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Shambetova C, Klein C. Genetic testing for non-parkinsonian movement disorders: Navigating the diagnostic maze. Parkinsonism Relat Disord 2024; 121:106033. [PMID: 38429185 DOI: 10.1016/j.parkreldis.2024.106033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 03/03/2024]
Abstract
Genetic testing has become a valuable diagnostic tool for movement disorders due to substantial advancements in understanding their genetic basis. However, the heterogeneity of movement disorders poses a significant challenge, with many genes implicated in different subtypes. This paper aims to provide a neurologist's perspective on approaching patients with hereditary hyperkinetic disorders with a focus on select forms of dystonia, paroxysmal dyskinesia, chorea, and ataxia. Age at onset, initial symptoms, and their severity, as well as the presence of any concurrent neurological and non-neurological features, contribute to the individual clinical profiles of hereditary non-parkinsonian movement disorders, aiding in the selection of appropriate genetic testing strategies. There are also more specific diagnostic clues that may facilitate the decision-making process and may be highly specific for certain conditions, such as diurnal fluctuations and l-dopa response in dopa-responsive dystonia, and triggering factors, duration and frequency of attacks in paroxysmal dyskinesia. While the genetic and mutational spectrum across non-parkinsonian movement disorders is broad, certain groups of diseases tend to be associated with specific types of pathogenic variants, such as repeat expansions in many of the ataxias. Some of these pathogenic variants cannot be detected by standard methods, such as panel or exome sequencing, but require the investigation of intronic regions for repeat expansions, such as Friedreich's or FGF14-linked ataxia. With our advancing knowledge of the genetic underpinnings of movement disorders, the incorporation of precise and personalized diagnostic strategies can enhance patient care, prognosis, and the application and development of targeted therapeutic interventions.
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Affiliation(s)
- Cholpon Shambetova
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany; Center for Continuing and Distance Learning, I. K. Akhunbaev Kyrgyz State Medical Academy, Bishkek, Kyrgyzstan
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.
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2
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Keller NA, Bracero LA, Kouba I, Steinberg A, Muscat J, Bergman D. Novel characterization of CASK variant c.1963 A>G (p.Asn655Asp) through whole-exome sequencing in a monochorionic diamniotic twin fetus with significant brain anomalies: A case report. Case Rep Womens Health 2024; 41:e00583. [PMID: 38440102 PMCID: PMC10910124 DOI: 10.1016/j.crwh.2024.e00583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 03/06/2024] Open
Abstract
Whole-exome sequencing is an evolving technology in perinatal diagnosis which allows identification of genetic etiologies that would otherwise go undetermined. In this case report, a 38-year-old Hispanic woman, G5P3013, with a monochorionic diamniotic twin gestation with one fetus displaying significant cranial abnormalities on prenatal ultrasound and magnetic resonance imaging (MRI) of the brain is presented. Fetal anomalies included bilateral ventriculomegaly, absent cavum septum pellucidum, and absent corpus callosum. Diagnostic amniocentesis with chromosome analysis, chromosomal microarray, alpha-fetoprotein, cytomegalovirus, toxoplasmosis, and parvovirus had normal results. Whole-exome sequencing for the anomalous fetus detected a de novo mosaic variant of uncertain significance (VUS) in the calcium/calmodulin dependent serine protein kinase (CASK) gene: c.1963 A > G (p.Asn655Asp). This variant was absent in the normal twin fetus, the mother, and the father. Pathogenic CASK gene mutations are associated with three syndromes: FG syndrome 4, intellectual developmental disorder and microcephaly with pontine and cerebellar hypoplasia (MICPCH), and intellectual developmental disorder with or without nystagmus. Whole-exome sequencing identified a potential etiology for the anomalies detected. The variant likely arose de novo and was the potential cause of the identified cranial abnormalities in one fetus of this monochorionic diamniotic twin gestation. Whole-exome sequencing may provide additional diagnostic utility when standard diagnostic testing is noncontributory.
