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Coschiera A, Yoshihara M, Lauter G, Ezer S, Pucci M, Li H, Kavšek A, Riedel CG, Kere J, Swoboda P. Primary cilia promote the differentiation of human neurons through the WNT signaling pathway. BMC Biol 2024; 22:48. [PMID: 38413974 PMCID: PMC10900739 DOI: 10.1186/s12915-024-01845-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Primary cilia emanate from most human cell types, including neurons. Cilia are important for communicating with the cell's immediate environment: signal reception and transduction to/from the ciliated cell. Deregulation of ciliary signaling can lead to ciliopathies and certain neurodevelopmental disorders. In the developing brain cilia play well-documented roles for the expansion of the neural progenitor cell pool, while information about the roles of cilia during post-mitotic neuron differentiation and maturation is scarce. RESULTS We employed ciliated Lund Human Mesencephalic (LUHMES) cells in time course experiments to assess the impact of ciliary signaling on neuron differentiation. By comparing ciliated and non-ciliated neuronal precursor cells and neurons in wild type and in RFX2 -/- mutant neurons with altered cilia, we discovered an early-differentiation "ciliary time window" during which transient cilia promote axon outgrowth, branching and arborization. Experiments in neurons with IFT88 and IFT172 ciliary gene knockdowns, leading to shorter cilia, confirm these results. Cilia promote neuron differentiation by tipping WNT signaling toward the non-canonical pathway, in turn activating WNT pathway output genes implicated in cyto-architectural changes. CONCLUSIONS We provide a mechanistic entry point into when and how ciliary signaling coordinates, promotes and translates into anatomical changes. We hypothesize that ciliary alterations causing neuron differentiation defects may result in "mild" impairments of brain development, possibly underpinning certain aspects of neurodevelopmental disorders.
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Affiliation(s)
- Andrea Coschiera
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba, Japan
- Chiba University, Chiba, Japan
| | - Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala, Sweden
- Uppsala University, Uppsala, Sweden
| | - Sini Ezer
- University of Helsinki, Stem Cells and Metabolism Research Program, and Folkhälsan Research Center, Helsinki, Finland
| | - Mariangela Pucci
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- Department of Bioscience and Technology for Food, Agriculture and Environment, Teramo, Italy
- University of Teramo, Teramo, Italy
| | - Haonan Li
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Alan Kavšek
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Christian G Riedel
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- University of Helsinki, Stem Cells and Metabolism Research Program, and Folkhälsan Research Center, Helsinki, Finland
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden.
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2
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Zaki ZMM, Ali SA, Ghazali MM, Jam FA. Genetic Modifications of Developmental Dyslexia and Its Representation Using In Vivo, In Vitro Model. Glob Med Genet 2024; 11:76-85. [PMID: 38414980 PMCID: PMC10898997 DOI: 10.1055/s-0044-1781456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024] Open
Abstract
Dyslexia is a genetic and heritable disorder that has yet to discover the treatment of it, especially at the molecular and drug intervention levels. This review provides an overview of the current findings on the environmental and genetic factors involved in developmental dyslexia. The latest techniques used in diagnosing the disease and macromolecular factors findings may contribute to a higher degree of development in detangling the proper management and treatment for dyslexic individuals. Furthermore, this review tried to put together all the models used in the current dyslexia research for references in future studies that include animal models as well as in vitro models and how the previous research has provided consistent data across many years and regions. Thus, we suggest furthering the studies using an organoid model based on the existing gene polymorphism, pathways, and neuronal function input.
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Affiliation(s)
- Zakiyyah M M Zaki
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Siti A Ali
- Department of Electronic Engineering, Faculty of Engineering and Green Technology, Universiti Tunku Abdul Rahman, Kampar, Perak, Malaysia
- Centre for Healthcare Science and Technology, Universiti Tunku Abdul Rahman, Kampar, Perak, Malaysia
| | - Mazira M Ghazali
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Terengganu, Malaysia
| | - Faidruz A Jam
- Department of Biochemistry, Faculty of Medicine, Manipal University College Malaysia, Melaka, Malaysia
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3
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Zhu X, Chen C, Song J, Dong S, Zeng X, Niu Z, Sha Y, Zhang X. A novel homozygous splice variant in DNAAF4 is associated with asthenozoospermia. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1689-1692. [PMID: 37674365 PMCID: PMC10577477 DOI: 10.3724/abbs.2023147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 06/25/2023] [Indexed: 09/08/2023] Open
Affiliation(s)
- Xiaobin Zhu
- Department of Gynecology and ObstetricsReproductive Medical CenterShanghai Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Chen Chen
- Institute of Reproductive MedicineSchool of MedicineNantong UniversityNantong226019China
| | - Jian Song
- Institute of Reproductive MedicineSchool of MedicineNantong UniversityNantong226019China
| | - Shijue Dong
- Institute of Reproductive MedicineSchool of MedicineNantong UniversityNantong226019China
| | - Xuhui Zeng
- Institute of Reproductive MedicineSchool of MedicineNantong UniversityNantong226019China
| | - Zhihong Niu
- Department of Gynecology and ObstetricsReproductive Medical CenterShanghai Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Yanwei Sha
- of AndrologyWomen and Children’s HospitalSchool of MedicineXiamen UniversityXiamen361005China
| | - Xiaoning Zhang
- Institute of Reproductive MedicineSchool of MedicineNantong UniversityNantong226019China
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4
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Bieder A, Chandrasekar G, Wason A, Erkelenz S, Gopalakrishnan J, Kere J, Tapia-Páez I. Genetic and protein interaction studies between the ciliary dyslexia candidate genes DYX1C1 and DCDC2. BMC Mol Cell Biol 2023; 24:20. [PMID: 37237337 DOI: 10.1186/s12860-023-00483-4] [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: 11/17/2022] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND DYX1C1 (DNAAF4) and DCDC2 are two of the most replicated dyslexia candidate genes in genetic studies. They both have demonstrated roles in neuronal migration, in cilia growth and function and they both are cytoskeletal interactors. In addition, they both have been characterized as ciliopathy genes. However, their exact molecular functions are still incompletely described. Based on these known roles, we asked whether DYX1C1 and DCDC2 interact on the genetic and the protein level. RESULTS Here, we report the physical protein-protein interaction of DYX1C1 and DCDC2 as well as their respective interactions with the centrosomal protein CPAP (CENPJ) on exogenous and endogenous levels in different cell models including brain organoids. In addition, we show a synergistic genetic interaction between dyx1c1 and dcdc2b in zebrafish exacerbating the ciliary phenotype. Finally, we show a mutual effect on transcriptional regulation among DYX1C1 and DCDC2 in a cellular model. CONCLUSIONS In summary, we describe the physical and functional interaction between the two genes DYX1C1 and DCDC2. These results contribute to the growing understanding of the molecular roles of DYX1C1 and DCDC2 and set the stage for future functional studies.
