1
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Garber A, Weingarten LS, Abreu NJ, Elloumi HZ, Haack T, Hildebrant C, Martínez-Gil N, Mathews J, Müller AJ, Valenzuela Palafoll I, Steigerwald C, Chung WK. Rare predicted deleterious FEZF2 variants are associated with a neurodevelopmental phenotype. Am J Med Genet A 2024; 194:e63578. [PMID: 38425142 PMCID: PMC11161304 DOI: 10.1002/ajmg.a.63578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/07/2024] [Accepted: 02/17/2024] [Indexed: 03/02/2024]
Abstract
FEZF2 encodes a transcription factor critical to neurodevelopment that regulates other neurodevelopment genes. Rare variants in FEZF2 have previously been suggested to play a role in autism, and cases of 3p14 microdeletions that include FEZF2 share a neurodevelopmental phenotype including mild dysmorphic features and intellectual disability. We identified seven heterozygous predicted deleterious variants in FEZF2 (three frameshifts, one recurrent missense in two independent cases, one nonsense, and one complete gene deletion) in unrelated individuals with neurodevelopmental disorders including developmental delay/intellectual disability, autism, and/or attention-deficit/hyperactivity. Variants were confirmed to be de novo in five of seven cases and paternally inherited from an affected father in one. Predicted deleterious variants in FEZF2 may affect the expression of genes that are involved in fate choice pathways in developing neurons, and thus contribute to the neurodevelopmental phenotype. Future studies are needed to clarify the mechanism by which FEZF2 leads to this neurodevelopmental disorder.
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Affiliation(s)
- Alison Garber
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Lisa S Weingarten
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Nicolas J Abreu
- Department of Neurology, NYU Grossman School of Medicine, New York, New York, USA
| | | | - Tobias Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Clara Hildebrant
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Núria Martínez-Gil
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, Barcelona, Spain
- Medical Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Jennifer Mathews
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Amelie Johanna Müller
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Irene Valenzuela Palafoll
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, Barcelona, Spain
- Medical Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Connolly Steigerwald
- Department of Neurology, NYU Grossman School of Medicine, New York, New York, USA
| | - Wendy K Chung
- Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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2
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Demin KA, Krotova NA, Ilyin NP, Galstyan DS, Kolesnikova TO, Strekalova T, de Abreu MS, Petersen EV, Zabegalov KN, Kalueff AV. Evolutionarily conserved gene expression patterns for affective disorders revealed using cross-species brain transcriptomic analyses in humans, rats and zebrafish. Sci Rep 2022; 12:20836. [PMID: 36460699 PMCID: PMC9718822 DOI: 10.1038/s41598-022-22688-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/18/2022] [Indexed: 12/03/2022] Open
Abstract
Widespread, debilitating and often treatment-resistant, depression and other stress-related neuropsychiatric disorders represent an urgent unmet biomedical and societal problem. Although animal models of these disorders are commonly used to study stress pathogenesis, they are often difficult to translate across species into valuable and meaningful clinically relevant data. To address this problem, here we utilized several cross-species/cross-taxon approaches to identify potential evolutionarily conserved differentially expressed genes and their sets. We also assessed enrichment of these genes for transcription factors DNA-binding sites down- and up- stream from their genetic sequences. For this, we compared our own RNA-seq brain transcriptomic data obtained from chronically stressed rats and zebrafish with publicly available human transcriptomic data for patients with major depression and their respective healthy control groups. Utilizing these data from the three species, we next analyzed their differential gene expression, gene set enrichment and protein-protein interaction networks, combined with validated tools for data pooling. This approach allowed us to identify several key brain proteins (GRIA1, DLG1, CDH1, THRB, PLCG2, NGEF, IKZF1 and FEZF2) as promising, evolutionarily conserved and shared affective 'hub' protein targets, as well as to propose a novel gene set that may be used to further study affective pathogenesis. Overall, these approaches may advance cross-species brain transcriptomic analyses, and call for further cross-species studies into putative shared molecular mechanisms of affective pathogenesis.
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Affiliation(s)
- Konstantin A Demin
- Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia.
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
| | - Nataliya A Krotova
- Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Nikita P Ilyin
- Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- Neurobiology Program, Sirius University of Science and Technology, Sochi, Russia
| | - David S Galstyan
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Preclinical Bioscreening, Granov Russian Research Center of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, Pesochny, Russia
| | | | | | | | | | | | - Allan V Kalueff
- Laboratory of Preclinical Bioscreening, Granov Russian Research Center of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, Pesochny, Russia.
- Institute of Neurosciences and Medicine, Novosibirsk, Russia.
- Ural Federal University, Ekaterinburg, Russia.