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Affiliation(s)
- Nathan A. Keller
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 376 East Main Street, Suite 202, Bay Shore, New York 11706, United States of America
| | - Luis A. Bracero
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 376 East Main Street, Suite 202, Bay Shore, New York 11706, United States of America
| | - Insaf Kouba
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 376 East Main Street, Suite 202, Bay Shore, New York 11706, United States of America
| | - Abigail Steinberg
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 376 East Main Street, Suite 202, Bay Shore, New York 11706, United States of America
| | - Jolene Muscat
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 376 East Main Street, Suite 202, Bay Shore, New York 11706, United States of America
| | - David Bergman
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 376 East Main Street, Suite 202, Bay Shore, New York 11706, United States of America
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3
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Lopes-Marques M, Mort M, Carneiro J, Azevedo A, Amaro AP, Cooper DN, Azevedo L. Meta-analysis of 46,000 germline de novo mutations linked to human inherited disease. Hum Genomics 2024; 18:20. [PMID: 38395944 PMCID: PMC10885371 DOI: 10.1186/s40246-024-00587-8] [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: 11/10/2023] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND De novo mutations (DNMs) are variants that occur anew in the offspring of noncarrier parents. They are not inherited from either parent but rather result from endogenous mutational processes involving errors of DNA repair/replication. These spontaneous errors play a significant role in the causation of genetic disorders, and their importance in the context of molecular diagnostic medicine has become steadily more apparent as more DNMs have been reported in the literature. In this study, we examined 46,489 disease-associated DNMs annotated by the Human Gene Mutation Database (HGMD) to ascertain their distribution across gene and disease categories. RESULTS Most disease-associated DNMs reported to date are found to be associated with developmental and psychiatric disorders, a reflection of the focus of sequencing efforts over the last decade. Of the 13,277 human genes in which DNMs have so far been found, the top-10 genes with the highest proportions of DNM relative to gene size were H3-3 A, DDX3X, CSNK2B, PURA, ZC4H2, STXBP1, SCN1A, SATB2, H3-3B and TUBA1A. The distribution of CADD and REVEL scores for both disease-associated DNMs and those mutations not reported to be de novo revealed a trend towards higher deleteriousness for DNMs, consistent with the likely lower selection pressure impacting them. This contrasts with the non-DNMs, which are presumed to have been subject to continuous negative selection over multiple generations. CONCLUSION This meta-analysis provides important information on the occurrence and distribution of disease-associated DNMs in association with heritable disease and should make a significant contribution to our understanding of this major type of mutation.
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Affiliation(s)
- Mónica Lopes-Marques
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - João Carneiro
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - António Azevedo
- CHUdSA-Centro Hospitalar Universitário de Santo António, Porto, Portugal
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - Andreia P Amaro
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Luísa Azevedo
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal.
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal.
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4
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Burke S. Hypoxia, NSAIDs, and autism: A biocultural analysis of stressors in gametogenesis. Am J Hum Biol 2024:e24042. [PMID: 38282542 DOI: 10.1002/ajhb.24042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/30/2024] Open
Abstract
Cultural and generational trends have increasingly favored "anti-inflammatory" action, innovating a new class of analgesic, non-steroidal anti-inflammatory drugs (NSAIDs) in the 20th century. The modern human body has been molded over evolutionary time and while acknowledging inflammation can be pathologically entwined, it also serves an important role in healthy folliculogenesis and ovulation, shaping cues that drive needed vascular change. This review argues that because of anti-inflammatory action, the cultural invention of NSAIDs represents a particular stressor on female reproductive-age bodies, interacting with natural, underlying variation and placing limits on healthy growth and development in the follicles, creating potential autism risk through hypoxia and mutagenic or epigenetic effects. Since testes are analogs to ovaries, the biological grounding extends naturally to spermatogenesis. This review suggests the introduction of over-the-counter NSAIDs in the 1980s failed to recognize the unique functioning of reproductive-age bodies, challenging the cyclical inflammation needed for healthy gamete development. NSAIDs are framed as one (notable) stressor in an anti-inflammatory era focused on taming the risks of inflammation in modern human life.
