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Khadija B, Rjiba K, Dimassi S, Dahleb W, Kammoun M, Hannechi H, Miladi N, Gouider-Khouja N, Saad A, Mougou-Zerelli S. Clinical and molecular characterization of 1q43q44 deletion and corpus callosum malformations: 2 new cases and literature review. Mol Cytogenet 2022; 15:42. [PMID: 36192753 PMCID: PMC9528098 DOI: 10.1186/s13039-022-00620-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/07/2022] [Indexed: 11/10/2022] Open
Abstract
Background Corpus callosum malformations (CCM) represent one of the most common congenital cerebral malformations with a prevalence of around one for 4000 births. There have been at least 230 reports in the literature concerning 1q43q44 deletions of varying sizes discovered using chromosomal microarrays. This disorder is distinguished by global developmental delay, seizures, hypotonia, corpus callosum defects, and significant craniofacial dysmorphism. In this study, we present a molecular cytogenetic analysis of 2 Tunisian patients with corpus callosum malformations. Patient 1 was a boy of 3 years old who presented psychomotor retardation, microcephaly, behavioral problems, interventricular septal defect, moderate pulmonary stenosis, hypospadias, and total CCA associated with delayed encephalic myelination. Patient 2 was a boy of 9 months. He presented a facial dysmorphia, a psychomotor retardation, an axial hypotonia, a quadri pyramidal syndrome, a micropenis, and HCC associated with decreased volume of the periventricular white matter. Both the array comparative genomic hybridization and fluorescence in situ hybridization techniques were used. Results Array CGH analysis reveals that patient 1 had the greater deletion size (11,7 Mb) at 1q43. The same region harbors a 2,7 Mb deletion in patient 2. Here, we notice that the larger the deletion, the more genes are likely to be involved, and the more severe the phenotype is likely to be. In both patients, the commonly deleted region includes six genes: PLD5, AKT3, ZNF238, HNRNPU, SDCCAG8 and CEP170. Based on the role of the ZNF238 gene in neuronal proliferation, migration, and cortex development, we hypothesized that the common deletion of ZNF238 in both patients seems to be the most responsible for corpus callosum malformations. Its absence may directly cause CCM. In addition, due to their high expression in the brain, PLD5 and FMN2 could modulate in the CCM phenotype. Conclusion Our findings support and improve the complex genotype–phenotype correlations previously reported in the 1qter microdeletion syndrome and define more precisely the neurodevelopmental phenotypes associated with genetic alterations of several genes related to this pathology.
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Affiliation(s)
- Bochra Khadija
- Laboratory of Human Cytogenetics, Department of Human Cytogenetics, Molecular Genetics and Biology of Reproduction, Farhat Hached University Hospital, Sousse, Tunisia.,Higher Institute of Biotechnology, Monastir University, Monastir, Tunisia.,Common Service Units for Research in Genetics, Faculty of Medicine of Sousse, University of Sousse, Sousse, Tunisia
| | - Khouloud Rjiba
- Laboratory of Human Cytogenetics, Department of Human Cytogenetics, Molecular Genetics and Biology of Reproduction, Farhat Hached University Hospital, Sousse, Tunisia.,Higher Institute of Biotechnology, Monastir University, Monastir, Tunisia.,Common Service Units for Research in Genetics, Faculty of Medicine of Sousse, University of Sousse, Sousse, Tunisia
| | - Sarra Dimassi
- Laboratory of Human Cytogenetics, Department of Human Cytogenetics, Molecular Genetics and Biology of Reproduction, Farhat Hached University Hospital, Sousse, Tunisia.,Common Service Units for Research in Genetics, Faculty of Medicine of Sousse, University of Sousse, Sousse, Tunisia
| | - Wafa Dahleb
- Laboratory of Human Cytogenetics, Department of Human Cytogenetics, Molecular Genetics and Biology of Reproduction, Farhat Hached University Hospital, Sousse, Tunisia.,Higher Institute of Biotechnology, Monastir University, Monastir, Tunisia
| | - Molka Kammoun
- Laboratory of Human Cytogenetics, Department of Human Cytogenetics, Molecular Genetics and Biology of Reproduction, Farhat Hached University Hospital, Sousse, Tunisia
| | - Hanen Hannechi
- Laboratory of Human Cytogenetics, Department of Human Cytogenetics, Molecular Genetics and Biology of Reproduction, Farhat Hached University Hospital, Sousse, Tunisia
| | - Najoua Miladi
- Medical Maghreb, El Manar 3, 2092, Tunis, Tunisia.,University of Tunis El Manar, 2092 El Manar 1, Tunis, Tunisia
| | - Neziha Gouider-Khouja
- Head of Department at the National Institute of Neurology Tunis Head of RU On Movement Disorders, Tunis, Tunisia
| | - Ali Saad
- Laboratory of Human Cytogenetics, Department of Human Cytogenetics, Molecular Genetics and Biology of Reproduction, Farhat Hached University Hospital, Sousse, Tunisia.,Common Service Units for Research in Genetics, Faculty of Medicine of Sousse, University of Sousse, Sousse, Tunisia
| | - Soumaya Mougou-Zerelli
- Laboratory of Human Cytogenetics, Department of Human Cytogenetics, Molecular Genetics and Biology of Reproduction, Farhat Hached University Hospital, Sousse, Tunisia. .,Common Service Units for Research in Genetics, Faculty of Medicine of Sousse, University of Sousse, Sousse, Tunisia.
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2
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Leitão F, Grangeia A, Pinto J, Passas A, Dória S. Clinical Findings on Chromosome 1 Copy Number Variations. Neuropediatrics 2022; 53:265-273. [PMID: 35835157 DOI: 10.1055/s-0042-1754162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Copy number variants (CNVs) are a major contribution to genome variability, and the presence of CNVs on chromosome 1 is a known cause of morbidity. The main objective of this study was to contribute to chromosome 1 disease map, through the analysis of patients with chromosome 1 CNVs.A cross-sectional study was performed using the array comparative genomic hybridization database of the Genetic Department of the Faculty of Medicine. Patients with pathogenic (P) or likely pathogenic (LP) CNVs on chromosome 1 were selected for the study. Clinical information was collected for all patients. Databases and related literature were used for genotype-phenotype correlation.From a total of 2,516 patients included in the database we identified 24 patients (0.95%) with P (9 patients) or LP (15 patients) CNVs on chromosome 1. These CNVs account for 6.1% (24/392 CNVs) of the total P/LP CNVs in the database. Most common CNVs found were in the 1q21.1-1q21.2 region.This study reinforces the association between chromosome 1 CNV and neurodevelopmental disorders and craniofacial dysmorphisms. Additionally, it also strengthened the idea that CNVs interpretation is not always a linear task due to the broad spectrum of variants that can be identified between benign and clearly pathogenic CNVs.