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Affiliation(s)
- Andrea Bieder
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | - Arpit Wason
- Center for Molecular Medicine, Institute for Biochemistry I of the University of Cologne, Cologne, Germany
| | - Steffen Erkelenz
- Institute of Human Genetics, Universitätsklinikum, Heinrich Heine University, Düsseldorf, Germany
| | - Jay Gopalakrishnan
- Institute of Human Genetics, Universitätsklinikum, Heinrich Heine University, Düsseldorf, Germany
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Molecular Neurology Research Program, University of Helsinki, Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Isabel Tapia-Páez
- Department of Medicine, Solna, Karolinska Institutet, Solnavägen 30, SE-171 76, Solna, Sweden.
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Coschiera A, Watts ME, Kere J, Tammimies K, Swoboda P. Human LUHMES and NES cells as models for studying primary cilia in neurons. Methods Cell Biol 2023; 176:27-41. [PMID: 37164541 DOI: 10.1016/bs.mcb.2022.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Primary cilia are antenna-like organelles emanating from the cell surface. They are involved in cell-to-cell communication and bidirectional signal transduction to/from the extracellular environment. During brain formation, cilia critically aid in neurogenesis and maturation of neuronal structures such as axons, dendrites and synapses. Aberrations in cilia function can induce neuron differentiation defects and pathological consequences of varying severity, resulting in ciliopathies and likely a number of neurodevelopmental disorders. Despite the documented relevance of cilia for proper brain development, human neuronal models to recognize and study cilia biology are still scarce. We have established two types of cell models, Lund Human Mesencephalic (LUHMES) cells and neuroepithelial stem (NES) cells derived from induced pluripotent stem cells (iPSC), to investigate cilia biology in both proliferating neuronal progenitors/precursors and during the entire neuron differentiation and maturation process. We employ improved immunocytochemistry assays able to specifically detect cilia by confocal and super-resolution microscopy. We provide straightforward and robust methods to easily maintain cells in culture, for immunostaining and characterization of cilia orientation, anatomy and shape in human neurons across all stages of differentiation.
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Affiliation(s)
- Andrea Coschiera
- Karolinska Institute, Department of Biosciences and Nutrition, Huddinge, Sweden
| | - Michelle Evelyn Watts
- Karolinska Institute, Department of Women's and Children's Health and Center for Psychiatry Research, Center of Neurodevelopmental Disorders (KIND), Division of Neuropsychiatry, Stockholm, Sweden; Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Juha Kere
- Karolinska Institute, Department of Biosciences and Nutrition, Huddinge, Sweden; University of Helsinki, Stem Cells and Metabolism Research Program and Folkhälsan Research Center, Helsinki, Finland
| | - Kristiina Tammimies
- Karolinska Institute, Department of Women's and Children's Health and Center for Psychiatry Research, Center of Neurodevelopmental Disorders (KIND), Division of Neuropsychiatry, Stockholm, Sweden; Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Peter Swoboda
- Karolinska Institute, Department of Biosciences and Nutrition, Huddinge, Sweden.
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6
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Mizukawa T, Nishida T, Akashi S, Kawata K, Kikuchi S, Kawaki H, Takigawa M, Kamioka H, Kubota S. RFX1-mediated CCN3 induction that may support chondrocyte survival under starved conditions. J Cell Physiol 2021; 236:6884-6896. [PMID: 33655492 DOI: 10.1002/jcp.30348] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/12/2021] [Accepted: 02/16/2021] [Indexed: 02/06/2023]
Abstract
Cellular communication network factor (CCN) family members are multifunctional matricellular proteins that manipulate and integrate extracellular signals. In our previous studies investigating the role of CCN family members in cellular metabolism, we found three members that might be under the regulation of energy metabolism. In this study, we confirmed that CCN2 and CCN3 are the only members that are tightly regulated by glycolysis in human chondrocytic cells. Interestingly, CCN3 was induced under a variety of impaired glycolytic conditions. This CCN3 induction was also observed in two breast cancer cell lines with a distinct phenotype, suggesting a basic role of CCN3 in cellular metabolism. Reporter gene assays indicated a transcriptional regulation mediated by an enhancer in the proximal promoter region. As a result of analyses in silico, we specified regulatory factor binding to the X-box 1 (RFX1) as a candidate that mediated the transcriptional activation by impaired glycolysis. Indeed, the inhibition of glycolysis induced the expression of RFX1, and RFX1 silencing nullified the CCN3 induction by impaired glycolysis. Subsequent experiments with an anti-CCN3 antibody indicated that CCN3 supported the survival of chondrocytes under impaired glycolysis. Consistent with these findings in vitro, abundant CCN3 production by chondrocytes in the deep zones of developing epiphysial cartilage, which are located far away from the synovial fluid, was confirmed in vivo. Our present study uncovered that RFX1 is the mediator that enables CCN3 induction upon cellular starvation, which may eventually assist chondrocytes in retaining their viability, even when there is an energy supply shortage.
