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Stassen SV, Kobashi M, Lam EY, Huang Y, Ho JWK, Tsia KK. StaVia: spatially and temporally aware cartography with higher-order random walks for cell atlases. Genome Biol 2024; 25:224. [PMID: 39152459 PMCID: PMC11328412 DOI: 10.1186/s13059-024-03347-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 07/23/2024] [Indexed: 08/19/2024] Open
Abstract
Single-cell atlases pose daunting computational challenges pertaining to the integration of spatial and temporal information and the visualization of trajectories across large atlases. We introduce StaVia, a computational framework that synergizes multi-faceted single-cell data with higher-order random walks that leverage the memory of cells' past states, fused with a cartographic Atlas View that offers intuitive graph visualization. This spatially aware cartography captures relationships between cell populations based on their spatial location as well as their gene expression and developmental stage. We demonstrate this using zebrafish gastrulation data, underscoring its potential to dissect complex biological landscapes in both spatial and temporal contexts.
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Affiliation(s)
- Shobana V Stassen
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong.
| | - Minato Kobashi
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Edmund Y Lam
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong
- AI Chip Center for Emerging Smart Systems, Hong Kong Science Park, Shatin, New Territories, Hong Kong
| | - Yuanhua Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
- Department of Statistics and Actuarial Science, The University of Hong Kong, Pokfulam, Hong Kong
| | - Joshua W K Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
- Laboratory of Data Discovery for Health, Hong Kong Science Park, Shatin, New Territories, Hong Kong
| | - Kevin K Tsia
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong.
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2
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Aerts T, Boonen A, Geenen L, Stulens A, Masin L, Pancho A, Francis A, Pepermans E, Baggerman G, Van Roy F, Wöhr M, Seuntjens E. Altered socio-affective communication and amygdala development in mice with protocadherin10-deficient interneurons. Open Biol 2024; 14:240113. [PMID: 38889770 DOI: 10.1098/rsob.240113] [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: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 06/20/2024] Open
Abstract
Autism spectrum disorder (ASD) is a group of neurodevelopmental conditions associated with deficits in social interaction and communication, together with repetitive behaviours. The cell adhesion molecule protocadherin10 (PCDH10) is linked to ASD in humans. Pcdh10 is expressed in the nervous system during embryonic and early postnatal development and is important for neural circuit formation. In mice, strong expression of Pcdh10 in the ganglionic eminences and in the basolateral complex (BLC) of the amygdala was observed at mid and late embryonic stages, respectively. Both inhibitory and excitatory neurons expressed Pcdh10 in the BLC at perinatal stages and vocalization-related genes were enriched in Pcdh10-expressing neurons in adult mice. An epitope-tagged Pcdh10-HAV5 mouse line revealed endogenous interactions of PCDH10 with synaptic proteins in the young postnatal telencephalon. Nuanced socio-affective communication changes in call emission rates, acoustic features and call subtype clustering were primarily observed in heterozygous pups of a conditional knockout (cKO) with selective deletion of Pcdh10 in Gsh2-lineage interneurons. These changes were less prominent in heterozygous ubiquitous Pcdh10 KO pups, suggesting that altered anxiety levels associated with Gsh2-lineage interneuron functioning might drive the behavioural effects. Together, loss of Pcdh10 specifically in interneurons contributes to behavioural alterations in socio-affective communication with relevance to ASD.