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Affiliation(s)
- Filipa Leitão
- Department of Pathology, Genetics Service, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Ana Grangeia
- Department of Pathology, Genetics Service, Faculty of Medicine, University of Porto, Porto, Portugal.,Medical Genetics Service, Centro Hospitalar Universitário de São João, Porto, Portugal.,I3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
| | - Joel Pinto
- Department of Pathology, Genetics Service, Faculty of Medicine, University of Porto, Porto, Portugal.,I3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
| | - Armanda Passas
- Neurodevelopment Unit- UNIA, Centro Hospitalar Vila Nova de Gaia/Espinho - CHVNG, Vila Nova de Gaia, Portugal
| | - Sofia Dória
- Department of Pathology, Genetics Service, Faculty of Medicine, University of Porto, Porto, Portugal.,I3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
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3
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Heng JIT, Viti L, Pugh K, Marshall OJ, Agostino M. Understanding the impact of ZBTB18 missense variation on transcription factor function in neurodevelopment and disease. J Neurochem 2022; 161:219-235. [PMID: 35083747 PMCID: PMC9302683 DOI: 10.1111/jnc.15572] [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: 09/28/2021] [Revised: 12/13/2021] [Accepted: 01/07/2022] [Indexed: 12/01/2022]
Abstract
Mutations to genes that encode DNA‐binding transcription factors (TFs) underlie a broad spectrum of human neurodevelopmental disorders. Here, we highlight the pathological mechanisms arising from mutations to TF genes that influence the development of mammalian cerebral cortex neurons. Drawing on recent findings for TF genes including ZBTB18, we discuss how functional missense mutations to such genes confer non‐native gene regulatory actions in developing neurons, leading to cell‐morphological defects, neuroanatomical abnormalities during foetal brain development and functional impairment. Further, we discuss how missense variation to human TF genes documented in the general population endow quantifiable changes to transcriptional regulation, with potential cell biological effects on the temporal progression of cerebral cortex neuron development and homeostasis. We offer a systematic approach to investigate the functional impact of missense variation in brain TFs and define their direct molecular and cellular actions in foetal neurodevelopment, tissue homeostasis and disease states.![]()
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Affiliation(s)
- Julian I-T Heng
- Curtin Health Innovation Research Institute, Bentley, WA, Australia.,Curtin Neuroscience Laboratories, Sarich Neuroscience Institute, Crawley, WA, Australia.,Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Leon Viti
- Curtin Health Innovation Research Institute, Bentley, WA, Australia.,Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Kye Pugh
- Curtin Health Innovation Research Institute, Bentley, WA, Australia.,Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Owen J Marshall
- Menzies Institute for Medical Research, The University of Tasmania, Hobart, Australia
| | - Mark Agostino
- Curtin Health Innovation Research Institute, Bentley, WA, Australia.,Curtin Institute for Computation, Curtin University, Bentley, Western Australia, Australia
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4
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Yue F, Sun M, Zhang H, Jiang Y, Li L, He J, Liu R. Molecular cytogenetic characterization of 1q42.3q44 deletion and 8q24.3 duplication in a fetus with single umbilical artery and ventricular septal defects. Taiwan J Obstet Gynecol 2021; 60:1126-1133. [PMID: 34794751 DOI: 10.1016/j.tjog.2021.09.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2021] [Indexed: 10/19/2022] Open
Abstract
OBJECTIVE We present prenatal diagnosis and molecular cytogenetic characterization of a chromosome 1q42.3q44 deletion and 8q24.3 duplication in a fetus with single umbilical artery and ventricular septal defects, and we discuss the genotype-phenotype correlation. CASE REPORT Here, we describe a fetus with abnormal sonography findings showing a single umbilical artery and ventricular septal defects. Conventional karyotyping initially described the fetus as 46,XX,1q? and molecular cytogenetic analysis (CMA) revealed a 13-Mb deletion and 4.6-Mb duplication of regions 1q42.3q44 and 8q24.3, respectively. The father's karyotype was 46,XY. The mother's karyotype was 46,XX,t(1;8)(q42;q24). Therefore, the karyotype of the fetus was identified as 46,XX,der(1)t(1;8)(q42;q24) mat. After genetic counseling, the couple chose to terminate the pregnancy. We suggest that the ACTN2, RYR2 and PUF60 genes may be responsible for the ultrasound abnormalities observed in the fetus. CONCLUSION To the best of our knowledge, this is the first report of a 1q deletion and 8q duplication identified by prenatal detection. The application of karyotype analysis and CMA provides more accurate characterization for unidentified chromosomal anomalies, and benefits appropriate genetic counseling in the clinic.
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Affiliation(s)
- Fagui Yue
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China; Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China
| | - Meiling Sun
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China; Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China
| | - Hongguo Zhang
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China; Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China
| | - Yuting Jiang
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China; Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China
| | - Leilei Li
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China; Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China
| | - Jing He
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China; Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China
| | - Ruizhi Liu
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China; Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China.
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5
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Benítez-Burraco A, Fernández-Urquiza M, Jiménez-Romero S. Language impairment with a microduplication in 1q42.3q43. CLINICAL LINGUISTICS & PHONETICS 2021; 35:610-635. [PMID: 32856472 DOI: 10.1080/02699206.2020.1812119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/11/2020] [Accepted: 08/16/2020] [Indexed: 06/11/2023]
Abstract
Deletions and duplications of the distal region of the long arm of chromosome 1 are associated with brain abnormalities and developmental delay. Because duplications are less frequent than deletions, no detailed account of the cognitive profile of the affected people is available, particularly, regarding their language (dis)abilities. In this paper we report on the cognitive and language capacities of a girl with one of the smallest interstitial duplications ever described in this region, affecting to 1q42.3q43 (arr[hg19] 1q42.3q43(235,963,632-236,972,276)x3), and advance potential candidate genes for the observed deficits. The proband's speech is severely impaired, exhibiting dysarthric-like features, with speech problems also resulting from a phonological deficit boiling down to a verbal auditory memory deficit. Lexical and grammatical knowledge are also impaired, impacting negatively on both expressive and receptive abilities, seemingly as a consequence of the phonological deficit. Still, her pragmatic abilities seem to be significantly spared, granting her a good command on the principles governing conversational exchanges. Genetic analyses point to several genes of interest. These include one gene within the duplicated region (LYST), one predicted functional partner (CMIP), and three genes outside the 1q42.3q43 region, which are all highly expressed in the cerebellum: DDIT4 and SLC29A1, found strongly downregulated in the proband compared to her healthy parents, and CNTNAP3, found strongly upregulated. The genes highlighted in the paper emerge as potential candidates for the phonological and speech deficits exhibited by the proband and ultimately, for her problems with language.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), University of Seville, Seville, Spain
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6
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Pirozzi F, Lee B, Horsley N, Burkardt DD, Dobyns WB, Graham JM, Dentici ML, Cesario C, Schallner J, Porrmann J, Di Donato N, Sanchez-Lara PA, Mirzaa GM. Proximal variants in CCND2 associated with microcephaly, short stature, and developmental delay: A case series and review of inverse brain growth phenotypes. Am J Med Genet A 2021; 185:2719-2738. [PMID: 34087052 DOI: 10.1002/ajmg.a.62362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 01/28/2023]
Abstract
Cyclin D2 (CCND2) is a critical cell cycle regulator and key member of the cyclin D2-CDK4 (DC) complex. De novo variants of CCND2 clustering in the distal part of the protein have been identified as pathogenic causes of brain overgrowth (megalencephaly, MEG) and severe cortical malformations in children including the megalencephaly-polymicrogyria-polydactyly-hydrocephalus (MPPH) syndrome. Megalencephaly-associated CCND2 variants are localized to the terminal exon and result in accumulation of degradation-resistant protein. We identified five individuals from three unrelated families with novel variants in the proximal region of CCND2 associated with microcephaly, mildly simplified cortical gyral pattern, symmetric short stature, and mild developmental delay. Identified variants include de novo frameshift variants and a dominantly inherited stop-gain variant segregating with the phenotype. This is the first reported association between proximal CCND2 variants and microcephaly, to our knowledge. This series expands the phenotypic spectrum of CCND2-related disorders and suggests that distinct classes of CCND2 variants are associated with reciprocal effects on human brain growth (microcephaly and megalencephaly due to possible loss or gain of protein function, respectively), adding to the growing paradigm of inverse phenotypes due to dysregulation of key brain growth genes.