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Affiliation(s)
- Stacie Burke
- Department of Anthropology, University of Manitoba, Winnipeg, Manitoba, Canada
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5
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de Smith AJ, Spector LG. In Utero Origins of Acute Leukemia in Children. Biomedicines 2024; 12:236. [PMID: 38275407 PMCID: PMC10813074 DOI: 10.3390/biomedicines12010236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Acute leukemias, mainly consisting of acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML), comprise a major diagnostic group among hematologic cancers. Due to the early age at onset of ALL, particularly, it has long been suspected that acute leukemias of childhood may have an in utero origin. This supposition has motivated many investigations seeking direct proof of prenatal leukemogenesis, in particular, twin and "backtracking studies". The suspected in utero origin has also focused on gestation as a critical window of risk, resulting in a rich literature on prenatal risk factors for pediatric acute leukemias. In this narrative review, we recount the circumstantial and direct evidence for an in utero origin of childhood acute leukemias.
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Affiliation(s)
- Adam J. de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Logan G. Spector
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
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Vado Y, Manero-Azua A, Pereda A, Perez de Nanclares G. Choosing the Best Tissue and Technique to Detect Mosaicism in Fibrous Dysplasia/McCune-Albright Syndrome (FD/MAS). Genes (Basel) 2024; 15:120. [PMID: 38255009 PMCID: PMC10815810 DOI: 10.3390/genes15010120] [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: 12/15/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
GNAS-activating somatic mutations give rise to Fibrous Dysplasia/McCune-Albright syndrome (FD/MAS). The low specificity of extra-skeletal signs of MAS and the mosaic status of the mutations generate some difficulties for a proper diagnosis. We studied the clinical and molecular statuses of 40 patients referred with a clinical suspicion of FD/MAS to provide some clues. GNAS was sequenced using both Sanger and Next-Generation Sequencing (NGS). We were able to identify the pathogenic variants in 25% of the patients. Most of them were identified in the affected tissue, but not in blood. Additionally, NGS demonstrated the ability to detect more patients with mosaicism (8/34) than Sanger sequencing (4/39). Even if in some cases, the clinical information was not complete, we confirmed that, as in previous works, when the patients were young children with a single manifestation, such as hyperpigmented skin macules or precocious puberty, the molecular diagnosis was usually negative. In conclusion, as FD/MAS is caused by mosaic variants, it is essential to use sensitive techniques that allow for the detection of low percentages and to choose the right tissue to study. When not possible, and due to the low positive genetic rate, patients with FD/MAS should only be genetically tested when the clinical diagnosis is really uncertain.
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Affiliation(s)
| | | | | | - Guiomar Perez de Nanclares
- Rare Disease Research Group, Molecular (Epi) Genetics Laboratory, Bioaraba Health Research Institute, Araba University Hospital, 01009 Vitoria-Gasteiz, Spain; (Y.V.); (A.M.-A.); (A.P.)
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7
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Shimomura R, Yanagishita T, Ishiguro K, Shichiji M, Sato T, Shimojima Yamamoto K, Nagata M, Ishihara Y, Miyashita Y, Ishigaki K, Nagata S, Asano Y, Yamamoto T. Rare mosaic variant of GJA1 in a patient with a neurodevelopmental disorder. Hum Genome Var 2024; 11:2. [PMID: 38221519 PMCID: PMC10788341 DOI: 10.1038/s41439-023-00262-9] [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: 10/19/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/16/2024] Open
Abstract
GJA1 is the causative gene for oculodentodigital dysplasia (ODDD). A novel de novo GJA1 variant, NM 000165:c263C > T [p.P88L], was identified in a mosaic state in a patient with short stature, seizures, delayed myelination, mild hearing loss, and tooth enamel hypoplasia. Although the patient exhibited severe neurodevelopmental delay, other clinical features of ODDD, including limb anomalies, were mild. This may be due to differences in the mosaic ratios in different organs.