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Affiliation(s)
- Tomomi Mizukawa
- Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- Department of Orthodontics, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Takashi Nishida
- Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, Okayama, Japan
| | - Sho Akashi
- Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- Department of Oral and Maxillofacial Reconstructive Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kazumi Kawata
- Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Sumire Kikuchi
- Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Harumi Kawaki
- Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- Department of Oral Biochemistry, Asahi University School of Dentistry, Mizuho, Japan
| | - Masaharu Takigawa
- Advanced Research Center for Oral and Craniofacial Sciences, Okayama University Dental School, Okayama, Japan
| | - Hiroshi Kamioka
- Department of Orthodontics, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Satoshi Kubota
- Department of Biochemistry and Molecular Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
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7
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The Polygenic Nature and Complex Genetic Architecture of Specific Learning Disorder. Brain Sci 2021; 11:brainsci11050631. [PMID: 34068951 PMCID: PMC8156942 DOI: 10.3390/brainsci11050631] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/16/2022] Open
Abstract
Specific Learning Disorder (SLD) is a multifactorial, neurodevelopmental disorder which may involve persistent difficulties in reading (dyslexia), written expression and/or mathematics. Dyslexia is characterized by difficulties with speed and accuracy of word reading, deficient decoding abilities, and poor spelling. Several studies from different, but complementary, scientific disciplines have investigated possible causal/risk factors for SLD. Biological, neurological, hereditary, cognitive, linguistic-phonological, developmental and environmental factors have been incriminated. Despite worldwide agreement that SLD is highly heritable, its exact biological basis remains elusive. We herein present: (a) an update of studies that have shaped our current knowledge on the disorder’s genetic architecture; (b) a discussion on whether this genetic architecture is ‘unique’ to SLD or, alternatively, whether there is an underlying common genetic background with other neurodevelopmental disorders; and, (c) a brief discussion on whether we are at a position of generating meaningful correlations between genetic findings and anatomical data from neuroimaging studies or specific molecular/cellular pathways. We conclude with open research questions that could drive future research directions.
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8
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Issac J, Raveendran PS, Das AV. RFX1: a promising therapeutic arsenal against cancer. Cancer Cell Int 2021; 21:253. [PMID: 33964962 PMCID: PMC8106159 DOI: 10.1186/s12935-021-01952-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 04/26/2021] [Indexed: 02/08/2023] Open
Abstract
Regulatory factor X1 (RFX1) is an evolutionary conserved transcriptional factor that influences a wide range of cellular processes such as cell cycle, cell proliferation, differentiation, and apoptosis, by regulating a number of target genes that are involved in such processes. On a closer look, these target genes also play a key role in tumorigenesis and associated events. Such observations paved the way for further studies evaluating the role of RFX1 in cancer. These studies were indispensable due to the failure of conventional chemotherapeutic drugs to target key cellular hallmarks such as cancer stemness, cellular plasticity, enhanced drug efflux, de-regulated DNA repair machinery, and altered pathways evading apoptosis. In this review, we compile significant evidence for the tumor-suppressive activities of RFX1 while also analyzing its oncogenic potential in some cancers. RFX1 induction decreased cellular proliferation, modulated the immune system, induced apoptosis, reduced chemoresistance, and sensitized cancer stem cells for chemotherapy. Thus, our review discusses the pleiotropic function of RFX1 in multitudinous gene regulations, decisive protein–protein interactions, and also its role in regulating key cell signaling events in cancer. Elucidation of these regulatory mechanisms can be further utilized for RFX1 targeted therapy.
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Affiliation(s)
- Joby Issac
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thycaud.P.O, Thiruvananthapuram, 695014, Kerala, India
| | - Pooja S Raveendran
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thycaud.P.O, Thiruvananthapuram, 695014, Kerala, India
| | - Ani V Das
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thycaud.P.O, Thiruvananthapuram, 695014, Kerala, India.
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9
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Lauter G, Coschiera A, Yoshihara M, Sugiaman-Trapman D, Ezer S, Sethurathinam S, Katayama S, Kere J, Swoboda P. Differentiation of ciliated human midbrain-derived LUHMES neurons. J Cell Sci 2020; 133:jcs249789. [PMID: 33115758 DOI: 10.1242/jcs.249789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022] Open
Abstract
Many human cell types are ciliated, including neural progenitors and differentiated neurons. Ciliopathies are characterized by defective cilia and comprise various disease states, including brain phenotypes, where the underlying biological pathways are largely unknown. Our understanding of neuronal cilia is rudimentary, and an easy-to-maintain, ciliated human neuronal cell model is absent. The Lund human mesencephalic (LUHMES) cell line is a ciliated neuronal cell line derived from human fetal mesencephalon. LUHMES cells can easily be maintained and differentiated into mature, functional neurons within one week. They have a single primary cilium as proliferating progenitor cells and as postmitotic, differentiating neurons. These developmental stages are completely separable within one day of culture condition change. The sonic hedgehog (SHH) signaling pathway is active in differentiating LUHMES neurons. RNA-sequencing timecourse analyses reveal molecular pathways and gene-regulatory networks critical for ciliogenesis and axon outgrowth at the interface between progenitor cell proliferation, polarization and neuronal differentiation. Gene expression dynamics of cultured LUHMES neurons faithfully mimic the corresponding in vivo dynamics of human fetal midbrain. In LUHMES cells, neuronal cilia biology can be investigated from proliferation through differentiation to mature neurons.
