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Qiao L, Welch CL, Hernan R, Wynn J, Krishnan US, Zalieckas JM, Buchmiller T, Khlevner J, De A, Farkouh-Karoleski C, Wagner AJ, Heydweiller A, Mueller AC, de Klein A, Warner BW, Maj C, Chung D, McCulley DJ, Schindel D, Potoka D, Fialkowski E, Schulz F, Kipfmuller F, Lim FY, Magielsen F, Mychaliska GB, Aspelund G, Reutter HM, Needelman H, Schnater JM, Fisher JC, Azarow K, Elfiky M, Nöthen MM, Danko ME, Li M, Kosiński P, Wijnen RMH, Cusick RA, Soffer SZ, Cochius-Den Otter SCM, Schaible T, Crombleholme T, Duron VP, Donahoe PK, Sun X, High FA, Bendixen C, Brosens E, Shen Y, Chung WK. Common variants increase risk for congenital diaphragmatic hernia within the context of de novo variants. Am J Hum Genet 2024:S0002-9297(24)00334-3. [PMID: 39332409 DOI: 10.1016/j.ajhg.2024.08.024] [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: 04/23/2024] [Revised: 08/24/2024] [Accepted: 08/30/2024] [Indexed: 09/29/2024] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly often accompanied by other structural anomalies and/or neurobehavioral manifestations. Rare de novo protein-coding variants and copy-number variations contribute to CDH in the population. However, most individuals with CDH remain genetically undiagnosed. Here, we perform integrated de novo and common-variant analyses using 1,469 CDH individuals, including 1,064 child-parent trios and 6,133 ancestry-matched, unaffected controls for the genome-wide association study. We identify candidate CDH variants in 15 genes, including eight novel genes, through deleterious de novo variants. We further identify two genomic loci contributing to CDH risk through common variants with similar effect sizes among Europeans and Latinx. Both loci are in putative transcriptional regulatory regions of developmental patterning genes. Estimated heritability in common variants is ∼19%. Strikingly, there is no significant difference in estimated polygenic risk scores between isolated and complex CDH or between individuals harboring deleterious de novo variants and individuals without these variants. The data support a polygenic model as part of the CDH genetic architecture.
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Affiliation(s)
- Lu Qiao
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Carrie L Welch
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rebecca Hernan
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Usha S Krishnan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jill M Zalieckas
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Anesthesiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Terry Buchmiller
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Julie Khlevner
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Aliva De
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Amy J Wagner
- Children's Hospital of Wisconsin, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Andreas Heydweiller
- Department of General, Visceral, Vascular, and Thoracic Surgery, Unit of Pediatric Surgery, University Hospital Bonn, Bonn, Germany
| | - Andreas C Mueller
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Brad W Warner
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Dai Chung
- Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN 37232, USA
| | - David J McCulley
- Department of Pediatrics, San Diego Medical School, University of California, San Diego, San Diego, CA 92092, USA
| | | | | | | | - Felicitas Schulz
- Department of Hematology, Oncology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Florian Kipfmuller
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Foong-Yen Lim
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Frank Magielsen
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | | | - Gudrun Aspelund
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Heiko Martin Reutter
- Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Howard Needelman
- University of Nebraska Medical Center College of Medicine, Omaha, NE 68114, USA
| | - J Marco Schnater
- Department of Pediatric Surgery, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Jason C Fisher
- New York University Grossman School of Medicine, Hassenfeld Children's Hospital at NYU Langone, New York, NY 10016, USA
| | - Kenneth Azarow
- Oregon Health and Science University, Portland, OR 97239, USA
| | | | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Melissa E Danko
- Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN 37232, USA
| | - Mindy Li
- Rush University Medical Center, Chicago, IL 60612, USA
| | - Przemyslaw Kosiński
- Department of Obstetrics, Perinatology and Gynecology, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Rene M H Wijnen
- Department of Pediatric Surgery, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Robert A Cusick
- University of Nebraska Medical Center College of Medicine, Omaha, NE 68114, USA
| | | | - Suzan C M Cochius-Den Otter
