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Ito S, Feldheim DA. The Mouse Superior Colliculus: An Emerging Model for Studying Circuit Formation and Function. Front Neural Circuits 2018; 12:10. [PMID: 29487505 PMCID: PMC5816945 DOI: 10.3389/fncir.2018.00010] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/22/2018] [Indexed: 11/30/2022] Open
Abstract
The superior colliculus (SC) is a midbrain area where visual, auditory and somatosensory information are integrated to initiate motor commands. The SC plays a central role in visual information processing in the mouse; it receives projections from 85% to 90% of the retinal ganglion cells (RGCs). While the mouse SC has been a long-standing model used to study retinotopic map formation, a number of technological advances in mouse molecular genetic techniques, large-scale physiological recordings and SC-dependent visual behavioral assays have made the mouse an even more ideal model to understand the relationship between circuitry and behavior.
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Affiliation(s)
- Shinya Ito
- Santa Cruz Institute for Particle Physics, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - David A Feldheim
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
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52
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Antinucci P, Hindges R. Orientation-Selective Retinal Circuits in Vertebrates. Front Neural Circuits 2018; 12:11. [PMID: 29467629 PMCID: PMC5808299 DOI: 10.3389/fncir.2018.00011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/23/2018] [Indexed: 11/24/2022] Open
Abstract
Visual information is already processed in the retina before it is transmitted to higher visual centers in the brain. This includes the extraction of salient features from visual scenes, such as motion directionality or contrast, through neurons belonging to distinct neural circuits. Some retinal neurons are tuned to the orientation of elongated visual stimuli. Such ‘orientation-selective’ neurons are present in the retinae of most, if not all, vertebrate species analyzed to date, with species-specific differences in frequency and degree of tuning. In some cases, orientation-selective neurons have very stereotyped functional and morphological properties suggesting that they represent distinct cell types. In this review, we describe the retinal cell types underlying orientation selectivity found in various vertebrate species, and highlight their commonalities and differences. In addition, we discuss recent studies that revealed the cellular, synaptic and circuit mechanisms at the basis of retinal orientation selectivity. Finally, we outline the significance of these findings in shaping our current understanding of how this fundamental neural computation is implemented in the visual systems of vertebrates.
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Affiliation(s)
- Paride Antinucci
- Centre for Developmental Neurobiology, King's College London, London, United Kingdom
| | - Robert Hindges
- Centre for Developmental Neurobiology, King's College London, London, United Kingdom.,MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom
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53
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Liu J, Sanes JR. Cellular and Molecular Analysis of Dendritic Morphogenesis in a Retinal Cell Type That Senses Color Contrast and Ventral Motion. J Neurosci 2017; 37:12247-12262. [PMID: 29114073 PMCID: PMC5729193 DOI: 10.1523/jneurosci.2098-17.2017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/27/2017] [Accepted: 10/17/2017] [Indexed: 01/08/2023] Open
Abstract
As neuronal dendrites develop, they acquire cell-type-specific features including characteristic size, shape, arborization, location and synaptic patterns. These features, in turn, are major determinants of type-specific neuronal function. Because neuronal diversity complicates the task of relating developmental programs to adult structure and function, we analyzed dendritic morphogenesis in a single retinal ganglion cell (RGC) type in mouse called J-RGC. We documented the emergence of five dendritic features that underlie J-RGC physiology: (1) dendritic field size, which approximate receptive field size; (2) dendritic complexity, which affects how J-RGCs sample space; (3) asymmetry, which contributes to direction-selectivity; (4) restricted lamination within the inner plexiform layer (IPL), which renders J-RGCs responsive to light decrements; and (5) distribution of synaptic inputs, which generate a color-opponent receptive field. We found dendritic growth in J-RGCs is accompanied by a refinement in dendritic self-crossing. Asymmetry arises by a combination of selective pruning and elaboration, whereas laminar restriction results from biased outgrowth toward the outermost IPL. Interestingly, asymmetry develops in a protracted dorsoventral wave, whereas lamination does so in a rapid centrifugal wave. As arbors mature, they acquire excitatory and inhibitory synapses, with the latter forming first and being concentrated in proximal dendrites. Thus, distinct mechanisms operate in different spatiotemporal dimensions of J-RGC dendritic patterning to generate the substrate for specific patterns of synaptogenesis. Finally, we asked whether the defining molecular signature of J-RGCs, the adhesion molecule JAM-B, regulates morphogenesis, and showed that it promotes dendro-dendritic interactions. Our results reveal multiple mechanisms that shape a dendritic arbor.SIGNIFICANCE STATEMENT Visual perception begins in the retina, where distinct types of retinal ganglion cells (RGCs) are tuned to specific visual features such as direction of motion. The features to which each RGC type responds are determined largely by the number and type of synaptic inputs it receives, and these, in turn, are greatly influenced by the size, shape, arborization pattern, and location of its dendrites. We analyzed dendritic morphogenesis in a functionally characterized RGC type, the J-RGC, demonstrating distinct mechanisms that operate in different dimensions to generate the dendritic scaffold and synaptic patterns for feature detection. Our work elucidates cellular and molecular mechanisms that shape dendritic arbors and synaptic distribution, enabling J-RGC connectivity and thus, function.