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Affiliation(s)
- Gilbert Lauter
- Karolinska Institute, Department of Biosciences and Nutrition, SE-141 83 Huddinge, Sweden
| | - Andrea Coschiera
- Karolinska Institute, Department of Biosciences and Nutrition, SE-141 83 Huddinge, Sweden
| | - Masahito Yoshihara
- Karolinska Institute, Department of Biosciences and Nutrition, SE-141 83 Huddinge, Sweden
| | | | - Sini Ezer
- University of Helsinki, Research Program of Molecular Neurology and Folkhälsan Institute of Genetics, FI-00290 Helsinki, Finland
| | - Shalini Sethurathinam
- Karolinska Institute, Department of Biosciences and Nutrition, SE-141 83 Huddinge, Sweden
| | - Shintaro Katayama
- Karolinska Institute, Department of Biosciences and Nutrition, SE-141 83 Huddinge, Sweden
- University of Helsinki, Stem Cells and Metabolism Research Program and Folkhälsan Research Center, FI-00290 Helsinki, Finland
| | - Juha Kere
- Karolinska Institute, Department of Biosciences and Nutrition, SE-141 83 Huddinge, Sweden
- University of Helsinki, Research Program of Molecular Neurology and Folkhälsan Institute of Genetics, FI-00290 Helsinki, Finland
| | - Peter Swoboda
- Karolinska Institute, Department of Biosciences and Nutrition, SE-141 83 Huddinge, Sweden
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10
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Bieder A, Yoshihara M, Katayama S, Krjutškov K, Falk A, Kere J, Tapia-Páez I. Dyslexia Candidate Gene and Ciliary Gene Expression Dynamics During Human Neuronal Differentiation. Mol Neurobiol 2020; 57:2944-2958. [PMID: 32445086 PMCID: PMC7320047 DOI: 10.1007/s12035-020-01905-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/19/2020] [Indexed: 11/30/2022]
Abstract
Developmental dyslexia (DD) is a neurodevelopmental condition with complex genetic mechanisms. A number of candidate genes have been identified, some of which are linked to neuronal development and migration and to ciliary functions. However, expression and regulation of these genes in human brain development and neuronal differentiation remain uncharted. Here, we used human long-term self-renewing neuroepithelial stem (lt-NES, here termed NES) cells derived from human induced pluripotent stem cells to study neuronal differentiation in vitro. We characterized gene expression changes during differentiation by using RNA sequencing and validated dynamics for selected genes by qRT-PCR. Interestingly, we found that genes related to cilia were significantly enriched among upregulated genes during differentiation, including genes linked to ciliopathies with neurodevelopmental phenotypes. We confirmed the presence of primary cilia throughout neuronal differentiation. Focusing on dyslexia candidate genes, 33 out of 50 DD candidate genes were detected in NES cells by RNA sequencing, and seven candidate genes were upregulated during differentiation to neurons, including DYX1C1 (DNAAF4), a highly replicated DD candidate gene. Our results suggest a role of ciliary genes in differentiating neuronal cells and show that NES cells provide a relevant human neuronal model to study ciliary and DD candidate genes.
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Affiliation(s)
- Andrea Bieder
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden.
| | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden.,Competence Centre on Health Technologies, Tartu, Estonia.,Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden. .,Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki, Finland. .,Folkhälsan Institute of Genetics, Helsinki, Finland. .,School of Basic and Medical Biosciences, King's College London, London, UK.
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11
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Bieder A, Einarsdottir E, Matsson H, Nilsson HE, Eisfeldt J, Dragomir A, Paucar M, Granberg T, Li TQ, Lindstrand A, Kere J, Tapia-Páez I. Rare variants in dynein heavy chain genes in two individuals with situs inversus and developmental dyslexia: a case report. BMC MEDICAL GENETICS 2020; 21:87. [PMID: 32357925 PMCID: PMC7193346 DOI: 10.1186/s12881-020-01020-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 04/05/2020] [Indexed: 02/08/2023]
Abstract
Background Developmental dyslexia (DD) is a neurodevelopmental learning disorder with high heritability. A number of candidate susceptibility genes have been identified, some of which are linked to the function of the cilium, an organelle regulating left-right asymmetry development in the embryo. Furthermore, it has been suggested that disrupted left-right asymmetry of the brain may play a role in neurodevelopmental disorders such as DD. However, it is unknown whether there is a common genetic cause to DD and laterality defects or ciliopathies. Case presentation Here, we studied two individuals with co-occurring situs inversus (SI) and DD using whole genome sequencing to identify genetic variants of importance for DD and SI. Individual 1 had primary ciliary dyskinesia (PCD), a rare, autosomal recessive disorder with oto-sino-pulmonary phenotype and SI. We identified two rare nonsynonymous variants in the dynein axonemal heavy chain 5 gene (DNAH5): a previously reported variant c.7502G > C; p.(R2501P), and a novel variant c.12043 T > G; p.(Y4015D). Both variants are predicted to be damaging. Ultrastructural analysis of the cilia revealed a lack of outer dynein arms and normal inner dynein arms. MRI of the brain revealed no significant abnormalities. Individual 2 had non-syndromic SI and DD. In individual 2, one rare variant (c.9110A > G;p.(H3037R)) in the dynein axonemal heavy chain 11 gene (DNAH11), coding for another component of the outer dynein arm, was identified. Conclusions We identified the likely genetic cause of SI and PCD in one individual, and a possibly significant heterozygosity in the other, both involving dynein genes. Given the present evidence, it is unclear if the identified variants also predispose to DD and further studies into the association between laterality, ciliopathies and DD are needed.