- Department of Neonatology and Pediatric Intensive Care, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Thomas Schaible
- Department of Neonatology, University Children's Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | | | - Vincent P Duron
- Department of Surgery (Pediatrics), Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Patricia K Donahoe
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Xin Sun
- Department of Pediatrics, San Diego Medical School, University of California, San Diego, San Diego, CA 92092, USA
| | - Frances A High
- Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Charlotte Bendixen
- Department of General, Visceral, Vascular, and Thoracic Surgery, Unit of Pediatric Surgery, University Hospital Bonn, Bonn, Germany
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA; JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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2
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Trevisan AJ, Han K, Chapman P, Kulkarni AS, Hinton JM, Ramirez C, Klein I, Gatto G, Gabitto MI, Menon V, Bikoff JB. The transcriptomic landscape of spinal V1 interneurons reveals a role for En1 in specific elements of motor output. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.18.613279. [PMID: 39345580 PMCID: PMC11429899 DOI: 10.1101/2024.09.18.613279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Neural circuits in the spinal cord are composed of diverse sets of interneurons that play crucial roles in shaping motor output. Despite progress in revealing the cellular architecture of the spinal cord, the extent of cell type heterogeneity within interneuron populations remains unclear. Here, we present a single-nucleus transcriptomic atlas of spinal V1 interneurons across postnatal development. We find that the core molecular taxonomy distinguishing neonatal V1 interneurons perdures into adulthood, suggesting conservation of function across development. Moreover, we identify a key role for En1, a transcription factor that marks the V1 population, in specifying one unique subset of V1 Pou6f2 interneurons. Loss of En1 selectively disrupts the frequency of rhythmic locomotor output but does not disrupt flexion/extension limb movement. Beyond serving as a molecular resource for this neuronal population, our study highlights how deep neuronal profiling provides an entry point for functional studies of specialized cell types in motor output.
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Wang B, Zhu Y, Wei B, Zeng H, Zhang P, Li L, Wang H, Wu X, Zheng Y, Sun M. miR-377-3p Regulates Hippocampal Neurogenesis via the Zfp462-Pbx1 Pathway and Mediates Anxiety-Like Behaviors in Prenatal Hypoxic Offspring. Mol Neurobiol 2024; 61:1920-1935. [PMID: 37817032 DOI: 10.1007/s12035-023-03683-3] [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: 03/01/2023] [Accepted: 09/29/2023] [Indexed: 10/12/2023]
Abstract
Prenatal hypoxia (PH) is one of the most common complications of obstetrics and is closely associated with many neurological disorders such as depression, anxiety, and cognitive impairment. Our previous study found that Zfp462 heterozygous (Het) mice exhibit significant anxiety-like behavior. Interestingly, offspring mice with PH also have anxiety-like behaviors in adulthood, accompanied by reduced expression of Zfp462 and increased expression of miR-377-3p; however, the exact regulatory mechanisms remain unclear. In this study, western blotting, gene knockdown, immunofluorescence, dual-luciferase reporter assay, immunoprecipitation, cell transfection with miR-377-3p mimics or inhibitors, quantitative real-time PCR, and rescue assay were used to detect changes in the miR-377-3p-Zfp462-Pbx1 (pre-B-cell leukemia homeobox1) pathway in the brains of prenatal hypoxic offspring to explain the pathogenesis of anxiety-like behaviors. We found that Zfp462 deficiency promoted Pbx1 protein degradation through ubiquitination and that Zfp462 Het mice showed downregulation of the protein kinase B (PKB, also called Akt)-glycogen synthase kinase-3β (GSK3β)-cAMP response element-binding protein (CREB) pathway and hippocampal neurogenesis with anxiety-like behavior. In addition, PH mice exhibited upregulation of miR-377-3p, downregulation of Zfp462/Pbx1-Akt-GSK3β-CREB pathway activity, reduced hippocampal neurogenesis, and an anxiety-like phenotype. Intriguingly, miR-377-3p directly targets the 3'UTR of Zfp462 mRNA to regulate Zfp462 expression. Importantly, microinjection of miR-377-3p antagomir into the hippocampal dentate gyrus of PH mice upregulated Zfp462/Pbx1-Akt-GSK3β-CREB pathway activity, increased hippocampal neurogenesis, and improved anxiety-like behaviors. Collectively, our findings demonstrated a crucial role for miR-377-3p in the regulation of hippocampal neurogenesis and anxiety-like behaviors via the Zfp462/Pbx1-Akt-GSK3β-CREB pathway. Therefore, miR-377-3p could be a potential therapeutic target for anxiety-like behavior in prenatal hypoxic offspring.