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Affiliation(s)
- Filomena Pirozzi
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Benson Lee
- Division of Medical Genetics, Department of Medicine, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, California, USA
| | - Nicole Horsley
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Deepika D Burkardt
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - William B Dobyns
- Division of Genetics and Metabolism, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - John M Graham
- Medical Genetics Institute, Cedars-Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Maria L Dentici
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, IRCSS, Rome, Italy.,Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCSS, Rome, Italy
| | - Claudia Cesario
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Jens Schallner
- Department of Neuropediatrics, School of Medicine, Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Joseph Porrmann
- Institute for Clinical Genetics, University Hospital, TU Dresden, Dresden, Germany
| | - Nataliya Di Donato
- Institute for Clinical Genetics, University Hospital, TU Dresden, Dresden, Germany
| | - Pedro A Sanchez-Lara
- Medical Genetics Institute, Cedars-Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Division of Medical Genetics, Department of Pediatrics, University of Washington, Seattle, Washington, USA.,Brotman-Baty Institute for Precision Medicine, Seattle, Washington, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA
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7
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Tung Y, Lu H, Lin W, Huang T, Kim S, Hu G, Zhang G, Zheng G. Case Report: Identification of a de novo Microdeletion 1q44 in a Patient With Seizures and Developmental Delay. Front Genet 2021; 12:648351. [PMID: 34093647 PMCID: PMC8173053 DOI: 10.3389/fgene.2021.648351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/06/2021] [Indexed: 02/04/2023] Open
Abstract
Objective: 1q44 microdeletion syndrome is difficult to diagnose due to the wide phenotypic spectrum and strong genetic heterogeneity. We explore the correlation between the chromosome microdeletions and phenotype in a child with 1q44 microdeletion syndrome, we collected the clinical features of the patient and combined them with adjacent copy number variation (CNV) regions previously reported. Methods: We collected the full medical history of the patient and summarized her clinical symptoms. Whole-exome sequencing (WES) and CapCNV analysis were performed with DNA extracted from both the patient's and her parents' peripheral blood samples. Fluorescent quantitative PCR (q-PCR) was performed for the use of verification to the CNV regions. Results: A 28.7 KB microdeletion was detected in the 1q44 region by whole-exome sequencing and low-depth whole-genome sequencing. The deleted region included the genes COX20 and HNRNPU. As verification, karyotype analysis showed no abnormality, and the results of qPCR were consistent with that of whole-exome sequencing and CapCNV analysis. Conclusion: The patient was diagnosed with 1q44 microdeletion syndrome with clinical and genetic analysis. Analyzing both whole-exome sequencing and CapCNV analysis can not only improve the diagnostic rate of clinically suspected syndromes that present with intellectual disability (ID) and multiple malformations but also support further study of the correlation between CNVs and clinical phenotypes. This study lays the foundation for the further study of the pathogenesis of complex diseases.
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Affiliation(s)
- Yiehen Tung
- Department of Neurology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Haiying Lu
- Department of Neurology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Wenxin Lin
- Department of Neurology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Tingting Huang
- Department of Neurology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Samuel Kim
- Department of Anesthesiology, Emory University School of Medicine, Atlanta, GA, United States
| | - Guo Hu
- Department of Neurology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Gang Zhang
- Department of Neurology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Guo Zheng
- Department of Neurology, Children's Hospital of Nanjing Medical University, Nanjing, China
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8
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Hemming IA, Blake S, Agostino M, Heng JI. General population ZBTB18 missense variants influence DNA binding and transcriptional regulation. Hum Mutat 2020; 41:1629-1644. [DOI: 10.1002/humu.24069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/28/2020] [Accepted: 06/22/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Isabel A. Hemming
- The Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands Western Australia Australia
- The Centre for Medical Research The University of Western Australia Crawley Western Australia Australia
- The Faculty of Health and Medical Sciences, Medical School The University of Western Australia Crawley Western Australia Australia
- Ralph and Patricia Sarich Neuroscience Research Institute Nedlands Western Australia Australia
- Curtin Health Innovation Research Institute Curtin University Bentley Western Australia Australia
| | - Steven Blake
- Ralph and Patricia Sarich Neuroscience Research Institute Nedlands Western Australia Australia
- Curtin Health Innovation Research Institute Curtin University Bentley Western Australia Australia
- School of Pharmacy and Biomedical Science Curtin University Bentley Western Australia Australia
| | - Mark Agostino
- Curtin Health Innovation Research Institute Curtin University Bentley Western Australia Australia
- School of Pharmacy and Biomedical Science Curtin University Bentley Western Australia Australia
- Curtin Institute for Computation Curtin University Bentley Western Australia Australia
| | - Julian I‐T. Heng
- Ralph and Patricia Sarich Neuroscience Research Institute Nedlands Western Australia Australia
- Curtin Health Innovation Research Institute Curtin University Bentley Western Australia Australia
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9
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Hemming IA, Clément O, Gladwyn-Ng IE, Cullen HD, Ng HL, See HB, Ngo L, Ulgiati D, Pfleger KDG, Agostino M, Heng JIT. Disease-associated missense variants in ZBTB18 disrupt DNA binding and impair the development of neurons within the embryonic cerebral cortex. Hum Mutat 2019; 40:1841-1855. [PMID: 31112317 DOI: 10.1002/humu.23803] [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: 12/19/2018] [Revised: 05/08/2019] [Accepted: 05/19/2019] [Indexed: 12/12/2022]
Abstract
The activities of DNA-binding transcription factors, such as the multi-zinc-finger protein ZBTB18 (also known as RP58, or ZNF238), are essential to coordinate mammalian neurodevelopment, including the birth and radial migration of newborn neurons within the fetal brain. In humans, the majority of disease-associated missense mutations in ZBTB18 lie within the DNA-binding zinc-finger domain and are associated with brain developmental disorder, yet the molecular mechanisms explaining their role in disease remain unclear. To address this, we developed in silico models of ZBTB18, bound to DNA, and discovered that half of the missense variants map to residues (Asn461, Arg464, Glu486) predicted to be essential to sequence-specific DNA contact, whereas others map to residues (Leu434, Tyr447, Arg495) with limited contributions to DNA binding. We studied pathogenic variants to residues with close (N461S) and limited (R495G) DNA contact and found that each bound DNA promiscuously, displayed altered transcriptional regulatory activity in vitro, and influenced the radial migration of newborn neurons in vivo in different ways. Taken together, our results suggest that altered transcriptional regulation could represent an important pathological mechanism for ZBTB18 missense variants in brain developmental disease.