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Affiliation(s)
- Andrea Bieder
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, 141 83, Huddinge, Sweden.
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, 141 83, Huddinge, Sweden.,Stem Cells and Metabolism Research Program (STEMM), University of Helsinki, Helsinki, Finland.,Folkhälsan Institute of Genetics, Helsinki, Finland.,Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of Technology, Solna, Sweden
| | - Hans Matsson
- Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Harriet E Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, 141 83, Huddinge, Sweden.,Department of Biomedical Engineering and Health Systems, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Huddinge, Sweden
| | - Jesper Eisfeldt
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Anca Dragomir
- Department of Pathology, Uppsala University Hospital, Uppsala, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Martin Paucar
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Tobias Granberg
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.,Department of Radiology, Karolinska University Hospital, Stockholm, Sweden
| | - Tie-Qiang Li
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Lindstrand
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, 141 83, Huddinge, Sweden.,Stem Cells and Metabolism Research Program (STEMM), University of Helsinki, Helsinki, Finland.,School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Isabel Tapia-Páez
- Department of Medicine, Solna, Karolinska Institutet, Solnavägen 30, 171 76 Solna, Stockholm, Sweden.
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12
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Landi N, Perdue M. Neuroimaging genetics studies of specific reading disability and developmental language disorder: A review. LANGUAGE AND LINGUISTICS COMPASS 2019; 13:e12349. [PMID: 31844423 PMCID: PMC6913889 DOI: 10.1111/lnc3.12349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Developmental disorders of spoken and written language are heterogeneous in nature with impairments observed across various linguistic, cognitive, and sensorimotor domains. These disorders are also associated with characteristic patterns of atypical neural structure and function that are observable early in development, often before formal schooling begins. Established patterns of heritability point toward genetic contributions, and molecular genetics approaches have identified genes that play a role in these disorders. Still, identified genes account for only a limited portion of phenotypic variance in complex developmental disorders, described as the problem of "missing heritability." The characterization of intermediate phenotypes at the neural level may fill gaps in our understanding of heritability patterns in complex disorders, and the emerging field of neuroimaging genetics offers a promising approach to accomplish this goal. The neuroimaging genetics approach is gaining prevalence in language- and reading-related research as it is well-suited to incorporate behavior, genetics, and neurobiology into coherent etiological models of complex developmental disorders. Here, we review research applying the neuroimaging genetics approach to the study of specific reading disability (SRD) and developmental language disorder (DLD), much of which links genes with known neurodevelopmental function to functional and structural abnormalities in the brain.
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Affiliation(s)
- Nicole Landi
- Department of Psychological Sciences, University of Connecticut, Storrs, Connecticut, United States; Haskins Laboratories, United States
| | - Meaghan Perdue
- Department of Psychological Sciences, University of Connecticut, Storrs, Connecticut, United States; Haskins Laboratories, United States
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13
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Hearn T. ALMS1 and Alström syndrome: a recessive form of metabolic, neurosensory and cardiac deficits. J Mol Med (Berl) 2018; 97:1-17. [PMID: 30421101 PMCID: PMC6327082 DOI: 10.1007/s00109-018-1714-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/25/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022]
Abstract
Alström syndrome (AS) is characterised by metabolic deficits, retinal dystrophy, sensorineural hearing loss, dilated cardiomyopathy and multi-organ fibrosis. Elucidating the function of the mutated gene, ALMS1, is critical for the development of specific treatments and may uncover pathways relevant to a range of other disorders including common forms of obesity and type 2 diabetes. Interest in ALMS1 is heightened by the recent discovery of its involvement in neonatal cardiomyocyte cell cycle arrest, a process with potential relevance to regenerative medicine. ALMS1 encodes a ~ 0.5 megadalton protein that localises to the base of centrioles. Some studies have suggested a role for this protein in maintaining centriole-nucleated sensory organelles termed primary cilia, and AS is now considered to belong to the growing class of human genetic disorders linked to ciliary dysfunction (ciliopathies). However, mechanistic details are lacking, and recent studies have implicated ALMS1 in several processes including endosomal trafficking, actin organisation, maintenance of centrosome cohesion and transcription. In line with a more complex picture, multiple isoforms of the protein likely exist and non-centrosomal sites of localisation have been reported. This review outlines the evidence for both ciliary and extra-ciliary functions of ALMS1.
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Affiliation(s)
- Tom Hearn
- Institute of Life Science, Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK.