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Affiliation(s)
- Tania Aerts
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Anneleen Boonen
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Lieve Geenen
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Anne Stulens
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Luca Masin
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Neural Circuit Development and Regeneration, KU Leuven , Leuven 3000, Belgium
| | - Anna Pancho
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
- Developmental Genetics, Department of Biomedicine, University of Basel , Basel 4058, Switzerland
| | - Annick Francis
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
| | - Elise Pepermans
- Centre for Proteomics, University of Antwerp , Antwerp, Belgium
| | - Geert Baggerman
- Centre for Proteomics, University of Antwerp , Antwerp, Belgium
- Department of Computer Science, University of Antwerp , Antwerp, Belgium
| | - Frans Van Roy
- Faculty of Science, Department of Biomedical Molecular Biology; Inflammation Research Center, VIB, Ghent University , Cancer Research Institute Ghent (CRIG) 9000, Belgium
| | - Markus Wöhr
- Faculty of Psychology and Educational Sciences, Research Unit Brain and Cognition, Laboratory of Biological Psychology, Social and Affective Neuroscience Research Group, KU Leuven , Leuven 3000, Belgium
- KU Leuven, Leuven Brain Institute , Leuven 3000, Belgium
- Faculty of Psychology, Experimental and Biological Psychology, Behavioral Neuroscience, Philipps-University of Marburg , Marburg 35032, Germany
- Center for Mind, Brain and Behavior, Philipps-University of Marburg , Marburg 35032, Germany
| | - Eve Seuntjens
- Faculty of Science, Department of Biology, Division of Animal Physiology and Neurobiology, Lab of Developmental Neurobiology, KU Leuven , Leuven 3000, Belgium
- KU Leuven, Leuven Brain Institute , Leuven 3000, Belgium
- KU Leuven, Leuven Institute for Single Cell Omics , Leuven 3000, Belgium
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3
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Wullimann MF, Mokayes N, Shainer I, Kuehn E, Baier H. Genoarchitectonics of the larval zebrafish diencephalon. J Comp Neurol 2024; 532:e25549. [PMID: 37983970 DOI: 10.1002/cne.25549] [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: 02/10/2023] [Revised: 07/15/2023] [Accepted: 10/03/2023] [Indexed: 11/22/2023]
Abstract
The brain is spatially organized into subdivisions, nuclei and areas, which often correspond to functional and developmental units. A segmentation of brain regions in the form of a consensus atlas facilitates mechanistic studies and is a prerequisite for sharing information among neuroanatomists. Gene expression patterns objectively delineate boundaries between brain regions and provide information about their developmental and evolutionary histories. To generate a detailed molecular map of the larval zebrafish diencephalon, we took advantage of the Max Planck Zebrafish Brain (mapzebrain) atlas, which aligns hundreds of transcript and transgene expression patterns in a shared coordinate system. Inspection and co-visualization of close to 50 marker genes have allowed us to resolve the tripartite prosomeric scaffold of the diencephalon at unprecedented resolution. This approach clarified the genoarchitectonic partitioning of the alar diencephalon into pretectum (alar part of prosomere P1), thalamus (alar part of prosomere P2, with habenula and pineal complex), and prethalamus (alar part of prosomere P3). We further identified the region of the nucleus of the medial longitudinal fasciculus, as well as the posterior and anterior parts of the posterior tuberculum, as molecularly distinct basal parts of prosomeres 1, 2, and 3, respectively. Some of the markers examined allowed us to locate glutamatergic, GABAergic, dopaminergic, serotoninergic, and various neuropeptidergic domains in the larval zebrafish diencephalon. Our molecular neuroanatomical approach has thus (1) yielded an objective and internally consistent interpretation of the prosomere boundaries within the zebrafish forebrain; has (2) produced a list of markers, which in sparse combinations label the subdivisions of the diencephalon; and is (3) setting the stage for further functional and developmental studies in this vertebrate brain.
