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Frankel E, Podder A, Sharifi M, Pillai R, Belnap N, Ramsey K, Dodson J, Venugopal P, Brzezinski M, Llaci L, Gerald B, Mills G, Sanchez-Castillo M, Balak CD, Szelinger S, Jepsen WM, Siniard AL, Richholt R, Naymik M, Schrauwen I, Craig DW, Piras IS, Huentelman MJ, Schork NJ, Narayanan V, Rangasamy S. Genetic and Protein Network Underlying the Convergence of Rett-Syndrome-like (RTT-L) Phenotype in Neurodevelopmental Disorders. Cells 2023; 12:1437. [PMID: 37408271 DOI: 10.3390/cells12101437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/20/2023] [Accepted: 04/29/2023] [Indexed: 07/07/2023] Open
Abstract
Mutations of the X-linked gene encoding methyl-CpG-binding protein 2 (MECP2) cause classical forms of Rett syndrome (RTT) in girls. A subset of patients who are recognized to have an overlapping neurological phenotype with RTT but are lacking a mutation in a gene that causes classical or atypical RTT can be described as having a 'Rett-syndrome-like phenotype (RTT-L). Here, we report eight patients from our cohort diagnosed as having RTT-L who carry mutations in genes unrelated to RTT. We annotated the list of genes associated with RTT-L from our patient cohort, considered them in the light of peer-reviewed articles on the genetics of RTT-L, and constructed an integrated protein-protein interaction network (PPIN) consisting of 2871 interactions connecting 2192 neighboring proteins among RTT- and RTT-L-associated genes. Functional enrichment analysis of RTT and RTT-L genes identified a number of intuitive biological processes. We also identified transcription factors (TFs) whose binding sites are common across the set of RTT and RTT-L genes and appear as important regulatory motifs for them. Investigation of the most significant over-represented pathway analysis suggests that HDAC1 and CHD4 likely play a central role in the interactome between RTT and RTT-L genes.
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Affiliation(s)
- Eric Frankel
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Avijit Podder
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Megan Sharifi
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Roshan Pillai
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Newell Belnap
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Julius Dodson
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Pooja Venugopal
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Molly Brzezinski
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Lorida Llaci
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Brittany Gerald
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Gabrielle Mills
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Meredith Sanchez-Castillo
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Chris D Balak
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Szabolcs Szelinger
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Wayne M Jepsen
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Ashley L Siniard
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Ryan Richholt
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Marcus Naymik
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Department of Neurology, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY 10032, USA
| | - David W Craig
- Department of Translational Genomics, University of Southern California, Los Angeles, CA 90033, USA
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Nicholas J Schork
- Quantitative Medicine Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Vinodh Narayanan
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Sampathkumar Rangasamy
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
- Center for Rare Childhood Disorders (C4RCD), Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
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JoJo Yang QZ, Porter BE, Axeen ET. GNAO1-related neurodevelopmental disorder: Literature review and caregiver survey. Epilepsy Behav Rep 2022; 21:100582. [PMID: 36654732 PMCID: PMC9841045 DOI: 10.1016/j.ebr.2022.100582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/01/2023] Open
Abstract
Background GNAO1-related neurodevelopmental disorder is a heterogeneous condition characterized by hypotonia, developmental delay, epilepsy, and movement disorder. This study aims to better understand the spectrum of epilepsy associated with GNAO1 variants and experience with anti-seizure medications, and to review published epilepsy phenotypes in GNAO1. Methods An online survey was distributed to caregivers of individuals diagnosed with GNAO1 pathogenic variants, and a literature review was conducted. Results Fifteen respondents completed the survey with the median age of 39 months, including a novel variant p.Q52P. Nine had epilepsy - six had onset in the first week of life, three in the first year of life - but two reported no ongoing seizures. Seizure types varied. Individuals were taking a median of 3 seizure medications without a single best treatment. Our cohort was compared to a literature review of epilepsy in GNAO1. In 86 cases, 38 discrete variants were described; epilepsy is reported in 53 % cases, and a developmental and epileptic encephalopathy in 36 %. Conclusions While GNAO1-related epilepsy is most often early-onset and severe, seizures may not always be drug resistant or lifelong. Experience with anti-seizure medications is varied. Certain variant "hotspots" may correlate with epilepsy phenotype though genotype-phenotype correlation is poorly understood.