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Affiliation(s)
- Rina Shimomura
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan
| | - Tomoe Yanagishita
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Kumiko Ishiguro
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Minobu Shichiji
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Takatoshi Sato
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Keiko Shimojima Yamamoto
- Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Miho Nagata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yasuki Ishihara
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yohei Miyashita
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genomic Medicine, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Keiko Ishigaki
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Satoru Nagata
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Yoshihiro Asano
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genomic Medicine, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Toshiyuki Yamamoto
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan.
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8
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Poli MC, Rebolledo-Jaramillo B, Lagos C, Orellana J, Moreno G, Martín LM, Encina G, Böhme D, Faundes V, Zavala MJ, Hasbún T, Fischer S, Brito F, Araya D, Lira M, de la Cruz J, Astudillo C, Lay-Son G, Cares C, Aracena M, Martin ES, Coban-Akdemir Z, Posey JE, Lupski JR, Repetto GM. Decoding complex inherited phenotypes in rare disorders: the DECIPHERD initiative for rare undiagnosed diseases in Chile. Eur J Hum Genet 2024:10.1038/s41431-023-01523-5. [PMID: 38177409 DOI: 10.1038/s41431-023-01523-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/30/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
Rare diseases affect millions of people worldwide, and most have a genetic etiology. The incorporation of next-generation sequencing into clinical settings, particularly exome and genome sequencing, has resulted in an unprecedented improvement in diagnosis and discovery in the past decade. Nevertheless, these tools are unavailable in many countries, increasing health care gaps between high- and low-and-middle-income countries and prolonging the "diagnostic odyssey" for patients. To advance genomic diagnoses in a setting of limited genomic resources, we developed DECIPHERD, an undiagnosed diseases program in Chile. DECIPHERD was implemented in two phases: training and local development. The training phase relied on international collaboration with Baylor College of Medicine, and the local development was structured as a hybrid model, where clinical and bioinformatics analysis were performed in-house and sequencing outsourced abroad, due to lack of high-throughput equipment in Chile. We describe the implementation process and findings of the first 103 patients. They had heterogeneous phenotypes, including congenital anomalies, intellectual disabilities and/or immune system dysfunction. Patients underwent clinical exome or research exome sequencing, as solo cases or with parents using a trio design. We identified pathogenic, likely pathogenic or variants of unknown significance in genes related to the patients´ phenotypes in 47 (45.6%) of them. Half were de novo informative variants, and half of the identified variants have not been previously reported in public databases. DECIPHERD ended the diagnostic odyssey for many participants. This hybrid strategy may be useful for settings of similarly limited genomic resources and lead to discoveries in understudied populations.
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Affiliation(s)
- M Cecilia Poli
- Program for Immunogenetics and Translational Immunology, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clinica Alemana Universidad del Desarrollo, Santiago, Chile
- Hospital Dr. Roberto del Río, Santiago, Chile
| | - Boris Rebolledo-Jaramillo
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Catalina Lagos
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Joan Orellana
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Gabriela Moreno
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Luz M Martín
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
- Unidad de Gestión Clínica del Niño, Hospital Padre Hurtado, Santiago, Chile
| | | | - Daniela Böhme
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
- Biosoluciones UDD, Santiago, Chile
| | - Víctor Faundes
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | | | - Trinidad Hasbún
- Department of Dermatology, Facultad de Medicina Universidad del Desarrollo, Clínica Alemana de Santiago, Vitacura, Chile
- Department of Dermatology, Hospital Exequiel González Cortés, Vitacura, Chile
| | - Sara Fischer
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Florencia Brito
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Diego Araya
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Manuel Lira
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Javiera de la Cruz
- Program for Immunogenetics and Translational Immunology, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | | | - Guillermo Lay-Son
- Division of Pediatrics, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carolina Cares
- Genetics Unit, Hospital Dr Luis Calvo Mackenna, Santiago, Chile
| | - Mariana Aracena
- Genetics Unit, Hospital Dr Luis Calvo Mackenna, Santiago, Chile
| | | | - Zeynep Coban-Akdemir
- University of Texas Health Science Center at Houston, School of Public Health, Department of Epidemiology, Human Genetics and Environmental Sciences, Santiago, Chile
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Gabriela M Repetto
- Rare Diseases Program, Center for Genetics and Genomics, Institute of Science and Innovation in Medicine, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile.