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Affiliation(s)
- Jinyue Liu
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, and
- Program in Neuroscience, Harvard Medical School, Boston, Massachusetts 02115
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, and
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54
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Guidance of retinal axons in mammals. Semin Cell Dev Biol 2017; 85:48-59. [PMID: 29174916 DOI: 10.1016/j.semcdb.2017.11.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 11/17/2017] [Accepted: 11/20/2017] [Indexed: 11/21/2022]
Abstract
In order to navigate through the surrounding environment many mammals, including humans, primarily rely on vision. The eye, composed of the choroid, sclera, retinal pigmented epithelium, cornea, lens, iris and retina, is the structure that receives the light and converts it into electrical impulses. The retina contains six major types of neurons involving in receiving and modifying visual information and passing it onto higher visual processing centres in the brain. Visual information is relayed to the brain via the axons of retinal ganglion cells (RGCs), a projection known as the optic pathway. The proper formation of this pathway during development is essential for normal vision in the adult individual. Along this pathway there are several points where visual axons face 'choices' in their direction of growth. Understanding how these choices are made has advanced significantly our knowledge of axon guidance mechanisms. Thus, the development of the visual pathway has served as an extremely useful model to reveal general principles of axon pathfinding throughout the nervous system. However, due to its particularities, some cellular and molecular mechanisms are specific for the visual circuit. Here we review both general and specific mechanisms involved in the guidance of mammalian RGC axons when they are traveling from the retina to the brain to establish precise and stereotyped connections that will sustain vision.
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55
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Graumann R, Di Capua GA, Oyarzún JE, Vásquez MA, Liao C, Brañes JA, Roa I, Casanello P, Corvalán AH, Owen GI, Delgado I, Zangemeister-Wittke U, Ziegler A. Expression of teneurins is associated with tumor differentiation and patient survival in ovarian cancer. PLoS One 2017; 12:e0177244. [PMID: 28472127 PMCID: PMC5417686 DOI: 10.1371/journal.pone.0177244] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/24/2017] [Indexed: 11/29/2022] Open
Abstract
Teneurins are a family of highly conserved pair-rule proteins involved in morphogenesis and development of the central nervous system. Their function in adult tissues and in disease is largely unknown. Recent evidence suggests a role for dysregulated expression of Teneurins in human tumors, but systematic investigations are missing. Here, we investigated Teneurin-2 and Teneurin-4 expression in various cancer cell lines and in ovarian tumor tissues. Teneurin-2 and Teneurin-4 were expressed in most of the breast cancer cell lines tested. Teneurin-4 was also detected in ovarian cancer cell lines, and throughout ovarian tumors and normal ovary tissue. Ovarian tumors with low Teneurin-4 expression showed less differentiated phenotypes and these patients had shorter mean overall survival. Similarly, Teneurin-2 expression correlated with overall survival as well, especially in patients with serous tumors. In the various cell lines, 5-Aza-cytidine-induced changes in DNA methylation did not alter expression of Teneurin-2 and Teneurin-4, despite the existence of predicted CpG islands in both genes. Interestingly, however, we found evidence for the control of Teneurin-2 expression by the oncogenic growth factor FGF8. Furthermore, we identified multiple transcript splicing variants for Teneurin-2 and Teneurin-4, indicating complex gene expression patterns in malignant cells. Finally, downregulation of Teneurin-4 expression using siRNA caused a cell-type dependent increase in proliferation and resistance to cisplatin. Altogether, our data suggest that low Teneurin-4 expression provides a growth advantage to cancer cells and marks an undifferentiated state characterized by increased drug resistance and clinical aggressiveness. We conclude that Teneurin-2 and Teneurin-4 expression levels could be of prognostic value in ovarian cancer.