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Affiliation(s)
- Qian-Zhou JoJo Yang
- Division of Child Neurology, Department of Neurology, University of North Carolina, Chapel Hill, NC, United States,Corresponding author at: 170 Manning Dr, Campus Box 7025, Chapel Hill, NC 27599, United States
| | - Brenda E Porter
- Division of Child Neurology, Department of Neurology, Stanford University, Palo Alto, CA, United States
| | - Erika T Axeen
- Division of Pediatric Neurology, Department of Neurology, University of Virginia, United States
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Akamine S, Okuzono S, Yamamoto H, Setoyama D, Sagata N, Ohgidani M, Kato TA, Ishitani T, Kato H, Masuda K, Matsushita Y, Ono H, Ishizaki Y, Sanefuji M, Saitsu H, Matsumoto N, Kang D, Kanba S, Nakabeppu Y, Sakai Y, Ohga S. GNAO1 organizes the cytoskeletal remodeling and firing of developing neurons. FASEB J 2020; 34:16601-16621. [PMID: 33107105 DOI: 10.1096/fj.202001113r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 09/03/2020] [Accepted: 10/13/2020] [Indexed: 01/03/2023]
Abstract
Developmental and epileptic encephalopathy (DEE) represents a group of neurodevelopmental disorders characterized by infantile-onset intractable seizures and unfavorable prognosis of psychomotor development. To date, hundreds of genes have been linked to the onset of DEE. GNAO1 is a DEE-associated gene encoding the alpha-O1 subunit of guanine nucleotide-binding protein (GαO ). Despite the increasing number of reported children with GNAO1 encephalopathy, the molecular mechanisms underlying their neurodevelopmental phenotypes remain elusive. We herein present that co-immunoprecipitation and mass spectrometry analyses identified another DEE-associated protein, SPTAN1, as an interacting partner of GαO . Silencing of endogenous Gnao1 attenuated the neurite outgrowth and calcium-dependent signaling. Inactivation of GNAO1 in human-induced pluripotent stem cells gave rise to anomalous brain organoids that only weakly expressed SPTAN1 and Ankyrin-G. Furthermore, GNAO1-deficient organoids failed to conduct synchronized firing to adjacent neurons. These data indicate that GαO and other DEE-associated proteins organize the cytoskeletal remodeling and functional polarity of neurons in the developing brain.
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Affiliation(s)
- Satoshi Akamine
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Sayaka Okuzono
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Yamamoto
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Daiki Setoyama
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Noriaki Sagata
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahiro Ohgidani
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takahiro A Kato
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tohru Ishitani
- Division of Integrated Signaling Systems, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan.,Department of Homeostatic Regulation, Division of Cellular and Molecular Biology. Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hiroki Kato
- Division of Oral Biological Sciences, Department of Molecular Cell Biology and Oral Anatomy, Graduate School of Dental Science, Kyushu University, Fukuoka, Japan
| | - Keiji Masuda
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Yuki Matsushita
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroaki Ono
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshito Ishizaki
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masafumi Sanefuji
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shigenobu Kanba
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yusaku Nakabeppu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yasunari Sakai
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shouichi Ohga
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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Customized multigene panels in epilepsy: the best things come in small packages. Neurogenetics 2019; 21:1-18. [PMID: 31834528 DOI: 10.1007/s10048-019-00598-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/12/2019] [Indexed: 12/13/2022]
Abstract
Over the past 10 years, the increasingly important role played by next-generation sequencing panels in the genetic diagnosis of epilepsy has led to a growing list of gene variants and a plethora of new scientific data. To date, however, there is still no consensus on what constitutes the "ideal panel design," or on the most rational criteria for selecting the best candidates for gene-panel analysis, even though both might optimize the cost-benefit ratio and the diagnostic efficiency of customized gene panels. Even though more and more laboratories are adopting whole-exome sequencing as a first-tier diagnostic approach, interpreting, "in silico," a set of epilepsy-related genes remains difficult. In the light of these considerations, we performed a systematic review of the targeted gene panels for epilepsy already reported in the available scientific literature, with a view to identifying the best criteria for selecting patients for gene-panel analysis, and the best way to design an "ideal," gold-standard panel that includes all genes with an established role in epilepsy pathogenesis, as well as those that might help to guide decisions regarding specific medical interventions and treatments. Our analyses suggest that the usefulness and diagnostic power of customized gene panels for epilepsy may be greatest when these panels are confined to rationally selected, relatively small, pools of genes, and applied in more carefully selected epilepsy patients (those with complex forms of epilepsy). A panel containing 64 genes, which includes the 45 genes harboring a significant number of pathogenic variants identified in previous literature, the 32 clinically actionable genes, and the 21 ILAE (International League Against Epilepsy) recommended genes, may represent an "ideal" core set likely able to provide the highest diagnostic efficiency and cost-effectiveness and facilitate gene prioritization when testing patients with whole-exome/whole-genome sequencing.