- Unidad de Gestión Clínica del Niño, Hospital Padre Hurtado, Santiago, Chile.
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9
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Zolzaya S, Narumoto A, Katsuyama Y. Genomic variation in neurons. Dev Growth Differ 2024; 66:35-42. [PMID: 37855730 DOI: 10.1111/dgd.12898] [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: 06/04/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 10/20/2023]
Abstract
Neurons born during the fetal period have extreme longevity and survive until the death of the individual because the human brain has highly limited tissue regeneration. The brain is comprised of an enormous variety of neurons each exhibiting different morphological and physiological characteristics and recent studies have further reported variations in their genome including chromosomal abnormalities, copy number variations, and single nucleotide mutations. During the early stages of brain development, the increasing number of neurons generated at high speeds has been proposed to lead to chromosomal instability. Additionally, mutations in the neuronal genome can occur in the mature brain. This observed genomic mosaicism in the brain can be produced by multiple endogenous and environmental factors and careful analyses of these observed variations in the neuronal genome remain central for our understanding of the genetic basis of neurological disorders.
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Affiliation(s)
- Sunjidmaa Zolzaya
- Division of Neuroanatomy, Department of Anatomy, Shiga University of Medical Science, Otsu, Japan
| | - Ayano Narumoto
- Division of Neuroanatomy, Department of Anatomy, Shiga University of Medical Science, Otsu, Japan
| | - Yu Katsuyama
- Division of Neuroanatomy, Department of Anatomy, Shiga University of Medical Science, Otsu, Japan
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10
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Birnbaum R. Rediscovering tandem repeat variation in schizophrenia: challenges and opportunities. Transl Psychiatry 2023; 13:402. [PMID: 38123544 PMCID: PMC10733427 DOI: 10.1038/s41398-023-02689-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Tandem repeats (TRs) are prevalent throughout the genome, constituting at least 3% of the genome, and often highly polymorphic. The high mutation rate of TRs, which can be orders of magnitude higher than single-nucleotide polymorphisms and indels, indicates that they are likely to make significant contributions to phenotypic variation, yet their contribution to schizophrenia has been largely ignored by recent genome-wide association studies (GWAS). Tandem repeat expansions are already known causative factors for over 50 disorders, while common tandem repeat variation is increasingly being identified as significantly associated with complex disease and gene regulation. The current review summarizes key background concepts of tandem repeat variation as pertains to disease risk, elucidating their potential for schizophrenia association. An overview of next-generation sequencing-based methods that may be applied for TR genome-wide identification is provided, and some key methodological challenges in TR analyses are delineated.
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Affiliation(s)
- Rebecca Birnbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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11
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Peel A, Saini A, Deluao JC, McPherson NO. Sperm DNA damage: The possible link between obesity and male infertility, an update of the current literature. Andrology 2023; 11:1635-1652. [PMID: 36789664 DOI: 10.1111/andr.13409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/13/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023]
Abstract
Obesity prevalence worldwide is increasing significantly. Whilst maternal obesity has clear detrimental impacts on fertility, pregnancy and foetal outcomes, more recently there has been an increasing focus on the role of paternal obesity in human fertility. Recent meta-analyses have indicated that obesity in men negatively affects basic sperm parameters such as sperm count, concentration and motility, increases the incidence of infertility and reduces the chances of conception. Sperm DNA damage, typically characterised by DNA strand breaks and oxidation of DNA nucleotides, is a specialised marker of sperm quality that has been independently associated with recurrent miscarriage, reduced assisted reproduction success and increased mutational loads in subsequent offspring. Whilst, there are still conflicting data in humans as to the association of obesity in men with sperm DNA damage, evidence from rodent models is clear, indicating that male obesity increases sperm DNA damage. Human data are often conflicting because of the large heterogeneity amongst studies, the use of body mass index as the indicator of obesity and the methods used for detection of sperm DNA damage. Furthermore, comorbidities of obesity (i.e., heat stress, adipokines, insulin resistance, changes in lipids, hypogonadism and obstructive sleep apnoea) are also independently associated with increased sperm DNA damage that is not always modified in men with obesity, and as such may provide a causative link to the discrepancies amongst human studies. In this review, we provide an update on the literature regarding the associations between obesity in men and fertility, basic sperm parameters and sperm DNA damage. We further discuss potential reasons for the discrepancies in the literature and outline possible direct and indirect mechanisms of increased sperm DNA damage resulting from obesity. Finally, we summarise intergenerational obesity through the paternal linage and how sperm DNA damage may contribute to the transmission.