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Affiliation(s)
- Rebecca Graumann
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Gabriella A. Di Capua
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Juan E. Oyarzún
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Marcos A. Vásquez
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Christine Liao
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - Jorge A. Brañes
- Division of Obstetrics and Gynecology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Iván Roa
- Division of Pathology, Clínica Alemana de Santiago, Santiago, Chile
| | - Paola Casanello
- Perinatology Research Laboratory, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro H. Corvalán
- Advanced Center for Chronic Diseases (ACCDiS), and UC-Center for Investigational Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gareth I. Owen
- Advanced Center for Chronic Diseases (ACCDiS), and UC-Center for Investigational Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Iris Delgado
- Center for Epidemiology and Health Policies, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | | | - Annemarie Ziegler
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
- * E-mail:
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56
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Vysokov NV, Silva JP, Lelianova VG, Ho C, Djamgoz MB, Tonevitsky AG, Ushkaryov YA. The Mechanism of Regulated Release of Lasso/Teneurin-2. Front Mol Neurosci 2016; 9:59. [PMID: 27499734 PMCID: PMC4956664 DOI: 10.3389/fnmol.2016.00059] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/08/2016] [Indexed: 01/25/2023] Open
Abstract
Teneurins are large cell-surface receptors involved in axon guidance. Teneurin-2 (also known as latrophilin-1-associated synaptic surface organizer (Lasso)) interacts across the synaptic cleft with presynaptic latrophilin-1, an adhesion G-protein-coupled receptor that participates in regulating neurotransmitter release. Lasso-latrophilin-1 interaction mediates synapse formation and calcium signaling, highlighting the important role of this trans-synaptic receptor pair. However, Lasso is thought to be proteolytically cleaved within its ectodomain and released into the medium, making it unclear whether it acts as a proper cell-surface receptor or a soluble protein. We demonstrate here that during its intracellular processing Lasso is constitutively cleaved at a furin site within its ectodomain. The cleaved fragment, which encompasses almost the entire ectodomain of Lasso, is potentially soluble; however, it remains anchored on the cell surface via its non-covalent interaction with the transmembrane fragment of Lasso. Lasso is also constitutively cleaved within the intracellular domain (ICD). Finally, Lasso can be further proteolytically cleaved within the transmembrane domain. The third cleavage is regulated and releases the entire ectodomain of Lasso into the medium. The released ectodomain of Lasso retains its functional properties and binds latrophilin-1 expressed on other cells; this binding stimulates intracellular Ca2+ signaling in the target cells. Thus, Lasso not only serves as a bona fide cell-surface receptor, but also as a partially released target-derived signaling factor.
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Affiliation(s)
- Nickolai V Vysokov
- School of Pharmacy, University of KentChatham, UK; Division of Cell and Molecular Biology, Imperial College LondonLondon, UK
| | - John-Paul Silva
- Division of Cell and Molecular Biology, Imperial College London London, UK
| | - Vera G Lelianova
- School of Pharmacy, University of KentChatham, UK; Division of Cell and Molecular Biology, Imperial College LondonLondon, UK
| | - Claudia Ho
- Division of Cell and Molecular Biology, Imperial College London London, UK
| | - Mustafa B Djamgoz
- Division of Cell and Molecular Biology, Imperial College London London, UK
| | - Alexander G Tonevitsky
- Department of Translational Oncology, P.A. Hertzen Moscow Oncology Research Institute, National Center of Medical Radiological Research Moscow, Russia
| | - Yuri A Ushkaryov
- School of Pharmacy, University of KentChatham, UK; Division of Cell and Molecular Biology, Imperial College LondonLondon, UK
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57
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Abstract
The larval zebrafish (Danio rerio) is an excellent vertebrate model for in vivo imaging of biological phenomena at subcellular, cellular and systems levels. However, the optical accessibility of highly pigmented tissues, like the eyes, is limited even in this animal model. Typical strategies to improve the transparency of zebrafish larvae require the use of either highly toxic chemical compounds (e.g. 1-phenyl-2-thiourea, PTU) or pigmentation mutant strains (e.g. casper mutant). To date none of these strategies produce normally behaving larvae that are transparent in both the body and the eyes. Here we present crystal, an optically clear zebrafish mutant obtained by combining different viable mutations affecting skin pigmentation. Compared to the previously described combinatorial mutant casper, the crystal mutant lacks pigmentation also in the retinal pigment epithelium, therefore enabling optical access to the eyes. Unlike PTU-treated animals, crystal larvae are able to perform visually guided behaviours, such as the optomotor response, as efficiently as wild type larvae. To validate the in vivo application of crystal larvae, we performed whole-brain light-sheet imaging and two-photon calcium imaging of neural activity in the retina. In conclusion, this novel combinatorial pigmentation mutant represents an ideal vertebrate tool for completely unobstructed structural and functional in vivo investigations of biological processes, particularly when imaging tissues inside or between the eyes.
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58
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Abstract
The larval zebrafish (Danio rerio) is an excellent vertebrate model for in vivo imaging of biological phenomena at subcellular, cellular and systems levels. However, the optical accessibility of highly pigmented tissues, like the eyes, is limited even in this animal model. Typical strategies to improve the transparency of zebrafish larvae require the use of either highly toxic chemical compounds (e.g. 1-phenyl-2-thiourea, PTU) or pigmentation mutant strains (e.g. casper mutant). To date none of these strategies produce normally behaving larvae that are transparent in both the body and the eyes. Here we present crystal, an optically clear zebrafish mutant obtained by combining different viable mutations affecting skin pigmentation. Compared to the previously described combinatorial mutant casper, the crystal mutant lacks pigmentation also in the retinal pigment epithelium, therefore enabling optical access to the eyes. Unlike PTU-treated animals, crystal larvae are able to perform visually guided behaviours, such as the optomotor response, as efficiently as wild type larvae. To validate the in vivo application of crystal larvae, we performed whole-brain light-sheet imaging and two-photon calcium imaging of neural activity in the retina. In conclusion, this novel combinatorial pigmentation mutant represents an ideal vertebrate tool for completely unobstructed structural and functional in vivo investigations of biological processes, particularly when imaging tissues inside or between the eyes.