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Affiliation(s)
- Bin Wang
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou City, 215006, Jiangsu, China.
| | - Yichen Zhu
- Cambridge-Suda Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases Research, Suzhou Medical College of Soochow University, Jiangsu, 215123, China
| | - Bin Wei
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou City, 215006, Jiangsu, China
| | - Hongtao Zeng
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou City, 215006, Jiangsu, China
| | - Pengjie Zhang
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou City, 215006, Jiangsu, China
| | - Lingjun Li
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou City, 215006, Jiangsu, China
| | - Hongyan Wang
- Obstetrics and Gynecology Hospital Research Center, Institute of Reproduction and Development, Fudan University, Shanghai, 200433, China
- State Key Laboratory of Genetic Engineering, MOE Key Laboratory of Contemporary Anthropology, and Collaborative Innovation Center for Genetics & Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xiaohui Wu
- State Key Laboratory of Genetic Engineering, MOE Key Laboratory of Contemporary Anthropology, and Collaborative Innovation Center for Genetics & Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Institute of Developmental Biology & Molecular Medicine, Fudan University, Shanghai, 200433, China
| | - Yufang Zheng
- Obstetrics and Gynecology Hospital Research Center, Institute of Reproduction and Development, Fudan University, Shanghai, 200433, China
- State Key Laboratory of Genetic Engineering, MOE Key Laboratory of Contemporary Anthropology, and Collaborative Innovation Center for Genetics & Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Institute of Developmental Biology & Molecular Medicine, Fudan University, Shanghai, 200433, China
| | - Miao Sun
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou City, 215006, Jiangsu, China.
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Han Y, Barasa P, Zeger L, Salomonsson SB, Zanotti F, Egli M, Zavan B, Trentini M, Florin G, Vaerneus A, Aldskogius H, Fredriksson R, Kozlova EN. Effects of microgravity on neural crest stem cells. Front Neurosci 2024; 18:1379076. [PMID: 38660221 PMCID: PMC11041629 DOI: 10.3389/fnins.2024.1379076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/15/2024] [Indexed: 04/26/2024] Open
Abstract
Exposure to microgravity (μg) results in a range of systemic changes in the organism, but may also have beneficial cellular effects. In a previous study we detected increased proliferation capacity and upregulation of genes related to proliferation and survival in boundary cap neural crest stem cells (BC) after MASER14 sounding rocket flight compared to ground-based controls. However, whether these changes were due to μg or hypergravity was not clarified. In the current MASER15 experiment BCs were exposed simultaneously to μg and 1 g conditions provided by an onboard centrifuge. BCs exposed to μg displayed a markedly increased proliferation capacity compared to 1 g on board controls, and genetic analysis of BCs harvested 5 h after flight revealed an upregulation, specifically in μg-exposed BCs, of Zfp462 transcription factor, a key regulator of cell pluripotency and neuronal fate. This was associated with alterations in exosome microRNA content between μg and 1 g exposed MASER15 specimens. Since the specimens from MASER14 were obtained for analysis with 1 week's delay, we examined whether gene expression and exosome content were different compared to the current MASER15 experiments, in which specimens were harvested 5 h after flight. The overall pattern of gene expression was different and Zfp462 expression was down-regulated in MASER14 BC μg compared to directly harvested specimens (MASER15). MicroRNA exosome content was markedly altered in medium harvested with delay compared to directly collected samples. In conclusion, our analysis indicates that even short exposure to μg alters gene expression, leading to increased BC capacity for proliferation and survival, lasting for a long time after μg exposure. With delayed harvest of specimens, a situation which may occur due to special post-flight circumstances, the exosome microRNA content is modified compared to fast specimen harvest, and the direct effects from μg exposure may be partially attenuated, whereas other effects can last for a long time after return to ground conditions.
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Affiliation(s)
- Yilin Han
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Povilas Barasa
- Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Lukas Zeger
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sara B. Salomonsson
- Department of Pharmaceutical Bioscience, Uppsala University, Uppsala, Sweden
| | - Federica Zanotti
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Marcel Egli
- Space Biology Group, School of Engineering and Architecture, Institute of Medical Engineering, Lucerne University of Applied Sciences and Arts, Hergiswil, Switzerland
- National Center for Biomedical Research in Space, Innovation Cluster Space and Aviation, University of Zurich, Zurich, Switzerland
| | - Barbara Zavan
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Martina Trentini
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | | | | | - Håkan Aldskogius
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Robert Fredriksson
- Department of Pharmaceutical Bioscience, Uppsala University, Uppsala, Sweden
| | - Elena N. Kozlova
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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Dillingham CM, Cormaty H, Morgan EC, Tak AI, Esgdaille DE, Boutz PL, Sridharan R. KDM3A and KDM3B Maintain Naïve Pluripotency Through the Regulation of Alternative Splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.31.543088. [PMID: 37398291 PMCID: PMC10312572 DOI: 10.1101/2023.05.31.543088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Histone modifying enzymes play a central role in maintaining cell identity by establishing a conducive chromatin environment for lineage specific transcription factor activity. Pluripotent embryonic stem cell (ESC) identity is characterized by a lower abundance of gene repression associated histone modifications that enables rapid response to differentiation cues. The KDM3 family of histone demethylases removes the repressive histone H3 lysine 9 dimethylation (H3K9me2). Here we uncover a surprising role for the KDM3 proteins in the maintenance of the pluripotent state through post-transcriptional regulation. We find that KDM3A and KDM3B interact with RNA processing factors such as EFTUD2 and PRMT5. Acute selective degradation of the endogenous KDM3A and KDM3B proteins resulted in altered splicing independent of H3K9me2 status or catalytic activity. These splicing changes partially resemble the splicing pattern of the more blastocyst-like ground state of pluripotency and occurred in important chromatin and transcription factors such as Dnmt3b, Tbx3 and Tcf12. Our findings reveal non-canonical roles of histone demethylating enzymes in splicing to regulate cell identity.