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3
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Tsyporin J, Tastad D, Ma X, Nehme A, Finn T, Huebner L, Liu G, Gallardo D, Makhamreh A, Roberts JM, Katzman S, Sestan N, McConnell SK, Yang Z, Qiu S, Chen B. Transcriptional repression by FEZF2 restricts alternative identities of cortical projection neurons. Cell Rep 2021; 35:109269. [PMID: 34161768 PMCID: PMC8327856 DOI: 10.1016/j.celrep.2021.109269] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/05/2021] [Accepted: 05/27/2021] [Indexed: 11/20/2022] Open
Abstract
Projection neuron subtype identities in the cerebral cortex are established by expressing pan-cortical and subtype-specific effector genes that execute terminal differentiation programs bestowing neurons with a glutamatergic neuron phenotype and subtype-specific morphology, physiology, and axonal projections. Whether pan-cortical glutamatergic and subtype-specific characteristics are regulated by the same genes or controlled by distinct programs remains largely unknown. Here, we show that FEZF2 functions as a transcriptional repressor, and it regulates subtype-specific identities of both corticothalamic and subcerebral neurons by selectively repressing expression of genes inappropriate for each neuronal subtype. We report that TLE4, specifically expressed in layer 6 corticothalamic neurons, is recruited by FEZF2 to inhibit layer 5 subcerebral neuronal genes. Together with previous studies, our results indicate that a cortical glutamatergic identity is specified by multiple parallel pathways active in progenitor cells, whereas projection neuron subtype-specific identity is achieved through selectively repressing genes associated with alternate identities in differentiating neurons.
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Affiliation(s)
- Jeremiah Tsyporin
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - David Tastad
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Xiaokuang Ma
- Department of Basic Medical Sciences, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Antoine Nehme
- Department of Basic Medical Sciences, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Thomas Finn
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Liora Huebner
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Guoping Liu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Daisy Gallardo
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Amr Makhamreh
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Jacqueline M Roberts
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Solomon Katzman
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | | | - Zhengang Yang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Shenfeng Qiu
- Department of Basic Medical Sciences, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Bin Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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4
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Kaur N, Han W, Li Z, Madrigal MP, Shim S, Pochareddy S, Gulden FO, Li M, Xu X, Xing X, Takeo Y, Li Z, Lu K, Imamura Kawasawa Y, Ballester-Lurbe B, Moreno-Bravo JA, Chédotal A, Terrado J, Pérez-Roger I, Koleske AJ, Sestan N. Neural Stem Cells Direct Axon Guidance via Their Radial Fiber Scaffold. Neuron 2020; 107:1197-1211.e9. [PMID: 32707082 DOI: 10.1016/j.neuron.2020.06.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/06/2020] [Accepted: 06/26/2020] [Indexed: 10/23/2022]
Abstract
Neural stem cells directly or indirectly generate all neurons and macroglial cells and guide migrating neurons by using a palisade-like scaffold made of their radial fibers. Here, we describe an unexpected role for the radial fiber scaffold in directing corticospinal and other axons at the junction between the striatum and globus pallidus. The maintenance of this scaffold, and consequently axon pathfinding, is dependent on the expression of an atypical RHO-GTPase, RND3/RHOE, together with its binding partner ARHGAP35/P190A, a RHO GTPase-activating protein, in the radial glia-like neural stem cells within the ventricular zone of the medial ganglionic eminence. This role is independent of RND3 and ARHGAP35 expression in corticospinal neurons, where they regulate dendritic spine formation, axon elongation, and pontine midline crossing in a FEZF2-dependent manner. The prevalence of neural stem cell scaffolds and their expression of RND3 and ARHGAP35 suggests that these observations might be broadly relevant for axon guidance and neural circuit formation.