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59
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Antinucci P, Suleyman O, Monfries C, Hindges R. Neural Mechanisms Generating Orientation Selectivity in the Retina. Curr Biol 2016; 26:1802-15. [PMID: 27374343 PMCID: PMC4963213 DOI: 10.1016/j.cub.2016.05.035] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/21/2016] [Accepted: 05/12/2016] [Indexed: 12/13/2022]
Abstract
The orientation of visual stimuli is a salient feature of visual scenes. In vertebrates, the first neural processing steps generating orientation selectivity take place in the retina. Here, we dissect an orientation-selective circuit in the larval zebrafish retina and describe its underlying synaptic, cellular, and molecular mechanisms. We genetically identify a class of amacrine cells (ACs) with elongated dendritic arbors that show orientation tuning. Both selective optogenetic ablation of ACs marked by the cell-adhesion molecule Teneurin-3 (Tenm3) and pharmacological interference with their function demonstrate that these cells are critical components for orientation selectivity in retinal ganglion cells (RGCs) by being a source of tuned GABAergic inhibition. Moreover, our morphological analyses reveal that Tenm3+ ACs and orientation-selective RGCs co-stratify their dendrites in the inner plexiform layer, and that Tenm3+ ACs require Tenm3 to acquire their correct dendritic stratification. Finally, we show that orientation tuning is present also among bipolar cell presynaptic terminals. Our results define a neural circuit underlying orientation selectivity in the vertebrate retina and characterize cellular and molecular requirements for its assembly. We identify Tenm3+ ACs with elongated dendritic arbors showing orientation tuning Tenm3+ AC GABAergic inhibition is crucial for orientation-selective RGC tuning Orientation tuning is present also among some bipolar cell presynaptic terminals We propose a model of how orientation selectivity is generated in ganglion cells
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Affiliation(s)
- Paride Antinucci
- MRC Centre for Developmental Neurobiology, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Oniz Suleyman
- MRC Centre for Developmental Neurobiology, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Clinton Monfries
- MRC Centre for Developmental Neurobiology, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Robert Hindges
- MRC Centre for Developmental Neurobiology, King's College London, Guy's Campus, London SE1 1UL, UK.
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60
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Chassaing N, Ragge N, Plaisancié J, Patat O, Geneviève D, Rivier F, Malrieu-Eliaou C, Hamel C, Kaplan J, Calvas P. Confirmation of TENM3 involvement in autosomal recessive colobomatous microphthalmia. Am J Med Genet A 2016; 170:1895-8. [PMID: 27103084 DOI: 10.1002/ajmg.a.37667] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/07/2016] [Indexed: 11/11/2022]
Abstract
Anophthalmia and microphthalmia are the most severe malformations of the eye, referring to a congenital absence, and a reduced size of the eyeball respectively. More than 20 genes have been shown to be mutated in patients with syndromic and non-syndromic forms of anophthalmia-microphthalmia. In a recent study combining autozygome and exome analysis, a homozygous loss of function mutation in TENM3 (previously named ODZ3) was reported in two siblings with isolated bilateral colobomatous microphthalmia from a consanguineous Saudi family. Herein, we report a third patient (not related to the previously reported family) with bilateral colobomatous microphthalmia and developmental delay in whom genetic studies identified a homozygous TENM3 splicing mutation c.2968-2A>T (p.Val990Cysfs*13). This report supports the association of TENM3 mutations with colobomatous microphthalmia and expands the phenotypic spectrum associated with mutations in this gene. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nicolas Chassaing
- CHU Toulouse, Service de Génétique Médicale, Hôpital Purpan, Toulouse, France.,UDEAR, Université de Toulouse, Inserm, UPS, CNRS, Toulouse, France
| | - Nicola Ragge
- Birmingham Women's Hospital Clinical Genetics Unit, Birmingham, UK.,School of Life Sciences, Oxford Brookes University, Oxford, UK
| | - Julie Plaisancié
- CHU Toulouse, Service de Génétique Médicale, Hôpital Purpan, Toulouse, France
| | - Oliver Patat
- CHU Toulouse, Service de Génétique Médicale, Hôpital Purpan, Toulouse, France
| | - David Geneviève
- CHRU Montpellier, Service de Génétique Médicale, Montpellier, France
| | - François Rivier
- CHRU Montpellier, Service de Neuropédiatrie, Montpellier, France
| | | | - Christian Hamel
- CHRU Montpellier, Maladies Sensorielles Génétiques, Montpellier, France
| | | | - Patrick Calvas
- CHU Toulouse, Service de Génétique Médicale, Hôpital Purpan, Toulouse, France.,UDEAR, Université de Toulouse, Inserm, UPS, CNRS, Toulouse, France
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61
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de Wit J, Ghosh A. Specification of synaptic connectivity by cell surface interactions. Nat Rev Neurosci 2015; 17:22-35. [PMID: 26656254 DOI: 10.1038/nrn.2015.3] [Citation(s) in RCA: 192] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The molecular diversification of cell surface molecules has long been postulated to impart specific surface identities on neuronal cell types. The existence of unique cell surface identities would allow neurons to distinguish one another and connect with their appropriate target cells. Although progress has been made in identifying cell type-specific surface molecule repertoires and in characterizing their extracellular interactions, determining how this molecular diversity contributes to the precise wiring of neural circuitry has proven challenging. Here, we review the role of the cadherin, neurexin, immunoglobulin and leucine-rich repeat protein superfamilies in the specification of connectivity. The emerging evidence suggests that the concerted actions of these proteins may critically contribute to the assembly of neural circuits.