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Affiliation(s)
- Mario F Wullimann
- Genes - Circuits - Behavior Max-Planck-Institute for Biological Intelligence, Martinsried, Germany
- Department Biology II, Division of Neurobiology, Ludwig-Maximilians-University (LMU Munich), Martinsried, Germany
| | - Nouwar Mokayes
- Genes - Circuits - Behavior Max-Planck-Institute for Biological Intelligence, Martinsried, Germany
| | - Inbal Shainer
- Genes - Circuits - Behavior Max-Planck-Institute for Biological Intelligence, Martinsried, Germany
| | - Enrico Kuehn
- Genes - Circuits - Behavior Max-Planck-Institute for Biological Intelligence, Martinsried, Germany
| | - Herwig Baier
- Genes - Circuits - Behavior Max-Planck-Institute for Biological Intelligence, Martinsried, Germany
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4
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Yao Z, van Velthoven CTJ, Kunst M, Zhang M, McMillen D, Lee C, Jung W, Goldy J, Abdelhak A, Aitken M, Baker K, Baker P, Barkan E, Bertagnolli D, Bhandiwad A, Bielstein C, Bishwakarma P, Campos J, Carey D, Casper T, Chakka AB, Chakrabarty R, Chavan S, Chen M, Clark M, Close J, Crichton K, Daniel S, DiValentin P, Dolbeare T, Ellingwood L, Fiabane E, Fliss T, Gee J, Gerstenberger J, Glandon A, Gloe J, Gould J, Gray J, Guilford N, Guzman J, Hirschstein D, Ho W, Hooper M, Huang M, Hupp M, Jin K, Kroll M, Lathia K, Leon A, Li S, Long B, Madigan Z, Malloy J, Malone J, Maltzer Z, Martin N, McCue R, McGinty R, Mei N, Melchor J, Meyerdierks E, Mollenkopf T, Moonsman S, Nguyen TN, Otto S, Pham T, Rimorin C, Ruiz A, Sanchez R, Sawyer L, Shapovalova N, Shepard N, Slaughterbeck C, Sulc J, Tieu M, Torkelson A, Tung H, Valera Cuevas N, Vance S, Wadhwani K, Ward K, Levi B, Farrell C, Young R, Staats B, Wang MQM, Thompson CL, Mufti S, Pagan CM, Kruse L, Dee N, Sunkin SM, Esposito L, Hawrylycz MJ, Waters J, Ng L, Smith K, Tasic B, Zhuang X, Zeng H. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Nature 2023; 624:317-332. [PMID: 38092916 PMCID: PMC10719114 DOI: 10.1038/s41586-023-06812-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
Abstract
The mammalian brain consists of millions to billions of cells that are organized into many cell types with specific spatial distribution patterns and structural and functional properties1-3. Here we report a comprehensive and high-resolution transcriptomic and spatial cell-type atlas for the whole adult mouse brain. The cell-type atlas was created by combining a single-cell RNA-sequencing (scRNA-seq) dataset of around 7 million cells profiled (approximately 4.0 million cells passing quality control), and a spatial transcriptomic dataset of approximately 4.3 million cells using multiplexed error-robust fluorescence in situ hybridization (MERFISH). The atlas is hierarchically organized into 4 nested levels of classification: 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters. We present an online platform, Allen Brain Cell Atlas, to visualize the mouse whole-brain cell-type atlas along with the single-cell RNA-sequencing and MERFISH datasets. We systematically analysed the neuronal and non-neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell-type organization in different brain regions-in particular, a dichotomy between the dorsal and ventral parts of the brain. The dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. Our study also uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types. Finally, we found that transcription factors are major determinants of cell-type classification and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole mouse brain transcriptomic and spatial cell-type atlas establishes a benchmark reference atlas and a foundational resource for integrative investigations of cellular and circuit function, development and evolution of the mammalian brain.
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Affiliation(s)
- Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA.
| | | | | | - Meng Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | | | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Won Jung
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Pamela Baker
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Daniel Carey
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Min Chen
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jennie Close
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Scott Daniel
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - James Gee
- University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Jessica Gloe
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - James Gray
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Windy Ho
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Mike Huang
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kelly Jin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Arielle Leon
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Su Li
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zach Madigan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Zoe Maltzer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Naomi Martin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Rachel McCue
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Ryan McGinty
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nicholas Mei
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jose Melchor
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Sven Otto
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Lane Sawyer
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Noah Shepard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Shane Vance
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Boaz Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Rob Young
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian Staats
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Shoaib Mufti
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA.