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Affiliation(s)
- Isabel A Hemming
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia.,Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, Australia
| | - Olivier Clément
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia.,Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, Australia.,School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia
| | - Ivan E Gladwyn-Ng
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia
| | - Hayley D Cullen
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia.,Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, Australia
| | - Han Leng Ng
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia
| | - Heng B See
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia
| | - Linh Ngo
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia
| | - Daniela Ulgiati
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia
| | - Kevin D G Pfleger
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia.,ARC Centre for Personalised Therapeutics Technologies, Melbourne, Australia
| | - Mark Agostino
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Australia.,Curtin Institute for Computation, Curtin University, Bentley, Australia
| | - Julian I-T Heng
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Australia.,ARC Centre for Personalised Therapeutics Technologies, Melbourne, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Australia
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10
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Small posterior fossa in Chiari I malformation affected families is significantly linked to 1q43-44 and 12q23-24.11 using whole exome sequencing. Eur J Hum Genet 2019; 27:1599-1610. [PMID: 31227808 DOI: 10.1038/s41431-019-0457-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 05/01/2019] [Accepted: 06/04/2019] [Indexed: 11/08/2022] Open
Abstract
The posterior fossa of the cranium contains the cerebellum and brainstem. Processes that reduce the volume of the posterior fossa squeeze the cerebellum and brainstem caudally, resulting in Chiari I malformation (CM1). CM1 causes neck pain, balance issues, decreased motor skills and headaches in those affected. We have posterior fossa measurements and whole exome sequence data on individuals from 7 extended families from Russia that have a family history of CM1. We performed parametric linkage analyses using an autosomal dominant inheritance model with a disease allele frequency of 0.01 and a penetrance of 0.8 for carriers and 0.0 for non-carriers. Variant-based two-point linkage analysis and gene-based linkage analysis was performed. Our results found a genome-wide significant signal on chromosome 1q43-44 (max HLOD = 3.3) in the variant-based analysis and 12q23 (max HLOD = 4.2) in the gene-based analysis. In both cases, the signal was driven by a single (different) family that contained a long, linked haplotype across the region in question. Using functional annotation, we were able to identify several rare nonsynonymous variants that were enriched in each family. The best candidate genes were rs765865412:G>A in MYBPC1 for the 12q haplotype and rs61749963:A>G in COX20 for the 1q haplotype. Good candidate variants in the 1q haplotype were also identified in CEP170 and AKT. Further laboratory work is planned to verify the causality of these genes.
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11
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Cheng X, Yang Q, Liu J, Ye J, Xiao H, Zhang G, Pan Y, Li X, Hao R, Li Y. Constitutional 763.3 Kb chromosome 1q43 duplication encompassing only CHRM3 gene identified by next generation sequencing (NGS) in a child with intellectual disability. Mol Cytogenet 2019; 12:16. [PMID: 31019551 PMCID: PMC6472087 DOI: 10.1186/s13039-019-0427-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 03/26/2019] [Indexed: 01/08/2023] Open
Abstract
Background Deletion or duplication on the distal portion of the long arm of chromosome 1 result in complex and highly variable clinical phenotype including. intellectual disability and autism. Case presentation We report on a patient with intellectual disability and a 763.3 Kb duplication on 1q43 that includes only CHRM3, which was detected by next generation sequencing (NGS). The patient presented with intellectual disability, developmental delay, autistic behavior, limited or no speech, social withdrawal, self-injurious, feeding difficulties, strabismus, short stature, hand anomalie, and no seizures, anxiety, or mood swings, and clinodactyly. Conclusions We propose that CHRM3 is the critical gene responsible for the common characteristics in the cases with 1q43 duplication and deletion.
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Affiliation(s)
- Xiaofei Cheng
- 1Department of Obstetrics and Gynecology, the First Hospital of Huhhot City, Inner Mongolia, China
| | - Qifang Yang
- 1Department of Obstetrics and Gynecology, the First Hospital of Huhhot City, Inner Mongolia, China
| | - Jun Liu
- 2Department of Radiology, the First Hospital of Huhhot City, Inner Mongolia, China
| | - Juan Ye
- 1Department of Obstetrics and Gynecology, the First Hospital of Huhhot City, Inner Mongolia, China
| | - Huiying Xiao
- 1Department of Obstetrics and Gynecology, the First Hospital of Huhhot City, Inner Mongolia, China
| | - Gaimei Zhang
- 1Department of Obstetrics and Gynecology, the First Hospital of Huhhot City, Inner Mongolia, China
| | - Yuanyuan Pan
- 1Department of Obstetrics and Gynecology, the First Hospital of Huhhot City, Inner Mongolia, China
| | - Xia Li
- 1Department of Obstetrics and Gynecology, the First Hospital of Huhhot City, Inner Mongolia, China
| | - Ruifeng Hao
- 1Department of Obstetrics and Gynecology, the First Hospital of Huhhot City, Inner Mongolia, China
| | - Yinfeng Li
- 1Department of Obstetrics and Gynecology, the First Hospital of Huhhot City, Inner Mongolia, China
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12
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Córdova-Fletes C, Arámbula-Meraz E, Zarazúa-Niño AI, Madueña-Molina J, Sáinz-Barraza ME, González-García JR, León-León C, López-López G, Lugo-Guzmán EG, Picos-Cárdenas VJ. Familial 3-Way Balanced Translocation Causes 1q43→qter Loss and 10q25.2→qter Gain in a Severely Affected Male Toddler. Cytogenet Genome Res 2019; 157:231-238. [PMID: 30933949 DOI: 10.1159/000498998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2018] [Indexed: 11/19/2022] Open
Abstract
Constitutional complex chromosomal rearrangements (CCRs) are rare events that typically involve 2 or more chromosomes with at least 3 breakpoints and can result in normal or abnormal phenotypes depending on whether they disturb the euchromatic neighborhood. Here, we report an unusual balanced CCR involving chromosomes 1, 9, and 10 that causes an unbalanced karyotype in a severely affected toddler. The CCR was initially reported as a maternal 2-way translocation but was reclassified as a 3-way translocation after a microarray analysis of the propositus revealed the involvement of another chromosome not identified by G-banding in his phenotypically normal mother. FISH assays on maternal metaphase cells confirmed that the 1qter region of der(1) was translocated to der(10), whereas the 10qter segment was translocated to der(9), which in turn donated a segment to der(1). Subsequently, this CCR was also identified in her phenotypically normal father (the patient's grandfather). Thus, the patient inherited the previously unreported pathogenic combination of der(1) with a loss of 1q43→qter (including AKT3, ZBTB18, HNRNPU, and SMYD3) and der(9) with a gain of 10q25.2→qter (including FGFR2), leading to a compound phenotype with key features of the 1q43→qter deletion and distal 10q trisomy syndromes. Our observations suggest that the loss of SMYD3 accounts for cardiac defects in a subset of patients. Moreover, due to recurrent miscarriages in this family, our findings allowed improved genetic counseling.