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Affiliation(s)
- Joris de Wit
- VIB Center for the Biology of Disease and Center for Human Genetics, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Anirvan Ghosh
- Neuroscience Discovery, Roche Innovation Center Basel, F. Hoffman-La Roche, Grenzacherstrasse 124, 4070 Basel, Switzerland
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62
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Gittelman RM, Hun E, Ay F, Madeoy J, Pennacchio L, Noble WS, Hawkins RD, Akey JM. Comprehensive identification and analysis of human accelerated regulatory DNA. Genome Res 2015; 25:1245-55. [PMID: 26104583 PMCID: PMC4561485 DOI: 10.1101/gr.192591.115] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/15/2015] [Indexed: 01/19/2023]
Abstract
It has long been hypothesized that changes in gene regulation have played an important role in human evolution, but regulatory DNA has been much more difficult to study compared with protein-coding regions. Recent large-scale studies have created genome-scale catalogs of DNase I hypersensitive sites (DHSs), which demark potentially functional regulatory DNA. To better define regulatory DNA that has been subject to human-specific adaptive evolution, we performed comprehensive evolutionary and population genetics analyses on over 18 million DHSs discovered in 130 cell types. We identified 524 DHSs that are conserved in nonhuman primates but accelerated in the human lineage (haDHS), and estimate that 70% of substitutions in haDHSs are attributable to positive selection. Through extensive computational and experimental analyses, we demonstrate that haDHSs are often active in brain or neuronal cell types; play an important role in regulating the expression of developmentally important genes, including many transcription factors such as SOX6, POU3F2, and HOX genes; and identify striking examples of adaptive regulatory evolution that may have contributed to human-specific phenotypes. More generally, our results reveal new insights into conserved and adaptive regulatory DNA in humans and refine the set of genomic substrates that distinguish humans from their closest living primate relatives.
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Affiliation(s)
- Rachel M Gittelman
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Enna Hun
- Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Ferhat Ay
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jennifer Madeoy
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Len Pennacchio
- Lawrence Berkeley National Laboratory, Genomics Division, Berkeley, California 94701, USA
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - R David Hawkins
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Joshua M Akey
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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63
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Reis LM, Semina EV. Conserved genetic pathways associated with microphthalmia, anophthalmia, and coloboma. ACTA ACUST UNITED AC 2015; 105:96-113. [PMID: 26046913 DOI: 10.1002/bdrc.21097] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 05/13/2015] [Indexed: 12/19/2022]
Abstract
The human eye is a complex organ whose development requires extraordinary coordination of developmental processes. The conservation of ocular developmental steps in vertebrates suggests possible common genetic mechanisms. Genetic diseases involving the eye represent a leading cause of blindness in children and adults. During the last decades, there has been an exponential increase in genetic studies of ocular disorders. In this review, we summarize current success in identification of genes responsible for microphthalmia, anophthalmia, and coloboma (MAC) phenotypes, which are associated with early defects in embryonic eye development. Studies in animal models for the orthologous genes identified overlapping phenotypes for most factors, confirming the conservation of their function in vertebrate development. These animal models allow for further investigation of the mechanisms of MAC, integration of various identified genes into common developmental pathways and finally, provide an avenue for the development and testing of therapeutic interventions.
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Affiliation(s)
- Linda M Reis
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Milwaukee, Wisconsin.,Department of Ophthalmology, Medical College of Wisconsin, Milwaukee, Wisconsin.,Department of Cell Biology Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin
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64
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Mosca TJ. On the Teneurin track: a new synaptic organization molecule emerges. Front Cell Neurosci 2015; 9:204. [PMID: 26074772 PMCID: PMC4444827 DOI: 10.3389/fncel.2015.00204] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/11/2015] [Indexed: 11/16/2022] Open
Abstract
To achieve proper synaptic development and function, coordinated signals must pass between the pre- and postsynaptic membranes. Such transsynaptic signals can be comprised of receptors and secreted ligands, membrane associated receptors, and also pairs of synaptic cell adhesion molecules. A critical open question bridging neuroscience, developmental biology, and cell biology involves identifying those signals and elucidating how they function. Recent work in Drosophila and vertebrate systems has implicated a family of proteins, the Teneurins, as a new transsynaptic signal in both the peripheral and central nervous systems. The Teneurins have established roles in neuronal wiring, but studies now show their involvement in regulating synaptic connections between neurons and bridging the synaptic membrane and the cytoskeleton. This review will examine the Teneurins as synaptic cell adhesion molecules, explore how they regulate synaptic organization, and consider how some consequences of human Teneurin mutations may have synaptopathic origins.