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14
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Montesion M, Williams ZH, Subramanian RP, Kuperwasser C, Coffin JM. Promoter expression of HERV-K (HML-2) provirus-derived sequences is related to LTR sequence variation and polymorphic transcription factor binding sites. Retrovirology 2018; 15:57. [PMID: 30126415 PMCID: PMC6102855 DOI: 10.1186/s12977-018-0441-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 08/13/2018] [Indexed: 12/29/2022] Open
Abstract
Background Increased transcription of the human endogenous retrovirus group HERV-K (HML-2) is often seen during disease. Although the mechanism of its tissue-specific activation is unclear, research shows that LTR CpG hypomethylation alone is not sufficient to induce its promoter activity and that the transcriptional milieu of a malignant cell contributes, at least partly, to differential HML-2 expression. Results We analyzed the relationship between LTR sequence variation and promoter expression patterns in human breast cancer cell lines, finding them to be positively correlated. In particular, two proviruses (3q12.3 and 11p15.4) displayed increased activity in almost all tumorigenic cell lines sampled. Using a transcription factor binding site prediction algorithm, we identified two unique binding sites in each 5′ LTR that appeared to be associated with inducing promoter activity during neoplasia. Genomic analysis of the homologous proviruses in several non-human primates indicated post-integration genetic drift in two transcription factor binding sites, away from the ancestral sequence and towards the active form. Based on the sequences of 2504 individuals from the 1000 Genomes Project, the active form of the 11p15.4 site was found to be polymorphic within the human population, with an allele frequency of 51%, whereas the activating mutation in the 3q12.3 provirus was fixed in humans but not present in the orthologous provirus in chimpanzees or gorillas. Conclusions These data suggest that stage-specific transcription factors at least partly contribute to LTR promoter activity during transformation and that, in some cases, transcription factor binding site polymorphisms may be responsible for the differential HML-2 expression often seen between individuals. Electronic supplementary material The online version of this article (10.1186/s12977-018-0441-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Meagan Montesion
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.,Foundation Medicine, Inc., Cambridge, MA, USA
| | - Zachary H Williams
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Ravi P Subramanian
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.,Excerpta Medica, New York, NY, USA
| | - Charlotte Kuperwasser
- Department of Developmental, Chemical, and Molecular Biology, Tufts University School of Medicine, Boston, MA, USA.,Raymond and Beverly Sackler Convergence Laboratory, Tufts University School of Medicine, Boston, MA, USA
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
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15
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The influence of DCDC2 risk genetic variants on reading: Testing main and haplotypic effects. Neuropsychologia 2018; 130:52-58. [PMID: 29803723 DOI: 10.1016/j.neuropsychologia.2018.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 04/17/2018] [Accepted: 05/23/2018] [Indexed: 12/28/2022]
Abstract
Developmental dyslexia (DD) is a complex neurodevelopmental heritable disorder. Among DD candidate genes, DCDC2 is one of the most replicated, with rs793862, READ1 and rs793842 likely contribute to phenotypic variability in reading (dis)ability. In this study, we tested the effects of these genetic variants on DD as a categorical trait and on quantitative reading-related measures in a sample of 555 Italian nuclear families with 930 offspring, of which 687 were diagnosed with DD. We conducted both single-marker and haplotype analyses, finding that the READ1-deletion was significantly associated with reading, whereas no significant haplotype associations were found. Our findings add further evidence to support the hypothesis of a DCDC2 contribution to inter-individual variation in distinct indicators of reading (dis)ability in transparent languages (i.e., reading accuracy and speed), suggesting a potential pleiotropic effect.
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16
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Sugiaman-Trapman D, Vitezic M, Jouhilahti EM, Mathelier A, Lauter G, Misra S, Daub CO, Kere J, Swoboda P. Characterization of the human RFX transcription factor family by regulatory and target gene analysis. BMC Genomics 2018; 19:181. [PMID: 29510665 PMCID: PMC5838959 DOI: 10.1186/s12864-018-4564-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/21/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Evolutionarily conserved RFX transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box. Thereby they regulate cellular specialization and terminal differentiation. Here, we provide a comprehensive analysis of all the eight human RFX genes (RFX1-8), their spatial and temporal expression profiles, potential upstream regulators and target genes. RESULTS We extracted all known human RFX1-8 gene expression profiles from the FANTOM5 database derived from transcription start site (TSS) activity as captured by Cap Analysis of Gene Expression (CAGE) technology. RFX genes are broadly (RFX1-3, RFX5, RFX7) and specifically (RFX4, RFX6) expressed in different cell types, with high expression in four organ systems: immune system, gastrointestinal tract, reproductive system and nervous system. Tissue type specific expression profiles link defined RFX family members with the target gene batteries they regulate. We experimentally confirmed novel TSS locations and characterized the previously undescribed RFX8 to be lowly expressed. RFX tissue and cell type specificity arises mainly from differences in TSS architecture. RFX transcript isoforms lacking a DNA binding domain (DBD) open up new possibilities for combinatorial target gene regulation. Our results favor a new grouping of the RFX family based on protein domain composition. We uncovered and experimentally confirmed the TFs SP2 and ESR1 as upstream regulators of specific RFX genes. Using TF binding profiles from the JASPAR database, we determined relevant patterns of X-box motif positioning with respect to gene TSS locations of human RFX target genes. CONCLUSIONS The wealth of data we provide will serve as the basis for precisely determining the roles RFX TFs play in human development and disease.