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Bernstein U, Demuth S, Puk O, Eichhorn B, Schulz S. Novel MECP2 Mutation c.1162_1172del; p.Pro388* in Two Patients with Symptoms of Atypical Rett Syndrome. Mol Syndromol 2019; 10:223-228. [PMID: 31602196 DOI: 10.1159/000501183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2019] [Indexed: 01/19/2023] Open
Abstract
We report 2 cases of girls with MECP2 gene variants who do not have typical clinical features of Rett syndrome except for intellectual disability and seizures. Both patients present with adipositas, macrocephalia, precocious puberty, and seizures. They have prominent eyebrows and a short neck as well as short and plump fingers. Sequencing by NGS revealed a novel variant c.1162_1172del; p.Pro388* in both patients.
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Affiliation(s)
- Ulrike Bernstein
- Center of Human Genetics, Jena University Hospital, Jena, Germany
| | | | | | | | - Solveig Schulz
- Center of Human Genetics, Jena University Hospital, Jena, Germany
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Proteomic Advances in Glial Tumors through Mass Spectrometry Approaches. ACTA ACUST UNITED AC 2019; 55:medicina55080412. [PMID: 31357616 PMCID: PMC6722920 DOI: 10.3390/medicina55080412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 01/25/2023]
Abstract
Being the fourth leading cause of cancer-related death, glial tumors are highly diverse tumor entities characterized by important heterogeneity regarding tumor malignancy and prognosis. However, despite the identification of important alterations in the genome of the glial tumors, there remains a gap in understanding the mechanisms involved in glioma malignancy. Previous research focused on decoding the genomic alterations in these tumors, but due to intricate cellular mechanisms, the genomic findings do not correlate with the functional proteins expressed at the cellular level. The development of mass spectrometry (MS) based proteomics allowed researchers to study proteins expressed at the cellular level or in serum that may provide new insights on the proteins involved in the proliferation, invasiveness, metastasis and resistance to therapy in glial tumors. The integration of data provided by genomic and proteomic approaches into clinical practice could allow for the identification of new predictive, diagnostic and prognostic biomarkers that will improve the clinical management of patients with glial tumors. This paper aims to provide an updated review of the recent proteomic findings, possible clinical applications, and future research perspectives in diffuse astrocytic and oligodendroglial tumors, pilocytic astrocytomas, and ependymomas.
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Smith HS, Swint JM, Lalani SR, Yamal JM, de Oliveira Otto MC, Castellanos S, Taylor A, Lee BH, Russell HV. Clinical Application of Genome and Exome Sequencing as a Diagnostic Tool for Pediatric Patients: a Scoping Review of the Literature. Genet Med 2018; 21:3-16. [PMID: 29760485 DOI: 10.1038/s41436-018-0024-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/20/2018] [Indexed: 12/17/2022] Open
Abstract
PURPOSE Availability of clinical genomic sequencing (CGS) has generated questions about the value of genome and exome sequencing as a diagnostic tool. Analysis of reported CGS application can inform uptake and direct further research. This scoping literature review aims to synthesize evidence on the clinical and economic impact of CGS. METHODS PubMed, Embase, and Cochrane were searched for peer-reviewed articles published between 2009 and 2017 on diagnostic CGS for infant and pediatric patients. Articles were classified according to sample size and whether economic evaluation was a primary research objective. Data on patient characteristics, clinical setting, and outcomes were extracted and narratively synthesized. RESULTS Of 171 included articles, 131 were case reports, 40 were aggregate analyses, and 4 had a primary economic evaluation aim. Diagnostic yield was the only consistently reported outcome. Median diagnostic yield in aggregate analyses was 33.2% but varied by broad clinical categories and test type. CONCLUSION Reported CGS use has rapidly increased and spans diverse clinical settings and patient phenotypes. Economic evaluations support the cost-saving potential of diagnostic CGS. Multidisciplinary implementation research, including more robust outcome measurement and economic evaluation, is needed to demonstrate clinical utility and cost-effectiveness of CGS.
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Affiliation(s)
- Hadley Stevens Smith
- Baylor College of Medicine, The University of Texas School of Public Health, Houston, Texas, USA
| | - J Michael Swint
- The University of Texas School of Public Health, The Center for Clinical Research and Evidence-Based Medicine, The University of Texas McGovern Medical School, Houston, Texas, USA
| | - Seema R Lalani
- Baylor College of Medicine, Baylor Genetics Laboratory, Houston, Texas, USA
| | - Jose-Miguel Yamal
- The University of Texas School of Public Health, Houston, Texas, USA
| | | | | | - Amy Taylor
- Texas Medical Center Library, Houston, Texas, USA
| | | | - Heidi V Russell
- Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, USA
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