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5
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Lobón-Iglesias MJ, Andrianteranagna M, Han ZY, Chauvin C, Masliah-Planchon J, Manriquez V, Tauziede-Espariat A, Turczynski S, Bouarich-Bourimi R, Frah M, Dufour C, Blauwblomme T, Cardoen L, Pierron G, Maillot L, Guillemot D, Reynaud S, Bourneix C, Pouponnot C, Surdez D, Bohec M, Baulande S, Delattre O, Piaggio E, Ayrault O, Waterfall JJ, Servant N, Beccaria K, Dangouloff-Ros V, Bourdeaut F. Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups. Nat Commun 2023; 14:6669. [PMID: 37863903 PMCID: PMC10589300 DOI: 10.1038/s41467-023-42371-7] [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: 06/10/2022] [Accepted: 10/09/2023] [Indexed: 10/22/2023] Open
Abstract
Atypical teratoid rhabdoid tumors (ATRT) are divided into MYC, TYR and SHH subgroups, suggesting diverse lineages of origin. Here, we investigate the imaging of human ATRT at diagnosis and the precise anatomic origin of brain tumors in the Rosa26-CreERT2::Smarcb1flox/flox model. This cross-species analysis points to an extra-cerebral origin for MYC tumors. Additionally, we clearly distinguish SHH ATRT emerging from the cerebellar anterior lobe (CAL) from those emerging from the basal ganglia (BG) and intra-ventricular (IV) regions. Molecular characteristics point to the midbrain-hindbrain boundary as the origin of CAL SHH ATRT, and to the ganglionic eminence as the origin of BG/IV SHH ATRT. Single-cell RNA sequencing on SHH ATRT supports these hypotheses. Trajectory analyses suggest that SMARCB1 loss induces a de-differentiation process mediated by repressors of the neuronal program such as REST, ID and the NOTCH pathway.
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Affiliation(s)
- María-Jesús Lobón-Iglesias
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Mamy Andrianteranagna
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
- INSERM U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Unit, Institut Curie, Mines Paris Tech, PSL Research University, Institut Curie Research Center, Paris, France
| | - Zhi-Yan Han
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Céline Chauvin
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Julien Masliah-Planchon
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Valeria Manriquez
- INSERM U932, Immunity and Cancer, PSL Research University, Institut Curie Research Center, Paris, France
| | - Arnault Tauziede-Espariat
- Department of Neuropathology, GHU Paris-Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
- Paris Psychiatry and Neurosciences Institute (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | - Sandrina Turczynski
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Rachida Bouarich-Bourimi
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Magali Frah
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France
| | - Christelle Dufour
- Department of Children and Adolescents Oncology, Gustave Roussy, Paris Saclay University, Villejuif, France
| | - Thomas Blauwblomme
- Department of Pediatric Neurosurgery-AP-HP, Necker Sick Kids Hospital, Université de Paris, Paris, France
| | | | - Gaelle Pierron
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Laetitia Maillot
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Delphine Guillemot
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Stéphanie Reynaud
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Christine Bourneix
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
| | - Célio Pouponnot
- CNRS UMR 3347, INSERM U1021, Institut Curie, PSL Research University, Université Paris-Saclay, Orsay, France
| | - Didier Surdez
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Mylene Bohec
- Institut Curie, PSL University, Single Cell Initiative, ICGex Next-Generation Sequencing Platform, PSL University, 75005, Paris, France
| | - Sylvain Baulande
- Institut Curie, PSL University, Single Cell Initiative, ICGex Next-Generation Sequencing Platform, PSL University, 75005, Paris, France
| | - Olivier Delattre
- Somatic Genetic Unit, Department of Pathology and Diagnostic and Theranostic Medecine, Institut Curie Hospital, Paris, France
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Eliane Piaggio
- INSERM U932, Immunity and Cancer, PSL Research University, Institut Curie Research Center, Paris, France
| | - Olivier Ayrault
- CNRS UMR 3347, INSERM U1021, Institut Curie, PSL Research University, Université Paris-Saclay, Orsay, France
| | - Joshua J Waterfall
- INSERM U830, Integrative Functional Genomics of Cancer Lab, PSL Research University, Institut Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Nicolas Servant
- INSERM U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Unit, Institut Curie, Mines Paris Tech, PSL Research University, Institut Curie Research Center, Paris, France
| | - Kevin Beccaria
- Department of Pediatric Neurosurgery-AP-HP, Necker Sick Kids Hospital, Université de Paris, Paris, France
| | - Volodia Dangouloff-Ros
- Pediatric Radiology Department, AP-HP, Necker Sick Kids Hospital and Paris Cite Universiy INSERM 1299 and UMR 1163, Institut Imagine, Paris, France
| | - Franck Bourdeaut
- INSERM U830, Laboratory of Translational Research In Pediatric Oncology, PSL Research University, SIREDO Oncology center, Institut Curie Research Center, Paris, France.