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Affiliation(s)
| | - Morana Vitezic
- Department of Biology, Bioinformatics Centre, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, Denmark
| | - Eeva-Mari Jouhilahti
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Anthony Mathelier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, Canada
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, University of Oslo, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Sougat Misra
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- School of Basic and Medical Biosciences, King's College London, London, UK
- Folkhälsan Institute of Genetics and Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
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17
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De Stasio EA, Mueller KP, Bauer RJ, Hurlburt AJ, Bice SA, Scholtz SL, Phirke P, Sugiaman-Trapman D, Stinson LA, Olson HB, Vogel SL, Ek-Vazquez Z, Esemen Y, Korzynski J, Wolfe K, Arbuckle BN, Zhang H, Lombard-Knapp G, Piasecki BP, Swoboda P. An Expanded Role for the RFX Transcription Factor DAF-19, with Dual Functions in Ciliated and Nonciliated Neurons. Genetics 2018; 208:1083-1097. [PMID: 29301909 PMCID: PMC5844324 DOI: 10.1534/genetics.117.300571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/02/2017] [Indexed: 02/06/2023] Open
Abstract
Regulatory Factor X (RFX) transcription factors (TFs) are best known for activating genes required for ciliogenesis in both vertebrates and invertebrates. In humans, eight RFX TFs have a variety of tissue-specific functions, while in the worm Caenorhabditis elegans, the sole RFX gene, daf-19, encodes a set of nested isoforms. Null alleles of daf-19 confer pleiotropic effects including altered development with a dauer constitutive phenotype, complete absence of cilia and ciliary proteins, and defects in synaptic protein maintenance. We sought to identify RFX/daf-19 target genes associated with neuronal functions other than ciliogenesis using comparative transcriptome analyses at different life stages of the worm. Subsequent characterization of gene expression patterns revealed one set of genes activated in the presence of DAF-19 in ciliated sensory neurons, whose activation requires the daf-19c isoform, also required for ciliogenesis. A second set of genes is downregulated in the presence of DAF-19, primarily in nonsensory neurons. The human orthologs of some of these neuronal genes are associated with human diseases. We report the novel finding that daf-19a is directly or indirectly responsible for downregulation of these neuronal genes in C. elegans by characterizing a new mutation affecting the daf-19a isoform (tm5562) and not associated with ciliogenesis, but which confers synaptic and behavioral defects. Thus, we have identified a new regulatory role for RFX TFs in the nervous system. The new daf-19 candidate target genes we have identified by transcriptomics will serve to uncover the molecular underpinnings of the pleiotropic effects that daf-19 exerts on nervous system function.
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Affiliation(s)
| | | | - Rosemary J Bauer
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | | | - Sophie A Bice
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Sophie L Scholtz
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Prasad Phirke
- Department of Biosciences and Nutrition, Karolinska Institute, 141 83 Huddinge, Sweden
| | | | - Loraina A Stinson
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Haili B Olson
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Savannah L Vogel
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | | | - Yagmur Esemen
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Jessica Korzynski
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Kelsey Wolfe
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Bonnie N Arbuckle
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - He Zhang
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | | | - Brian P Piasecki
- Department of Biology, Lawrence University, Appleton, Wisconsin 54911
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institute, 141 83 Huddinge, Sweden
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18
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Julien L, Chassagne J, Peccate C, Lorain S, Piétri-Rouxel F, Danos O, Benkhelifa-Ziyyat S. RFX1 and RFX3 Transcription Factors Interact with the D Sequence of Adeno-Associated Virus Inverted Terminal Repeat and Regulate AAV Transduction. Sci Rep 2018; 8:210. [PMID: 29317724 PMCID: PMC5760533 DOI: 10.1038/s41598-017-18604-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/13/2017] [Indexed: 12/31/2022] Open
Abstract
Adeno-associated virus (AAV) transduction efficiency depends on the way in which cellular proteins process viral genomes in the nucleus. In this study, we have investigated the binding of nuclear proteins to the double stranded D (dsD) sequence of the AAV inverted terminal repeat (ITRs) by electromobility shift assay. We present here several lines of evidence that transcription factors belonging to the RFX protein family bind specifically and selectively to AAV2 and AAV1 dsD sequences. Using supershift experiments, we characterize complexes containing RFX1 homodimers and RFX1/RFX3 heterodimers. Following transduction of HEK-293 cells, the AAV genome can be pulled-down by RFX1 and RFX3 antibodies. Moreover, our data suggest that RFX proteins which interact with transcriptional enhancers of several mammalian DNA viruses, can act as regulators of AAV mediated transgene expression.
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Affiliation(s)
- Laura Julien
- Sorbonne Universités UPMC Univ Paris 06, Inserm, Institut de Myologie, Centre de Recherche en Myologie (CRM), GH Pitié Salpêtrière, 105 bd de l'Hôpital, Paris, 13, France
| | - Julie Chassagne
- Sorbonne Universités UPMC Univ Paris 06, Inserm, Institut de Myologie, Centre de Recherche en Myologie (CRM), GH Pitié Salpêtrière, 105 bd de l'Hôpital, Paris, 13, France
| | - Cécile Peccate
- Sorbonne Universités UPMC Univ Paris 06, Inserm, Institut de Myologie, Centre de Recherche en Myologie (CRM), GH Pitié Salpêtrière, 105 bd de l'Hôpital, Paris, 13, France
| | - Stéphanie Lorain
- Sorbonne Universités UPMC Univ Paris 06, Inserm, Institut de Myologie, Centre de Recherche en Myologie (CRM), GH Pitié Salpêtrière, 105 bd de l'Hôpital, Paris, 13, France
| | - France Piétri-Rouxel
- Sorbonne Universités UPMC Univ Paris 06, Inserm, Institut de Myologie, Centre de Recherche en Myologie (CRM), GH Pitié Salpêtrière, 105 bd de l'Hôpital, Paris, 13, France
| | - Olivier Danos
- REGENXBIO, 9600 Blackwell Rd, Rockville, MD, 20850, USA
| | - Sofia Benkhelifa-Ziyyat
- Sorbonne Universités UPMC Univ Paris 06, Inserm, Institut de Myologie, Centre de Recherche en Myologie (CRM), GH Pitié Salpêtrière, 105 bd de l'Hôpital, Paris, 13, France.