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MESH Headings
- Abnormalities, Multiple/diagnostic imaging
- Abnormalities, Multiple/genetics
- Child, Preschool
- Chromosomes, Human, Pair 1/genetics
- Chromosomes, Human, Pair 10/genetics
- Chromosomes, Human, Pair 9/genetics
- Comparative Genomic Hybridization
- Genetic Counseling
- Histone-Lysine N-Methyltransferase/genetics
- Humans
- In Situ Hybridization, Fluorescence/methods
- Male
- Tomography, X-Ray Computed
- Translocation, Genetic
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13
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Lopes F, Torres F, Soares G, van Karnebeek CD, Martins C, Antunes D, Silva J, Muttucomaroe L, Botelho LF, Sousa S, Rendeiro P, Tavares P, Van Esch H, Rajcan-Separovic E, Maciel P. The Role of AKT3 Copy Number Changes in Brain Abnormalities and Neurodevelopmental Disorders: Four New Cases and Literature Review. Front Genet 2019; 10:58. [PMID: 30853971 PMCID: PMC6395382 DOI: 10.3389/fgene.2019.00058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 01/24/2019] [Indexed: 11/19/2022] Open
Abstract
Microdeletions at 1q43-q44 have been described as resulting in a clinically recognizable phenotype of intellectual disability (ID), facial dysmorphisms and microcephaly (MIC). In contrast, the reciprocal microduplications of 1q43-q44 region have been less frequently reported and patients showed a variable phenotype, including macrocephaly. Reports of a large number of patients with copy number variations involving this region highlighted the AKT3 gene as a likely key player in head size anomalies. We report four novel patients with copy number variations in the 1q43-q44 region: one with a larger deletion (3.7Mb), two with smaller deletions affecting AKT3 and SDCCAG8 genes (0.16 and 0.18Mb) and one with a quadruplication (1Mb) that affects the entire AKT3 gene. All patients with deletions presented MIC without structural brain abnormalities, whereas the patient with quadruplication had macrocephaly, but his carrier father had normal head circumference. Our report also includes a comparison of phenotypes in cases with 1q43-q44 duplications to assist future genotype-phenotype correlations. Our observations implicate AKT3 as a contributor to ID/development delay (DD) and head size but raise doubts about its straightforward impact on the latter aspect of the phenotype in patients with 1q43-q44 deletion/duplication syndrome.
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Affiliation(s)
- Fátima Lopes
- School of Medicine, Life and Health Sciences Research Institute (ICVS), University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Guimarães, Portugal
| | - Fátima Torres
- CGC Genetics, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Gabriela Soares
- Center for Medical Genetics Dr. Jacinto Magalhães, National Health Institute Dr. Ricardo Jorge, Porto, Portugal
| | - Clara D van Karnebeek
- Department of Pediatrics, Centre for Molecular Medicine, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada.,Academic Medical Centre, Department of Pediatrics and Clinical Genetics, Amsterdam, Netherlands
| | - Cecília Martins
- Department of Pediatrics, Médio Ave Hospital Center, Vila Nova de Famalicão, Portugal
| | - Diana Antunes
- Medical Genetics Department, Hospital D. Estefânia, Centro Hospitalar Lisboa Central, Lisbon, Portugal
| | - João Silva
- Center for Medical Genetics Dr. Jacinto Magalhães, National Health Institute Dr. Ricardo Jorge, Porto, Portugal
| | - Lauren Muttucomaroe
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Luís Filipe Botelho
- Department of Neuroradiology, Hospital de Santo António, Porto Hospital Center, Porto, Portugal
| | - Susana Sousa
- School of Medicine, Life and Health Sciences Research Institute (ICVS), University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Guimarães, Portugal
| | | | | | - Hilde Van Esch
- Laboratories for Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | - Patrícia Maciel
- School of Medicine, Life and Health Sciences Research Institute (ICVS), University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Guimarães, Portugal
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14
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Corbett MA, van Eyk CL, Webber DL, Bent SJ, Newman M, Harper K, Berry JG, Azmanov DN, Woodward KJ, Gardner AE, Slee J, Pérez-Jurado LA, MacLennan AH, Gecz J. Pathogenic copy number variants that affect gene expression contribute to genomic burden in cerebral palsy. NPJ Genom Med 2018; 3:33. [PMID: 30564460 PMCID: PMC6294788 DOI: 10.1038/s41525-018-0073-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/26/2018] [Indexed: 11/10/2022] Open
Abstract
Cerebral palsy (CP) is the most frequent movement disorder of childhood affecting 1 in 500 live births in developed countries. We previously identified likely pathogenic de novo or inherited single nucleotide variants (SNV) in 14% (14/98) of trios by exome sequencing and a further 5% (9/182) from evidence of outlier gene expression using RNA sequencing. Here, we detected copy number variants (CNV) from exomes of 186 unrelated individuals with CP (including our original 98 trios) using the CoNIFER algorithm. CNV were validated with Illumina 850 K SNP arrays and compared with RNA-Seq outlier gene expression analysis from lymphoblastoid cell lines (LCL). Gene expression was highly correlated with gene dosage effect. We resolved an additional 3.7% (7/186) of this cohort with pathogenic or likely pathogenic CNV while a further 7.7% (14/186) had CNV of uncertain significance. We identified recurrent genomic rearrangements previously associated with CP due to 2p25.3 deletion, 22q11.2 deletions and duplications and Xp monosomy. We also discovered a deletion of a single gene, PDCD6IP, and performed additional zebrafish model studies to support its single allele loss in CP aetiology. Combined SNV and CNV analysis revealed pathogenic and likely pathogenic variants in 22.7% of unselected individuals with CP.