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Affiliation(s)
- Andrew Peel
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- Freemasons Centre for Male Health and Wellbeing, The University of Adelaide, Adelaide, South Australia, Australia
- Adelaide Health and Medical School, School of Biomedicine, Discipline of Reproduction and Development, The University of Adelaide, Adelaide, South Australia, Australia
| | - Anmol Saini
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- Adelaide Health and Medical School, School of Biomedicine, Discipline of Reproduction and Development, The University of Adelaide, Adelaide, South Australia, Australia
| | - Joshua C Deluao
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- Freemasons Centre for Male Health and Wellbeing, The University of Adelaide, Adelaide, South Australia, Australia
- Adelaide Health and Medical School, School of Biomedicine, Discipline of Reproduction and Development, The University of Adelaide, Adelaide, South Australia, Australia
| | - Nicole O McPherson
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- Freemasons Centre for Male Health and Wellbeing, The University of Adelaide, Adelaide, South Australia, Australia
- Adelaide Health and Medical School, School of Biomedicine, Discipline of Reproduction and Development, The University of Adelaide, Adelaide, South Australia, Australia
- Repromed IVF Adelaide, Dulwich, South Australia, Australia
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12
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Núñez-Núñez ME, Lona-Reyes JC, López-Barragán B, Cruz-Osorio RM, Gutiérrez-Zepeda BM, Quintero-Ramos A, Becerra-Loaiza DS. Case Report: Characterization of known (c.607G>C) and novel (c.416C>G) ELANE mutations in two Mexican families with congenital neutropenia. Front Immunol 2023; 14:1194262. [PMID: 37795094 PMCID: PMC10547563 DOI: 10.3389/fimmu.2023.1194262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/30/2023] [Indexed: 10/06/2023] Open
Abstract
The most common causes of congenital neutropenia are mutations in the ELANE (Elastase, Neutrophil Expressed) gene (19p13.3), mostly in exon 5 and the distal portion of exon 4, which result in different clinical phenotypes of neutropenia. Here, we report two pathogenic mutations in ELANE, namely, c.607G>C (p.Gly203Arg) and a novel variant c.416C>G (p.Pro139Arg), found in two Mexican families ascertained via patients with congenital neutropenia who responded positively to the granulocyte colony-stimulating factor (G-CSF) treatment. These findings highlight the usefulness of identifying variants in patients with inborn errors of immunity for early clinical management and the need to rule out mosaicism in noncarrier parents with more than one case in the family.