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19
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Waye MMY, Poo LK, Ho CSH. Study of Genetic Association With DCDC2 and Developmental Dyslexia in Hong Kong Chinese Children. Clin Pract Epidemiol Ment Health 2017; 13:104-114. [PMID: 29081827 PMCID: PMC5633722 DOI: 10.2174/1745017901713010104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/21/2017] [Accepted: 07/25/2017] [Indexed: 11/30/2022]
Abstract
Background: Doublecortin domain-containing 2 (DCDC2) is a doublecortin domain-containing gene family member and the doublecortin domain has been demonstrated to bind to tubulin and enhance microtubule polymerization. It has been associated with developmental dyslexia and this protein family member is thought to function in neuronal migration where it may affect the signaling of primary cilia. Objectives: The objective of the study is to find out if there is any association of genetic variants of DCDC2 with developmental dyslexia in Chinese children from Hong Kong. Methods: The dyslexic children were diagnosed as developmental dyslexia (DD) using the Hong Kong Test of Specific Learning Difficulties in Reading and Writing (HKT-SpLD) by the Department of Health, Hong Kong. Saliva specimens were collected and their genotypes of DCDC2 were studied by DNA sequencing or TaqMan Real Time PCR Assays. Results: The most significant marker is rs6940827 which is associated with DD with nominal p-value (0.011). However, this marker did not remain significant after multiple testing corrections and the adjusted p-value from permutation test was 0.1329. Using sliding window haplotype analysis, several haplotypes were found to be nominally associated with DD. The smallest nominal p values was 0.0036 (rs2996452-rs1318700, C-A). However, none of the p values could withstand the multiple testing corrections. Conclusion: Despite early findings that DCDC2 is a strong candidate for developmental dyslexia and that some of the genetic variants have been linked to brain structure and functions, our findings showed that DCDC2 is not strongly associated with dyslexia.
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Affiliation(s)
- Mary M Y Waye
- The Nethersole School of Nursing, The Nethersole School of Nursing, The Chinese University of Hong Kong, Hong Kong
| | - Lim K Poo
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Connie S-H Ho
- Department of Psychology, The University of Hong Kong, Hong Kong
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20
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The role of READ1 and KIAA0319 genetic variations in developmental dyslexia: testing main and interactive effects. J Hum Genet 2017; 62:949-955. [DOI: 10.1038/jhg.2017.80] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/30/2017] [Accepted: 07/02/2017] [Indexed: 12/23/2022]
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21
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Genes, Gender, Environment, and Novel Functions of Estrogen Receptor Beta in the Susceptibility to Neurodevelopmental Disorders. Brain Sci 2017; 7:brainsci7030024. [PMID: 28241485 PMCID: PMC5366823 DOI: 10.3390/brainsci7030024] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/14/2017] [Accepted: 02/17/2017] [Indexed: 12/30/2022] Open
Abstract
Many neurological disorders affect men and women differently regarding prevalence, progression, and severity. It is clear that many of these disorders may originate from defective signaling during fetal or perinatal brain development, which may affect males and females differently. Such sex-specific differences may originate from chromosomal or sex-hormone specific effects. This short review will focus on the estrogen receptor beta (ERβ) signaling during perinatal brain development and put it in the context of sex-specific differences in neurodevelopmental disorders. We will discuss ERβ’s recent discovery in directing DNA de-methylation to specific sites, of which one such site may bear consequences for the susceptibility to the neurological reading disorder dyslexia. We will also discuss how dysregulations in sex-hormone signaling, like those evoked by endocrine disruptive chemicals, may affect this and other neurodevelopmental disorders in a sex-specific manner through ERβ.
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22
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Neurogenetics of developmental dyslexia: from genes to behavior through brain neuroimaging and cognitive and sensorial mechanisms. Transl Psychiatry 2017; 7:e987. [PMID: 28045463 PMCID: PMC5545717 DOI: 10.1038/tp.2016.240] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 10/15/2016] [Indexed: 01/18/2023] Open
Abstract
Developmental dyslexia (DD) is a complex neurodevelopmental deficit characterized by impaired reading acquisition, in spite of adequate neurological and sensorial conditions, educational opportunities and normal intelligence. Despite the successful characterization of DD-susceptibility genes, we are far from understanding the molecular etiological pathways underlying the development of reading (dis)ability. By focusing mainly on clinical phenotypes, the molecular genetics approach has yielded mixed results. More optimally reduced measures of functioning, that is, intermediate phenotypes (IPs), represent a target for researching disease-associated genetic variants and for elucidating the underlying mechanisms. Imaging data provide a viable IP for complex neurobehavioral disorders and have been extensively used to investigate both morphological, structural and functional brain abnormalities in DD. Performing joint genetic and neuroimaging studies in humans is an emerging strategy to link DD-candidate genes to the brain structure and function. A limited number of studies has already pursued the imaging-genetics integration in DD. However, the results are still not sufficient to unravel the complexity of the reading circuit due to heterogeneous study design and data processing. Here, we propose an interdisciplinary, multilevel, imaging-genetic approach to disentangle the pathways from genes to behavior. As the presence of putative functional genetic variants has been provided and as genetic associations with specific cognitive/sensorial mechanisms have been reported, new hypothesis-driven imaging-genetic studies must gain momentum. This approach would lead to the optimization of diagnostic criteria and to the early identification of 'biologically at-risk' children, supporting the definition of adequate and well-timed prevention strategies and the implementation of novel, specific remediation approach.
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