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Affiliation(s)
- Caleb M Dillingham
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Harshini Cormaty
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ellen C Morgan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Andrew I Tak
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Dakarai E Esgdaille
- Department of Biochemistry and Biophysics, Center for RNA Biology, Wilmot Cancer Center, University of Rochester School of Medicine and Dentistry
| | - Paul L Boutz
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
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Ge C, Tian Y, Hu C, Mei L, Li D, Dong P, Zhang Y, Li H, Sun D, Peng W, Xu X, Jiang Y, Xu Q. Clinical impact and in vitro characterization of ADNP variants in pediatric patients. Mol Autism 2024; 15:5. [PMID: 38254177 PMCID: PMC10804707 DOI: 10.1186/s13229-024-00584-7] [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: 10/27/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Helsmoortel-Van der Aa syndrome (HVDAS) is a rare genetic disorder caused by variants in the activity-dependent neuroprotector homeobox (ADNP) gene; hence, it is also called ADNP syndrome. ADNP is a multitasking protein with the function as a transcription factor, playing a critical role in brain development. Furthermore, ADNP variants have been identified as one of the most common single-gene causes of autism spectrum disorder (ASD) and intellectual disability. METHODS We assembled a cohort of 15 Chinese pediatric patients, identified 13 variants in the coding region of ADNP gene, and evaluated their clinical phenotypes. Additionally, we constructed the corresponding ADNP variants and performed western blotting and immunofluorescence analysis to examine their protein expression and subcellular localization in human HEK293T and SH-SY5Y cells. RESULTS Our study conducted a thorough characterization of the clinical manifestations in 15 children with ADNP variants, and revealed a broad spectrum of symptoms including global developmental delay, intellectual disability, ASD, facial abnormalities, and other features. In vitro studies were carried out to check the expression of ADNP with identified variants. Two cases presented missense variants, while the remainder exhibited nonsense or frameshift variants, leading to truncated mutants in in vitro overexpression systems. Both overexpressed wildtype ADNP and all the different mutants were found to be confined to the nuclei in HEK293T cells; however, the distinctive pattern of nuclear bodies formed by the wildtype ADNP was either partially or entirely disrupted by the mutant proteins. Moreover, two variants of p.Y719* on the nuclear localization signal (NLS) of ADNP disrupted the nuclear expression pattern, predominantly manifesting in the cytoplasm in SH-SY5Y cells. LIMITATIONS Our study was limited by a relatively small sample size and the absence of a longitudinal framework to monitor the progression of patient conditions over time. Additionally, we lacked in vivo evidence to further indicate the causal implications of the identified ADNP variants. CONCLUSIONS Our study reported the first cohort of HVDAS patients in the Chinese population and provided systematic clinical presentations and laboratory examinations. Furthermore, we identified multiple genetic variants and validated them in vitro. Our findings offered valuable insights into the diverse genetic variants associated with HVDAS.
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Affiliation(s)
- Chuanhui Ge
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Yuxin Tian
- Department of Child Health Care, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Chunchun Hu
- Department of Child Health Care, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Lianni Mei
- Department of Child Health Care, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Dongyun Li
- Department of Child Health Care, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Ping Dong
- Department of Child Health Care, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Ying Zhang
- Department of Child Health Care, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Huiping Li
- Department of Child Health Care, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Daijing Sun
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Wenzhu Peng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Xiu Xu
- Department of Child Health Care, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Yan Jiang
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Qiong Xu
- Department of Child Health Care, Children's Hospital of Fudan University, Shanghai, 201102, China.