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Affiliation(s)
- María Enriqueta Núñez-Núñez
- Departamento de Alergia e Inmunología Clínica Pediátrica, Nuevo Hospital Civil de Guadalajara “Dr. Juan I. Menchaca”, Guadalajara, Mexico
| | - Juan Carlos Lona-Reyes
- Departamento de Infectología, Nuevo Hospital Civil de Guadalajara “Dr. Juan I. Menchaca”, Guadalajara, Mexico
- Clínicas de Pediatría, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Brenda López-Barragán
- Departamento de Pediatría, Nuevo Hospital Civil de Guadalajara “Dr. Juan I. Menchaca”, Guadalajara, Mexico
| | - Rosa Margarita Cruz-Osorio
- Clínicas de Pediatría, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Departamento de Hemato-Oncología Pediátrica, Nuevo Hospital Civil de Guadalajara “Dr. Juan I. Menchaca”, Guadalajara, Mexico
| | - Bricia Melissa Gutiérrez-Zepeda
- Laboratorio de Inmunología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Antonio Quintero-Ramos
- Laboratorio de Inmunología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Unidad de Investigación Biomédica 02, Hospital de Especialidades, Centro Médico Nacional de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico
| | - Denisse Stephania Becerra-Loaiza
- Laboratorio de Inmunología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
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13
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Ma Y, Duan X, Liu X, Fan D. Clinical and mutational spectrum of paediatric Charcot-Marie-Tooth disease in a large cohort of Chinese patients. Front Genet 2023; 14:1188361. [PMID: 37519884 PMCID: PMC10381926 DOI: 10.3389/fgene.2023.1188361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/03/2023] [Indexed: 08/01/2023] Open
Abstract
Background: Charcot-Marie-Tooth disease (CMT) is the most common inherited neurological disorder suffered in childhood. To date, the disease features have not been extensively characterized in the Chinese paediatric population. In this study, we aimed to analyse the clinical profiles and genetic distributions of a paediatric CMT cohort in China. Methods: A total of 181 paediatric CMT patients were enrolled. After preexcluding PMP22 duplication/deletion by multiplex ligation-dependent probe amplification (MLPA), Sanger sequencing, targeted next-generation sequencing (NGS) or whole-exome sequencing (WES) was performed to obtain a genetic diagnosis. Detailed information was collected to explore the spectrum of subtypes and genotype-phenotype correlations. Results: Pathogenic mutations were identified in 68% of patients in this study; with PMP22 duplication, MFN2 and GJB1 were the most frequent disease-causing genes. Of note, respect to the higher prevalence worldwide, CMT1A (18.2%) was relatively lower in our cohort. Besides, the mean age at onset (8.3 ± 5.7 years) was significantly older in our series. In genotype-phenotype analyse, PMP22 point mutations were considered the most severe genotypes and were mostly de novo. In addition, the de novo mutations were identified in up to 12.7% of all patients, which was higher than that in other studies. Conclusion: We identified a relatively lower detection rate of PMP22 duplication and a higher frequency of de novo variants among paediatric patients in China. We also identified the genetic and phenotypic heterogeneity of this cohort, which may provide clues for clinicians in directing genetic testing strategies for Chinese patients with early-onset CMT.
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Affiliation(s)
- Yan Ma
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
| | | | - Xiaoxuan Liu
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
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Aluri J, Cooper MA. Somatic mosaicism in inborn errors of immunity: Current knowledge, challenges, and future perspectives. Semin Immunol 2023; 67:101761. [PMID: 37062181 DOI: 10.1016/j.smim.2023.101761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/18/2023]
Abstract
Inborn errors of immunity (IEI) are a diverse group of monogenic disorders of the immune system due to germline variants in genes important for the immune response. Over the past decade there has been increasing recognition that acquired somatic variants present in a subset of cells can also lead to immune disorders or 'phenocopies' of IEI. Discovery of somatic mosaicism causing IEI has largely arisen from investigation of seemingly sporadic cases of IEI with predominant symptoms of autoinflammation and/or autoimmunity in which germline disease-causing variants are not detected. Disease-causing somatic mosaicism has been identified in genes that also cause germline IEI, such as FAS, and in genes without significant corresponding germline disease, such as UBA1 and TLR8. There are challenges in detecting low-level somatic variants, and it is likely that the extent of the somatic mosaicism causing IEI is largely uncharted. Here we review the field of somatic mosaicism leading to IEI and discuss challenges and methods for somatic variant detection, including diagnostic approaches for molecular diagnoses of patients.
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Affiliation(s)
- Jahnavi Aluri
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Megan A Cooper
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA.
