghent 9000, Belgium
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Sabine Endele
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Joep de Ligt
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Bregje W M van Bon
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Dorien Lugtenberg
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Petra F de Vries
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Department of Cognitive Neurosciences, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8603 Schwerzenbach-Zurich, Switzerland; Neuroscience Center Zurich, University of Zurich, 8603 Schwerzenbach-Zurich, Switzerland; Zurich Center of Integrative Human Physiology, University of Zurich, 8603 Schwerzenbach-Zurich, Switzerland
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Department of Cognitive Neurosciences, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Gemma L Carvill
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent 9000, Belgium
| | - Michael W Collard
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
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