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Affiliation(s)
- Timothy J Mosca
- Department of Biology, Stanford University Stanford, CA, USA
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Missaire M, Hindges R. The role of cell adhesion molecules in visual circuit formation: from neurite outgrowth to maps and synaptic specificity. Dev Neurobiol 2015; 75:569-83. [PMID: 25649254 PMCID: PMC4855686 DOI: 10.1002/dneu.22267] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/08/2015] [Accepted: 01/09/2015] [Indexed: 11/08/2022]
Abstract
The formation of visual circuitry is a multistep process that involves cell–cell interactions based on a range of molecular mechanisms. The correct implementation of individual events, including axon outgrowth and guidance, the formation of the topographic map, or the synaptic targeting of specific cellular subtypes, are prerequisites for a fully functional visual system that is able to appropriately process the information captured by the eyes. Cell adhesion molecules (CAMs) with their adhesive properties and their high functional diversity have been identified as key actors in several of these fundamental processes. Because of their growth‐promoting properties, CAMs play an important role in neuritogenesis. Furthermore, they are necessary to control additional neurite development, regulating dendritic spacing and axon pathfinding. Finally, trans‐synaptic interactions of CAMs ensure cell type‐specific connectivity as a basis for the establishment of circuits processing distinct visual features. Recent discoveries implicating CAMs in novel mechanisms have led to a better general understanding of neural circuit formation, but also revealed an increasing complexity of their function. This review aims at describing the different levels of action for CAMs to shape neural connectivity, with a special focus on the visual system. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 75: 569–583, 2015
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Affiliation(s)
- Mégane Missaire
- MRC Centre for Developmental Neurobiology, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, United Kingdom
| | - Robert Hindges
- MRC Centre for Developmental Neurobiology, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, United Kingdom
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66
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Kita EM, Scott EK, Goodhill GJ. Topographic wiring of the retinotectal connection in zebrafish. Dev Neurobiol 2015; 75:542-56. [PMID: 25492632 DOI: 10.1002/dneu.22256] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 12/03/2014] [Accepted: 12/08/2014] [Indexed: 11/08/2022]
Abstract
The zebrafish retinotectal projection provides an attractive model system for studying many aspects of topographic map formation and maintenance. Visual connections initially start to form between 3 and 5 days postfertilization, and remain plastic throughout the life of the fish. Zebrafish are easily manipulated surgically, genetically, and chemically, and a variety of molecular tools exist to enable visualization and control of various aspects of map development. Here, we review zebrafish retinotectal map formation, focusing particularly on the detailed structure and dynamics of the connections, the molecules that are important in map creation, and how activity regulates the maintenance of the map.
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Affiliation(s)
- Elizabeth M Kita
- Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia
| | - Ethan K Scott
- School of Biomedical Sciences, The University of Queensland, Brisbane QLD 4072, Australia
| | - Geoffrey J Goodhill
- Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia.,School of Mathematics and Physics, The University of Queensland, Brisbane QLD 4072, Australia
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67
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Abstract
The visual system is beautifully crafted to transmit information of the external world to visual processing and cognitive centers in the brain. For visual information to be relayed to the brain, a series of axon pathfinding events must take place to ensure that the axons of retinal ganglion cells, the only neuronal cell type in the retina that sends axons out of the retina, find their way out of the eye to connect with targets in the brain. In the past few decades, the power of molecular and genetic tools, including the generation of genetically manipulated mouse lines, have multiplied our knowledge about the molecular mechanisms involved in the sculpting of the visual system. Here, we review major advances in our understanding of the mechanisms controlling the differentiation of RGCs, guidance of their axons from the retina to the primary visual centers, and the refinement processes essential for the establishment of topographic maps and eye-specific axon segregation. Human disorders, such as albinism and achiasmia, that impair RGC axon growth and guidance and, thus, the establishment of a fully functioning visual system will also be discussed.