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7
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Kuroda Y, Iwata-Otsubo A, Dias KR, Temple SEL, Nagao K, De Hayr L, Zhu Y, Isobe SY, Nishibuchi G, Fiordaliso SK, Fujita Y, Rippert AL, Baker SW, Leung ML, Koboldt DC, Harman A, Keena BA, Kazama I, Subramanian GM, Manickam K, Schmalz B, Latsko M, Zackai EH, Edwards M, Evans CA, Dulik MC, Buckley MF, Yamashita T, O'Brien WT, Harvey RJ, Obuse C, Roscioli T, Izumi K. Dominant-negative variants in CBX1 cause a neurodevelopmental disorder. Genet Med 2023; 25:100861. [PMID: 37087635 DOI: 10.1016/j.gim.2023.100861] [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: 01/17/2023] [Revised: 04/16/2023] [Accepted: 04/16/2023] [Indexed: 04/24/2023] Open
Abstract
PURPOSE This study aimed to establish variants in CBX1, encoding heterochromatin protein 1β (HP1β), as a cause of a novel syndromic neurodevelopmental disorder. METHODS Patients with CBX1 variants were identified, and clinician researchers were connected using GeneMatcher and physician referrals. Clinical histories were collected from each patient. To investigate the pathogenicity of identified variants, we performed in vitro cellular assays and neurobehavioral and cytological analyses of neuronal cells obtained from newly generated Cbx1 mutant mouse lines. RESULTS In 3 unrelated individuals with developmental delay, hypotonia, and autistic features, we identified heterozygous de novo variants in CBX1. The identified variants were in the chromodomain, the functional domain of HP1β, which mediates interactions with chromatin. Cbx1 chromodomain mutant mice displayed increased latency-to-peak response, suggesting the possibility of synaptic delay or myelination deficits. Cytological and chromatin immunoprecipitation experiments confirmed the reduction of mutant HP1β binding to heterochromatin, whereas HP1β interactome analysis demonstrated that the majority of HP1β-interacting proteins remained unchanged between the wild-type and mutant HP1β. CONCLUSION These collective findings confirm the role of CBX1 in developmental disabilities through the disruption of HP1β chromatin binding during neurocognitive development. Because HP1β forms homodimers and heterodimers, mutant HP1β likely sequesters wild-type HP1β and other HP1 proteins, exerting dominant-negative effects.
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Affiliation(s)
- Yukiko Kuroda
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Aiko Iwata-Otsubo
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kerith-Rae Dias
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia; Neuroscience Research Australia (NeuRA) and Prince of Wales Clinical School, University of New South Wales, Kensington, NSW, Australia
| | - Suzanna E L Temple
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Koji Nagao
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Lachlan De Hayr
- School of Health, University of the Sunshine Coast, Maroochydore, QLD, Australia; Sunshine Coast Health Institute, Birtinya, QLD, Australia
| | - Ying Zhu
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Shin-Ya Isobe
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Gohei Nishibuchi
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Sarah K Fiordaliso
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Yuki Fujita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Alyssa L Rippert
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Samuel W Baker
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Marco L Leung
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH; Department of Pathology, The Ohio State University College of Medicine, Columbus, OH
| | - Daniel C Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH
| | - Adele Harman
- Transgenic core, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Beth A Keena
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Izumi Kazama
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Kandamurugu Manickam
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH; Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Betsy Schmalz
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Maeson Latsko
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Elaine H Zackai
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Matt Edwards
- Hunter Genetics, Newcastle, NSW, Australia; University of Western Sydney School of Medicine, Sydney, NSW, Australia
| | - Carey-Anne Evans
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia; Neuroscience Research Australia (NeuRA) and Prince of Wales Clinical School, University of New South Wales, Kensington, NSW, Australia
| | - Matthew C Dulik
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Michael F Buckley
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - W Timothy O'Brien
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Robert J Harvey
- School of Health, University of the Sunshine Coast, Maroochydore, QLD, Australia; Sunshine Coast Health Institute, Birtinya, QLD, Australia
| | - Chikashi Obuse
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Tony Roscioli
- Randwick Genomics Laboratory, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia; Neuroscience Research Australia (NeuRA) and Prince of Wales Clinical School, University of New South Wales, Kensington, NSW, Australia
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Roberts Individualized Medical Genetics Center, The Children's Hospital of Philadelphia, Philadelphia, PA; Laboratory of Rare Disease Research, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan; Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX.
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