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Affiliation(s)
- Navjot Kaur
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Wenqi Han
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Zhuo Li
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Graduate Program in Histology and Embryology, Zhengzhou University, 450001 Zhengzhou, China
| | - M Pilar Madrigal
- Department of Biomedical Sciences, School of Health Sciences and Veterinary School, Universidad Cardenal Herrera-CEU, CEU Universities, Moncada, 46113 Valencia, Spain
| | - Sungbo Shim
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Biochemistry, Chungbuk National University, Cheongju 28644, Korea
| | - Sirisha Pochareddy
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Forrest O Gulden
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Mingfeng Li
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Xuming Xu
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Xiaojun Xing
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Genome Editing Center, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yutaka Takeo
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Zhen Li
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Kangrong Lu
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yuka Imamura Kawasawa
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology and of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Begoña Ballester-Lurbe
- Department of Biomedical Sciences, School of Health Sciences and Veterinary School, Universidad Cardenal Herrera-CEU, CEU Universities, Moncada, 46113 Valencia, Spain
| | | | - Alain Chédotal
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France
| | - José Terrado
- Department of Biomedical Sciences, School of Health Sciences and Veterinary School, Universidad Cardenal Herrera-CEU, CEU Universities, Moncada, 46113 Valencia, Spain
| | - Ignacio Pérez-Roger
- Department of Biomedical Sciences, School of Health Sciences and Veterinary School, Universidad Cardenal Herrera-CEU, CEU Universities, Moncada, 46113 Valencia, Spain
| | - Anthony J Koleske
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Molecular Biochemistry and Biophysics, Yale University, New Haven, CT 06520, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Departments of Genetics, Psychiatry, and Comparative Medicine, Kavli Institute for Neuroscience, Program in Cellular Neuroscience, Neurodegeneration, and Repair, and Yale Child Study Center, Yale University School of Medicine, New Haven, CT 06510, USA.
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5
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Clare AJ, Day RC, Empson RM, Hughes SM. Transcriptome Profiling of Layer 5 Intratelencephalic Projection Neurons From the Mature Mouse Motor Cortex. Front Mol Neurosci 2018; 11:410. [PMID: 30483051 PMCID: PMC6240696 DOI: 10.3389/fnmol.2018.00410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 10/22/2018] [Indexed: 11/17/2022] Open
Abstract
The mature cortex contains hugely diverse populations of pyramidal projection neurons (PNs), critical to normal forebrain circuits. In order to understand the healthy cortex, it is essential to characterize this neuronal complexity. We recently demonstrated different identities for Fezf2-positive (Fezf2+ve) and Fezf2-negative (Fezf2−ve) intratelencephalic-PNs (IT-PNs) from layer 5 of the motor cortex (M1). Comparatively, each IT-PN type has a distinct electrophysiological phenotype and the Fezf2+ve IT-PNs display a unique apical dendritic tuft. Here, we aimed to expand our understanding of the molecular underpinnings defining these unique IT-PN types. Using a validated Fezf2-GFP reporter mouse, retrograde labeling techniques and fluorescence activated cell sorting (FACS), combined with a novel approach for low-input RNA-sequencing, we isolated mature Fezf2+ve and Fezf2−ve IT-PNs for transcriptome profiling. Through the comparison of Fezf2+ve and Fezf2−ve IT-PN gene expression profiles, we identified significant enrichment of 81 genes in the Fezf2+ve IT-PNs and 119 genes in the Fezf2−ve IT-PNs. Term enrichment analysis of these enriched genes demonstrated significant overrepresentation of the calcium-binding EF-hand domain in Fezf2+ve IT-PNs, suggesting a greater importance for calcium handling in these neurons. Of the Fezf2−ve IT-PN enriched genes an unexpected and unique enrichment of genes, previously associated with microglia were identified. Our dataset identifies the molecular profiles of two unique IT-PN types in the mature M1, providing important targets to investigate for their maintenance in the healthy mature brain.
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Affiliation(s)
- Alison J Clare
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Brain Health Research Centre, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Genetics Otago, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Robert C Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Genetics Otago, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Ruth M Empson
- Brain Health Research Centre, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Stephanie M Hughes
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Brain Health Research Centre, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Genetics Otago, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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6
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Haendel MA, McMurry JA, Relevo R, Mungall CJ, Robinson PN, Chute CG. A Census of Disease Ontologies. Annu Rev Biomed Data Sci 2018. [DOI: 10.1146/annurev-biodatasci-080917-013459] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For centuries, humans have sought to classify diseases based on phenotypic presentation and available treatments. Today, a wide landscape of strategies, resources, and tools exist to classify patients and diseases. Ontologies can provide a robust foundation of logic for precise stratification and classification along diverse axes such as etiology, development, treatment, and genetics. Disease and phenotype ontologies are used in four primary ways: ( a) search, retrieval, and annotation of knowledge; ( b) data integration and analysis; ( c) clinical decision support; and ( d) knowledge discovery. Computational inference can connect existing knowledge and generate new insights and hypotheses about drug targets, prognosis prediction, or diagnosis. In this review, we examine the rise of disease and phenotype ontologies and the diverse ways they are represented and applied in biomedicine.
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Affiliation(s)
- Melissa A. Haendel
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon 97239, USA
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon 97331, USA
| | - Julie A. McMurry
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Rose Relevo
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Christopher J. Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | - Christopher G. Chute
- School of Medicine, School of Public Health, and School of Nursing, Johns Hopkins University, Baltimore, Maryland 21205, USA
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