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Affiliation(s)
- Lynda Erskine
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Scotland, UK
| | - Eloisa Herrera
- Instituto de Neurosciencias de Alicante, CSIC-UMH, San Juan de Alicante, Spain
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68
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Meza-Aguilar DG, Boucard AA. Latrophilins updated. Biomol Concepts 2014; 5:457-78. [DOI: 10.1515/bmc-2014-0032] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/07/2014] [Indexed: 01/26/2023] Open
Abstract
AbstractLatrophilins (LPHN) are part of a yet unexplored family of receptors comprising three isoforms, LPHN1-3, and belonging to a unique branch of G protein-coupled receptors (GPCR) named adhesion GPCR (aGPCR). LPHN are considered to be prototypical models for the study of aGPCR as they are one of the most evolutionary conserved members. Previously described as the target for a potent neurotoxin from the black widow spider venom, LPHN are now being studied under a whole new perspective. Indeed, recent advances have provided a better understanding of different aspects of this prototypical family of receptors: 1) elucidation of LPHN ectodomain organization by crystallography has unveiled a new functional domain with great repercussion on all the other members of the aGPCR family, 2) proteomic approaches have opened the gate to unsuspected functional characteristics of LPHN cellular role, and 3) genetic approaches have provided hints into the physiological functions of LPHN in specific systems and organisms. Moreover, genomic linkage studies screening human patients from diverse genetic backgrounds have involved LPHN gene defects in human disorders such as attention-deficit hyperactivity disorder and cancer. In this review, we will provide a historical perspective addressing experimental research on these receptors while highlighting the new advances and discoveries concerning LPHN functions. As GPCR still represent the most studied targets for the development of pharmacological approaches aiming at alleviating human disorders, the relevance of studying LPHN retains a high pertinence to better understand these receptors for the treatment of human diseases.
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Affiliation(s)
- Diana G. Meza-Aguilar
- 1Av. Instituto Politécnico Nacional, Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, No 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México D.F., México
| | - Antony A. Boucard
- 1Av. Instituto Politécnico Nacional, Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, No 2508, Col. San Pedro Zacatenco, Gustavo A. Madero, C.P. 07360, México D.F., México
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69
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Tran H, Sawatari A, Leamey CA. The glycoprotein Ten-m3 mediates topography and patterning of thalamostriatal projections from the parafascicular nucleus in mice. Eur J Neurosci 2014; 41:55-68. [PMID: 25406022 DOI: 10.1111/ejn.12767] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 11/27/2022]
Abstract
The striatum is the key input nucleus of the basal ganglia, and is implicated in motor control and learning. Despite the importance of striatal circuits, the mechanisms associated with their development are not well established. Previously, Ten-m3, a member of the Ten-m/teneurin/odz family of transmembrane glycoproteins, was found to be important in the mapping of binocular visual pathways. Here, we investigated a potential role for Ten-m3 in striatal circuit formation. In situ hybridisation revealed a patchy distribution of Ten-m3 mRNA expression superimposed on a high-dorsal to low-ventral gradient in a subregion of the striatal matrix. A survey of afferent/efferent structures associated with the matrix identified the parafascicular thalamic nucleus (PF) as a potential locus of action. Ten-m3 was also found to be expressed in a high-dorsal to low-ventral gradient in the PF, corresponding topographically to its expression in the striatum. Further, a subset of thalamic terminal clusters overlapped with Ten-m3-positive domains within the striatal matrix. Studies in wild-type (WT) and Ten-m3 knockout (KO) mice revealed no differences in overall striatal or PF structure. Thalamostriatal terminals in KOs, however, while still confined to the matrix subregion, lost their clustered appearance. Topography was also altered, with terminals from the lateral PF projecting ectopically to ventral and medial striatum, rather than remaining confined dorsolaterally as in WTs. Behaviorally, Ten-m3 KOs displayed delayed motor skill acquisition. This study demonstrates that Ten-m3 plays a key role in directing the formation of thalamostriatal circuitry, the first molecular candidate reported to regulate connectivity within this pathway.
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Affiliation(s)
- Heidi Tran
- Discipline of Physiology, Bosch Institute and School of Medical Sciences, University of Sydney, Sydney, NSW, 2006, Australia
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70
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Mosca TJ, Luo L. Synaptic organization of the Drosophila antennal lobe and its regulation by the Teneurins. eLife 2014; 3:e03726. [PMID: 25310239 PMCID: PMC4194450 DOI: 10.7554/elife.03726] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 09/18/2014] [Indexed: 12/11/2022] Open
Abstract
Understanding information flow through neuronal circuits requires knowledge of their synaptic organization. In this study, we utilized fluorescent pre- and postsynaptic markers to map synaptic organization in the Drosophila antennal lobe, the first olfactory processing center. Olfactory receptor neurons (ORNs) produce a constant synaptic density across different glomeruli. Each ORN within a class contributes nearly identical active zone number. Active zones from ORNs, projection neurons (PNs), and local interneurons have distinct subglomerular and subcellular distributions. The correct number of ORN active zones and PN acetylcholine receptor clusters requires the Teneurins, conserved transmembrane proteins involved in neuromuscular synapse organization and synaptic partner matching. Ten-a acts in ORNs to organize presynaptic active zones via the spectrin cytoskeleton. Ten-m acts in PNs autonomously to regulate acetylcholine receptor cluster number and transsynaptically to regulate ORN active zone number. These studies advanced our ability to assess synaptic architecture in complex CNS circuits and their underlying molecular mechanisms.