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Affiliation(s)
- Mark A. Corbett
- Robinson Research Institute & Adelaide Medical School, University of Adelaide, Adelaide, South Australia 5000 Australia
| | - Clare L. van Eyk
- Robinson Research Institute & Adelaide Medical School, University of Adelaide, Adelaide, South Australia 5000 Australia
| | - Dani L. Webber
- Robinson Research Institute & Adelaide Medical School, University of Adelaide, Adelaide, South Australia 5000 Australia
| | - Stephen J. Bent
- Data61, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, Brisbane, QLD 4102 Australia
| | - Morgan Newman
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005 Australia
| | - Kelly Harper
- Robinson Research Institute & Adelaide Medical School, University of Adelaide, Adelaide, South Australia 5000 Australia
| | - Jesia G. Berry
- Robinson Research Institute & Adelaide Medical School, University of Adelaide, Adelaide, South Australia 5000 Australia
| | - Dimitar N. Azmanov
- Department of Diagnostic Genomics, Queen Elizabeth II Medical Centre, PathWest, Nedlands, WA 6009 Australia
| | - Karen J. Woodward
- Department of Diagnostic Genomics, Queen Elizabeth II Medical Centre, PathWest, Nedlands, WA 6009 Australia
- School of Biomedical Sciences, University of Western Australia, Perth, WA 6009 Australia
| | - Alison E. Gardner
- Robinson Research Institute & Adelaide Medical School, University of Adelaide, Adelaide, South Australia 5000 Australia
| | - Jennie Slee
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA 6008 Australia
| | - Luís A. Pérez-Jurado
- Genetics Unit, Universitat Pompeu Fabra, Barcelona, 08003 Spain
- Hospital del Mar Research Institute (IMIM) and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, 08003 Spain
- SA Clinical Genetics, Women’s and Children’s Hospital & University of Adelaide, Adelaide, South Australia 5006 Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia 5000 Australia
| | - Alastair H. MacLennan
- Robinson Research Institute & Adelaide Medical School, University of Adelaide, Adelaide, South Australia 5000 Australia
| | - Jozef Gecz
- Robinson Research Institute & Adelaide Medical School, University of Adelaide, Adelaide, South Australia 5000 Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia 5000 Australia
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15
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Cytogenomic characterization of 1q43q44 deletion associated with 4q32.1q35.2 duplication and phenotype correlation. Mol Cytogenet 2018; 11:57. [PMID: 30410579 PMCID: PMC6219057 DOI: 10.1186/s13039-018-0406-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 10/17/2018] [Indexed: 11/10/2022] Open
Abstract
Background Microdeletion of 1q43q44 causes a syndrome characterized by intellectual disability (ID), speech delay, seizures, microcephaly (MIC), corpus callosum abnormalities (CCA) and characteristic facial features. Duplication of 4q is presented with minor to severe ID, MIC and facial dysmorphism. We aimed to verify the correlation between genotype/phenotype in a patient with 1q43q44 deletion associated with 4q32.1q35.2 duplication. Case presentation We report on a 3 year-old female patient with delayed motor and mental milestones, MIC and facial dysmorphism. She is a child of non-consanguineous parents and no similarly affected family members. CT brain showed abnormal gyral patterns, hypogenesis of corpus callosum and bilateral deep Sylvian fissure. Electroencephalogram showed frontotemporal epileptogenic focus. Her karyotype was revealed as 46,XX,add(1)(q44). Fluorescence in situ hybridization (FISH) using whole chromosome paint (WCP1) and subtelomere 1q revealed that the add segment was not derived from chromosome 1 and there was the deletion of subtelomere 1q. Multiple ligation probe amplification (MLPA) subtelomere kit revealed the deletion of 1q and duplication of 4q. Array CGH demonstrated the 6.5 Mb deletion of 1q and 31 Mb duplication of chromosome 4q. Conclusion The phenotype of our patient mainly reflects the effects of haploinsufficiency of AKT3, HNRNPU, ZBTB18 genes associated with duplication of GLRA3, GMP6A, HAND2 genes. Patients presented with ID, seizures, MIC together with CCA are candidates for prediction of 1q43q44 microdeletion and cytogenomic analysis.
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16
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Luo A, Cheng D, Yuan S, Li H, Du J, Zhang Y, Yang C, Lin G, Zhang W, Tan YQ. Maternal interchromosomal insertional translocation leading to 1q43-q44 deletion and duplication in two siblings. Mol Cytogenet 2018; 11:24. [PMID: 29636822 PMCID: PMC5883343 DOI: 10.1186/s13039-018-0371-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/08/2018] [Indexed: 12/05/2022] Open
Abstract
Background 1q43-q44 deletion syndrome is a well-defined chromosomal disorder which is characterized by moderate to severe mental retardation, and variable but characteristic facial features determined by the size of the segment and the number of genes involved. However, patients with 1q43-q44 duplication with a clinical phenotype comparable to that of 1q43-q44 deletion are rarely reported. Moreover, pure 1q43-q44 deletions and duplications derived from balanced insertional translocation within the same family with precisely identified breakpoints have not been reported. Case presentation The proband is a 6-year-old girl with profound developmental delay, mental retardation, microcephaly, epilepsy, agenesis of the corpus callosum and hearing impairment. Her younger brother is a 3-month-old boy with macrocephaly and mild developmental delay in gross motor functions. G-banding analysis of the subjects at the 400-band level did not reveal any subtle structural changes in their karyotypes. However, single-nucleotide polymorphism (SNP) array analysis showed a deletion and a duplication of approximately 6.0 Mb at 1q43-q44 in the proband and her younger brother, respectively. The Levicare analysis pipeline of whole-genome sequencing (WGS) further demonstrated that a segment of 1q43-q44 was inserted at 14q23.1 in the unaffected mother, which indicated that the mother was a carrier of a 46,XX,ins(14;1)(q23.1;q43q44) insertional translocation. Moreover, Sanger sequencing was used to assist the mapping of the breakpoints and the final validation of those breakpoints. The breakpoint on chromosome 1 disrupted the EFCAB2 gene in the first intron, and the breakpoint on chromosome 14 disrupted the PRKCH gene within the 12th intron. In addition, fluorescence in situ hybridization (FISH) further confirmed that the unaffected older sister of the proband carried the same karyotype as the mother. Conclusion Here, we describe a rare family exhibiting pure 1q43-q44 deletion and duplication in two siblings caused by a maternal balanced insertional translocation. Our study demonstrates that WGS with a carefully designed analysis pipeline is a powerful tool for identifying cryptic genomic balanced translocations and mapping the breakpoints at the nucleotide level and could be an effective method for explaining the relationship between karyotype and phenotype. Electronic supplementary material The online version of this article (10.1186/s13039-018-0371-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aixiang Luo
- 1Institute of Reproduction and Stem Cell Engineering, Xiangya School of Medicine, Central South University, Changsha, Hunan 410078 People's Republic of China
| | - Dehua Cheng
- 1Institute of Reproduction and Stem Cell Engineering, Xiangya School of Medicine, Central South University, Changsha, Hunan 410078 People's Republic of China.,2Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan 410078 People's Republic of China
| | - Shimin Yuan
- 2Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan 410078 People's Republic of China
| | - Haiyu Li
- 1Institute of Reproduction and Stem Cell Engineering, Xiangya School of Medicine, Central South University, Changsha, Hunan 410078 People's Republic of China
| | - Juan Du
- 1Institute of Reproduction and Stem Cell Engineering, Xiangya School of Medicine, Central South University, Changsha, Hunan 410078 People's Republic of China.,2Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan 410078 People's Republic of China
| | - Yang Zhang
- 3School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong, 999077 People's Republic of China
| | - Chuanchun Yang
- Cheerland Precision Biomed Co., Ltd., Shenzhen, Guangdong 518055 People's Republic of China
| | - Ge Lin
- 1Institute of Reproduction and Stem Cell Engineering, Xiangya School of Medicine, Central South University, Changsha, Hunan 410078 People's Republic of China.,2Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan 410078 People's Republic of China
| | - Wenyong Zhang
- Southern University of Science and Technology, Shenzhen, Guangdong 518055 People's Republic of China
| | - Yue-Qiu Tan
- 1Institute of Reproduction and Stem Cell Engineering, Xiangya School of Medicine, Central South University, Changsha, Hunan 410078 People's Republic of China.,2Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan 410078 People's Republic of China
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17
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van der Schoot V, de Munnik S, Venselaar H, Elting M, Mancini GMS, Ravenswaaij-Arts CMA, Anderlid BM, Brunner HG, Stevens SJC. Toward clinical and molecular understanding of pathogenic variants in the ZBTB18 gene. Mol Genet Genomic Med 2018; 6:393-400. [PMID: 29573576 PMCID: PMC6014478 DOI: 10.1002/mgg3.387] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 12/25/2022] Open
Abstract
Background Patients with pathogenic variants in ZBTB18 present with Intellectual Disability (ID) with frequent co‐occurrence of corpus callosum (CC) anomalies, hypotonia, microcephaly, growth problems and variable facial dysmorphologies. These features illustrate a key role for ZBTB18 in brain development. Methods Patients with a pathogenic variant in ZBTB18 were detected by diagnostic whole exome sequencing (WES) performed in our center. We reviewed the literature and used GeneMatcher to include other cases. YASARA and WHAT IF were used to provide insight into the structural effect of missense variants located in the C2H2 zinc finger domains of the ZBTB18 protein. Results We give a complete overview of pathogenic variants in ZBTB18 detected to date, showing inconsistent presence of clinical features, including CC anomalies. We present four new cases with a de novo pathogenic variant in the ZBTB18 gene, including the fourth case in which a de novo p.Arg464His variant was found. Conclusion Homology modeling of protein structure points to a variable degree of impaired DNA binding caused by missense variants in these domains probably leading to Loss of Function (LoF). Putative partial LoF may present with a less distinctive phenotype than complete LoF, as seen in truncating variants, which presents with an extensive variability in the phenotypic spectrum. Our data do not support a clear genotype to phenotype correlation.