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15
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D'Incal CP, Van Rossem KE, De Man K, Konings A, Van Dijck A, Rizzuti L, Vitriolo A, Testa G, Gozes I, Vanden Berghe W, Kooy RF. Chromatin remodeler Activity-Dependent Neuroprotective Protein (ADNP) contributes to syndromic autism. Clin Epigenetics 2023; 15:45. [PMID: 36945042 PMCID: PMC10031977 DOI: 10.1186/s13148-023-01450-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/16/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Individuals affected with autism often suffer additional co-morbidities such as intellectual disability. The genes contributing to autism cluster on a relatively limited number of cellular pathways, including chromatin remodeling. However, limited information is available on how mutations in single genes can result in such pleiotropic clinical features in affected individuals. In this review, we summarize available information on one of the most frequently mutated genes in syndromic autism the Activity-Dependent Neuroprotective Protein (ADNP). RESULTS Heterozygous and predicted loss-of-function ADNP mutations in individuals inevitably result in the clinical presentation with the Helsmoortel-Van der Aa syndrome, a frequent form of syndromic autism. ADNP, a zinc finger DNA-binding protein has a role in chromatin remodeling: The protein is associated with the pericentromeric protein HP1, the SWI/SNF core complex protein BRG1, and other members of this chromatin remodeling complex and, in murine stem cells, with the chromodomain helicase CHD4 in a ChAHP complex. ADNP has recently been shown to possess R-loop processing activity. In addition, many additional functions, for instance, in association with cytoskeletal proteins have been linked to ADNP. CONCLUSIONS We here present an integrated evaluation of all current aspects of gene function and evaluate how abnormalities in chromatin remodeling might relate to the pleiotropic clinical presentation in individual"s" with Helsmoortel-Van der Aa syndrome.
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Affiliation(s)
- Claudio Peter D'Incal
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Kirsten Esther Van Rossem
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium
| | - Kevin De Man
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Anthony Konings
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Anke Van Dijck
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium
| | - Ludovico Rizzuti
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, V. Le Rita Levi-Montalcini, 1, 20157, Milan, Italy
| | - Alessandro Vitriolo
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, V. Le Rita Levi-Montalcini, 1, 20157, Milan, Italy
| | - Giuseppe Testa
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, V. Le Rita Levi-Montalcini, 1, 20157, Milan, Italy
| | - Illana Gozes
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Adams Super Center for Brain Studies and Sagol School of Neuroscience, Tel Aviv University, Sackler School of Medicine, 727, 69978, Tel Aviv, Israel
| | - Wim Vanden Berghe
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium.
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium.
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16
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Miao C, Du L, Zhang Y, Jia F, Shan L. Novel de novo ZNF148 truncating variant causing autism spectrum disorder, attention deficit hyperactivity disorder, and intellectual disability. Clin Genet 2023; 103:364-368. [PMID: 36444493 DOI: 10.1111/cge.14272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022]
Abstract
ZNF148 gene is a Krüppel-type transcription factor that has transcriptional regulatory function. Heterozygous variant in ZNF148 gene causes an intellectual disability syndrome characterized by global developmental delay, absence, or hypoplasia of corpus callosum, wide intracerebral ventricles, and dysmorphic facial features, while its associations with ASD and ADHD have not been reported. We report a new patient with intellectual disability, autism spectrum disorder (ASD) and attention-deficit hyperactivity disorder (ADHD). The patient had a novel heterozygous truncating variant c.1818dupC (p.Lys607Glnfs*11) in the ZNF148 gene. This variation produces a ZNF148 truncated protein with a deletion of the C-terminal activation domain and may destabilize the protein by affecting the transcriptional activation function. Brain MRI shows normal brain development. Here, we identify a novel ZNF148 heterozygous truncating variant in a patient with distinct phenotypes of ASD and ADHD, which expands the genotype-phenotype spectrum of ZNF148, and indicates ZNF148 is also a potential target gene for ASD.
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Affiliation(s)
- Chunyue Miao
- Department of Developmental and Behavioral Pediatrics, The First Hospital of Jilin University, Jilin, China
| | - Lin Du
- Department of Developmental and Behavioral Pediatrics, The First Hospital of Jilin University, Jilin, China
| | - Yu Zhang
- Department of Developmental and Behavioral Pediatrics, The First Hospital of Jilin University, Jilin, China
| | - Feiyong Jia
- Department of Developmental and Behavioral Pediatrics, The First Hospital of Jilin University, Jilin, China
| | - Ling Shan
- Department of Developmental and Behavioral Pediatrics, The First Hospital of Jilin University, Jilin, China
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