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Affiliation(s)
- Timothy J Mosca
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Liqun Luo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, United States
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71
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The teneurins: new players in the generation of visual topography. Semin Cell Dev Biol 2014; 35:173-9. [PMID: 25152333 DOI: 10.1016/j.semcdb.2014.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 08/08/2014] [Accepted: 08/15/2014] [Indexed: 01/03/2023]
Abstract
A functionally critical feature of the nervous system is the precision of its connectivity. An emerging molecular mediator of this process is the teneurin/ten-m/odz family of transmembrane proteins. A number of recent studies have provided compelling evidence that teneurins have homophilic adhesive properties which, together with their corresponding expression patterns in interconnected groups of neurons, enables them to promote appropriate patterns of connectivity. Particularly important roles have been demonstrated in the visual, olfactory and motor systems. This review attempts to relate new insights into the complex biology of these molecules to their roles in the establishment of functional neural circuits.
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72
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Robles E, Laurell E, Baier H. The retinal projectome reveals brain-area-specific visual representations generated by ganglion cell diversity. Curr Biol 2014; 24:2085-2096. [PMID: 25155513 DOI: 10.1016/j.cub.2014.07.080] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 07/29/2014] [Accepted: 07/31/2014] [Indexed: 11/29/2022]
Abstract
BACKGROUND Visual information is transmitted to the vertebrate brain exclusively via the axons of retinal ganglion cells (RGCs). The functional diversity of RGCs generates multiple representations of the visual environment that are transmitted to several brain areas. However, in no vertebrate species has a complete wiring diagram of RGC axonal projections been constructed. We employed sparse genetic labeling and in vivo imaging of the larval zebrafish to generate a cellular-resolution map of projections from the retina to the brain. RESULTS Our data define 20 stereotyped axonal projection patterns, the majority of which innervate multiple brain areas. Morphometric analysis of pre- and postsynaptic RGC structure revealed more than 50 structural RGC types with unique combinations of dendritic and axonal morphologies, exceeding current estimates of RGC diversity in vertebrates. These single-cell projection mapping data indicate that specific projection patterns are nonuniformly specified in the retina to generate retinotopically biased visual maps throughout the brain. The retinal projectome also successfully predicted a functional subdivision of the pretectum. CONCLUSIONS Our data indicate that RGC projection patterns are precisely coordinated to generate brain-area-specific visual representations originating from RGCs with distinct dendritic morphologies and topographic distributions.
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Affiliation(s)
- Estuardo Robles
- Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Eva Laurell
- Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Herwig Baier
- Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany
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73
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de Wit J, Ghosh A. Control of neural circuit formation by leucine-rich repeat proteins. Trends Neurosci 2014; 37:539-50. [PMID: 25131359 DOI: 10.1016/j.tins.2014.07.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/02/2014] [Accepted: 07/24/2014] [Indexed: 01/19/2023]
Abstract
The function of neural circuits depends on the precise connectivity between populations of neurons. Increasing evidence indicates that disruptions in excitatory or inhibitory synapse formation or function lead to excitation/inhibition (E/I) imbalances and contribute to neurodevelopmental and psychiatric disorders. Leucine-rich repeat (LRR)-containing surface proteins have emerged as key organizers of excitatory and inhibitory synapses. Distinct LRR proteins are expressed in different cell types and interact with key pre- and postsynaptic proteins. These protein interaction networks allow LRR proteins to coordinate pre- and postsynaptic elements during synapse formation and differentiation, pathway-specific synapse development, and synaptic plasticity. LRR proteins, therefore, play a critical role in organizing synaptic connections into functional neural circuits, and their dysfunction may contribute to neuropsychiatric disorders.
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Affiliation(s)
- Joris de Wit
- VIB Center for the Biology of Disease, 3000 Leuven, Belgium; KU Leuven, Center for Human Genetics, 3000 Leuven, Belgium.
| | - Anirvan Ghosh
- Neuroscience Discovery, F. Hoffman-La Roche, 4070 Basel, Switzerland
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Retinal overexpression of Ten-m3 alters ipsilateral retinogeniculate projections in the wallaby (Macropus eugenii). Neurosci Lett 2014; 566:167-71. [PMID: 24602979 DOI: 10.1016/j.neulet.2014.02.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 02/10/2014] [Accepted: 02/23/2014] [Indexed: 12/27/2022]
Abstract
The dorsal lateral geniculate nucleus (dLGN) contains a retinotopic map where input from the two eyes map in register to provide a substrate for binocular vision. Ten-m3, a transmembrane protein, mediates homophilic interactions and has been implicated in the patterning of ipsilateral visual projections. Ease of access to early developmental stages in a marsupial wallaby has been used to manipulate levels of Ten-m3 during the development of retinogeniculate projections. In situ hybridisation showed a high dorsomedial to low ventrolateral gradient of Ten-m3 in the developing dLGN, matching retinotopically with the previously reported high ventral to low dorsal retinal gradient. Overexpression of Ten-m3 in ventronasal but not dorsonasal retina resulted in an extension of ipsilateral projections beyond the normal binocular zone. These results demonstrate that Ten-m3 influences ipsilateral projections and support a role for it in binocular mapping.
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