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Affiliation(s)
- Vyne van der Schoot
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Sonja de Munnik
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, the Netherlands
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Centre Nijmegen, Nijmegen, the Netherlands
| | - Mariet Elting
- Department of Clinical Genetics, Vrije Universiteit, Amsterdam, the Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Centre, Rotterdam, the Netherlands
| | - Conny M A Ravenswaaij-Arts
- University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, the Netherlands
| | - Britt-Marie Anderlid
- Department of Clinical Genetics, Karolinska Universitetssjukhuset, Solna, Sweden
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands.,Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, the Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
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18
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Raun N, Mailo J, Spinelli E, He X, McAvena S, Brand L, O'Sullivan J, Andersen J, Richer L, Tang-Wai R, Bolduc FV. Quantitative phenotypic and network analysis of 1q44 microdeletion for microcephaly. Am J Med Genet A 2017; 173:972-977. [PMID: 28328126 DOI: 10.1002/ajmg.a.38139] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 11/07/2016] [Accepted: 12/05/2016] [Indexed: 11/10/2022]
Abstract
As genome wide techniques become more common, an increasing proportion of patients with intellectual disability (ID) are found to have genetic defects allowing genotype-phenotype correlations. Previously, AKT3 deletion was suggested to be responsible for microcephaly in patients with 1q43-q44 deletion syndrome, but this does not correspond to all cases. We report a case of a de novo 1q44 deletion in an 8-year-old boy with microcephaly in whom AKT3 is not deleted. We used a systematic review of the literature, our patient, and network analysis to gain a better understanding of the genetic basis of microcephaly in 1q deletion patients. Our analysis showed that while AKT3 deletion is associated with more severe (≤3 SD) microcephaly in 1q43-q44 deletion patients, other genes may contribute to microcephaly in AKT3 intact patients with microcephaly and 1q43-44 deletion syndrome. We identified a potential role for HNRNPU, SMYD3, NLRP3, and KIF26B in microcephaly. Overall, our study highlights the need for network analysis and quantitative measures reporting in the phenotypic analysis of a complex genetic syndrome related to copy number variation.
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Affiliation(s)
- Nicholas Raun
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Janette Mailo
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Egidio Spinelli
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Xu He
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Sarah McAvena
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Logan Brand
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Julia O'Sullivan
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - John Andersen
- Division of Neurodevelopmental and Neuromotor Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Lawrence Richer
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Richard Tang-Wai
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
| | - Francois V Bolduc
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada.,Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta, Canada.,Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
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19
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Alcantara D, Timms AE, Gripp K, Baker L, Park K, Collins S, Cheng C, Stewart F, Mehta SG, Saggar A, Sztriha L, Zombor M, Caluseriu O, Mesterman R, Van Allen MI, Jacquinet A, Ygberg S, Bernstein JA, Wenger AM, Guturu H, Bejerano G, Gomez-Ospina N, Lehman A, Alfei E, Pantaleoni C, Conti V, Guerrini R, Moog U, Graham Jr. JM, Hevner R, Dobyns WB, O’Driscoll M, Mirzaa GM. Mutations of AKT3 are associated with a wide spectrum of developmental disorders including extreme megalencephaly. Brain 2017; 140:2610-2622. [PMID: 28969385 PMCID: PMC6080423 DOI: 10.1093/brain/awx203] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/13/2017] [Accepted: 07/04/2017] [Indexed: 11/12/2022] Open
Abstract
Mutations of genes within the phosphatidylinositol-3-kinase (PI3K)-AKT-MTOR pathway are well known causes of brain overgrowth (megalencephaly) as well as segmental cortical dysplasia (such as hemimegalencephaly, focal cortical dysplasia and polymicrogyria). Mutations of the AKT3 gene have been reported in a few individuals with brain malformations, to date. Therefore, our understanding regarding the clinical and molecular spectrum associated with mutations of this critical gene is limited, with no clear genotype-phenotype correlations. We sought to further delineate this spectrum, study levels of mosaicism and identify genotype-phenotype correlations of AKT3-related disorders. We performed targeted sequencing of AKT3 on individuals with these phenotypes by molecular inversion probes and/or Sanger sequencing to determine the type and level of mosaicism of mutations. We analysed all clinical and brain imaging data of mutation-positive individuals including neuropathological analysis in one instance. We performed ex vivo kinase assays on AKT3 engineered with the patient mutations and examined the phospholipid binding profile of pleckstrin homology domain localizing mutations. We identified 14 new individuals with AKT3 mutations with several phenotypes dependent on the type of mutation and level of mosaicism. Our comprehensive clinical characterization, and review of all previously published patients, broadly segregates individuals with AKT3 mutations into two groups: patients with highly asymmetric cortical dysplasia caused by the common p.E17K mutation, and patients with constitutional AKT3 mutations exhibiting more variable phenotypes including bilateral cortical malformations, polymicrogyria, periventricular nodular heterotopia and diffuse megalencephaly without cortical dysplasia. All mutations increased kinase activity, and pleckstrin homology domain mutants exhibited enhanced phospholipid binding. Overall, our study shows that activating mutations of the critical AKT3 gene are associated with a wide spectrum of brain involvement ranging from focal or segmental brain malformations (such as hemimegalencephaly and polymicrogyria) predominantly due to mosaic AKT3 mutations, to diffuse bilateral cortical malformations, megalencephaly and heterotopia due to constitutional AKT3 mutations. We also provide the first detailed neuropathological examination of a child with extreme megalencephaly due to a constitutional AKT3 mutation. This child has one of the largest documented paediatric brain sizes, to our knowledge. Finally, our data show that constitutional AKT3 mutations are associated with megalencephaly, with or without autism, similar to PTEN-related disorders. Recognition of this broad clinical and molecular spectrum of AKT3 mutations is important for providing early diagnosis and appropriate management of affected individuals, and will facilitate targeted design of future human clinical trials using PI3K-AKT pathway inhibitors.
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Affiliation(s)
- Diana Alcantara
- Genome Damage and Stability Centre, University of Sussex, Sussex, UK
| | - Andrew E Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Karen Gripp
- Department of Pediatrics, Sidney Kimmel Medical School, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
- Division of Medical Genetics, A.I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Laura Baker
- Department of Pediatrics, Sidney Kimmel Medical School, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
- Division of Medical Genetics, A.I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Kaylee Park
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Sarah Collins
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Chi Cheng
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Fiona Stewart
- Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK
| | - Sarju G Mehta
- East Anglian Medical Genetics Service, Addenbrookes Hospital, Cambridge, UK
| | - Anand Saggar
- South West Thames Regional Genetic Services, St. George’s NHS Trust and St. George’s Hospital Medical School, London, UK
| | - László Sztriha
- Department of Pediatrics, University of Szeged, Szeged, Hungary
| | - Melinda Zombor
- Department of Pediatrics, University of Szeged, Szeged, Hungary
| | - Oana Caluseriu
- Department of Medical Genetics, Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Ronit Mesterman
- Division of Pediatric Neurology, Developmental Pediatric Rehabilitation and Autism Spectrum Disorder, McMaster University, Hamilton, ON, Canada
| | - Margot I Van Allen
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- B.C. Children’s Hospital Research Centre, Vancouver, BC Canada
| | - Adeline Jacquinet
- Center for Human Genetics, Centre Hospitalier Universitaire and University of Liège, Liège, Belgium
| | - Sofia Ygberg
- Neuropediatric Unit and Centre for Inherited Metabolic Diseases (CMMS), Karolinska University Hospital, Stockholm, Sweden
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Aaron M Wenger
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Harendra Guturu
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Gill Bejerano
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
- Department of Computer Science, School of Engineering, Stanford University School of Medicine, Stanford, California, USA
- Department of Developmental Biology, School of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Natalia Gomez-Ospina
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Enrico Alfei
- Developmental Neurology Unit, Department of Pediatric Neurosciences, Carlo Besta Neurological Institute, IRCCS Foundation, Milan, Italy
| | - Chiara Pantaleoni
- Developmental Neurology Unit, Department of Pediatric Neurosciences, Carlo Besta Neurological Institute, IRCCS Foundation, Milan, Italy
| | - Valerio Conti
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, A. Meyer Children’s Hospital, Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, A. Meyer Children’s Hospital, Florence, Italy
- IRCCS Stella Maris, Pisa, Italy
| | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - John M Graham Jr.
- Department of Pediatrics, Cedars-Sinai Medical Center, Harbor-UCLA Medical Center, David Geffen School of Medicine Los Angeles, California, USA
| | - Robert Hevner
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Neurological Surgery, University of Washington, Seattle, Washington, USA
| | - William B Dobyns
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Mark O’Driscoll
- Genome Damage and Stability Centre, University of Sussex, Sussex, UK
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
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20
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Ehmke N, Karge S, Buchmann J, Korinth D, Horn D, Reis O, Häßler F. A de novo nonsense mutation in ZBTB18 plus a de novo 15q13.3 microdeletion in a 6-year-old female. Am J Med Genet A 2017; 173:1251-1256. [PMID: 28345786 DOI: 10.1002/ajmg.a.38145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 12/21/2016] [Accepted: 01/02/2017] [Indexed: 12/11/2022]
Abstract
ZBTB18 has been proposed as candidate gene for microcephaly and abnormalities of the corpus callosum based on overlapping microdeletions of 1q43q44. More recently, de novo mutations of ZBTB18 have been identified in patients with syndromic and non-syndromic intellectual disability. Heterozygous microdeletions of 15q13.3 encompassing the candidate gene CHRNA7 are associated with developmental delay or intellectual disability with speech problems, hypotonia, and seizures. They are characterized by significant variability and reduced penetrance. We report on a patient with a de novo ZBTB18 nonsense mutation and a de novo 15q13.3 microdeletion, both in a heterozygous state, identified by next generation sequencing and array-CGH. The 6-year-old girl showed global developmental delay, absent speech, therapy-refractory seizures, ataxia, muscular hypotonia, and discrete facial dysmorphisms. Almost all of these features have been reported for both genetic aberrations, but the severity could hardly been explained by the microdeletion 15q13.3 alone. We assume an additive effect of haploinsufficiency of ZBTB18 and CHRNA7 in our patient. Assembling the features of our patient and the published patients, we noted that only one of them showed mild anomalies of the corpus callosum. Moreover, we hypothesize that nonsense mutations of ZBTB18 are associated with a more severe phenotype than missense mutations. This report indicates that haploinsufficiency of additional genes beside ZBTB18 causes the high frequency of corpus callosum anomalies in patients with microdeletions of 1q43q44 and underlines the importance of an NGS-based molecular diagnostic in complex phenotypes.
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Affiliation(s)
- Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Sylvio Karge
- Clinics for Child and Adolescent Psychiatry of the University of Rostock, Rostock, Germany
| | - Johannes Buchmann
- Clinics for Child and Adolescent Psychiatry of the University of Rostock, Rostock, Germany
| | | | - Denise Horn
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Olaf Reis
- Clinics for Child and Adolescent Psychiatry of the University of Rostock, Rostock, Germany
| | - Frank Häßler
- Clinics for Child and Adolescent Psychiatry of the University of Rostock, Rostock, Germany
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21
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Genetic and phenotypic dissection of 1q43q44 microdeletion syndrome and neurodevelopmental phenotypes associated with mutations in ZBTB18 and HNRNPU. Hum Genet 2017; 136:463-479. [PMID: 28283832 PMCID: PMC5360844 DOI: 10.1007/s00439-017-1772-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 02/21/2017] [Indexed: 11/09/2022]
Abstract
Subtelomeric 1q43q44 microdeletions cause a syndrome associating intellectual disability, microcephaly, seizures and anomalies of the corpus callosum. Despite several previous studies assessing genotype-phenotype correlations, the contribution of genes located in this region to the specific features of this syndrome remains uncertain. Among those, three genes, AKT3, HNRNPU and ZBTB18 are highly expressed in the brain and point mutations in these genes have been recently identified in children with neurodevelopmental phenotypes. In this study, we report the clinical and molecular data from 17 patients with 1q43q44 microdeletions, four with ZBTB18 mutations and seven with HNRNPU mutations, and review additional data from 37 previously published patients with 1q43q44 microdeletions. We compare clinical data of patients with 1q43q44 microdeletions with those of patients with point mutations in HNRNPU and ZBTB18 to assess the contribution of each gene as well as the possibility of epistasis between genes. Our study demonstrates that AKT3 haploinsufficiency is the main driver for microcephaly, whereas HNRNPU alteration mostly drives epilepsy and determines the degree of intellectual disability. ZBTB18 deletions or mutations are associated with variable corpus callosum anomalies with an incomplete penetrance. ZBTB18 may also contribute to microcephaly and HNRNPU to thin corpus callosum, but with a lower penetrance. Co-deletion of contiguous genes has additive effects. Our results confirm and refine the complex genotype-phenotype correlations existing in the 1qter microdeletion syndrome and define more precisely the neurodevelopmental phenotypes associated with genetic alterations of AKT3, ZBTB18 and HNRNPU in humans.
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