- Department of Pediatric Oncology, SIREDO Oncology Center, Institut Curie Hospital, Paris, and Université de Paris, Paris, France.
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6
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Kim CN, Shin D, Wang A, Nowakowski TJ. Spatiotemporal molecular dynamics of the developing human thalamus. Science 2023; 382:eadf9941. [PMID: 37824646 PMCID: PMC10758299 DOI: 10.1126/science.adf9941] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 09/15/2023] [Indexed: 10/14/2023]
Abstract
The thalamus plays a central coordinating role in the brain. Thalamic neurons are organized into spatially distinct nuclei, but the molecular architecture of thalamic development is poorly understood, especially in humans. To begin to delineate the molecular trajectories of cell fate specification and organization in the developing human thalamus, we used single-cell and multiplexed spatial transcriptomics. We show that molecularly defined thalamic neurons differentiate in the second trimester of human development and that these neurons organize into spatially and molecularly distinct nuclei. We identified major subtypes of glutamatergic neuron subtypes that are differentially enriched in anatomically distinct nuclei and six subtypes of γ-aminobutyric acid-mediated (GABAergic) neurons that are shared and distinct across thalamic nuclei.
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Affiliation(s)
- Chang N Kim
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94143, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - David Shin
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94143, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - Albert Wang
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
| | - Tomasz J Nowakowski
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94143, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
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7
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Kim CN, Shin D, Wang A, Nowakowski TJ. Spatiotemporal molecular dynamics of the developing human thalamus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554174. [PMID: 37662287 PMCID: PMC10473600 DOI: 10.1101/2023.08.21.554174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The thalamus plays a central coordinating role in the brain. Thalamic neurons are organized into spatially-distinct nuclei, but the molecular architecture of thalamic development is poorly understood, especially in humans. To begin to delineate the molecular trajectories of cell fate specification and organization in the developing human thalamus, we used single cell and multiplexed spatial transcriptomics. Here we show that molecularly-defined thalamic neurons differentiate in the second trimester of human development, and that these neurons organize into spatially and molecularly distinct nuclei. We identify major subtypes of glutamatergic neuron subtypes that are differentially enriched in anatomically distinct nuclei. In addition, we identify six subtypes of GABAergic neurons that are shared and distinct across thalamic nuclei. One-Sentence Summary Single cell and spatial profiling of the developing thalamus in the first and second trimester yields molecular mechanisms of thalamic nuclei development.
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Park G, Jang WE, Kim S, Gonzales EL, Ji J, Choi S, Kim Y, Park JH, Mohammad HB, Bang G, Kang M, Kim S, Jeon SJ, Kim JY, Kim KP, Shin CY, An JY, Kim MS, Lee YS. Dysregulation of the Wnt/β-catenin signaling pathway via Rnf146 upregulation in a VPA-induced mouse model of autism spectrum disorder. Exp Mol Med 2023; 55:1783-1794. [PMID: 37524878 PMCID: PMC10474298 DOI: 10.1038/s12276-023-01065-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/15/2023] [Accepted: 05/29/2023] [Indexed: 08/02/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder associated with impaired social behavior and communication, repetitive behaviors, and restricted interests. In addition to genetic factors, environmental factors such as prenatal drug exposure contribute to the development of ASD. However, how those prenatal factors induce behavioral deficits in the adult stage is not clear. To elucidate ASD pathogenesis at the molecular level, we performed a high-resolution mass spectrometry-based quantitative proteomic analysis on the prefrontal cortex (PFC) of mice exposed to valproic acid (VPA) in utero, a widely used animal model of ASD. Differentially expressed proteins (DEPs) in VPA-exposed mice showed significant overlap with ASD risk genes, including differentially expressed genes from the postmortem cortex of ASD patients. Functional annotations of the DEPs revealed significant enrichment in the Wnt/β-catenin signaling pathway, which is dysregulated by the upregulation of Rnf146 in VPA-exposed mice. Consistently, overexpressing Rnf146 in the PFC impaired social behaviors and altered the Wnt signaling pathway in adult mice. Furthermore, Rnf146-overexpressing PFC neurons showed increased excitatory synaptic transmission, which may underlie impaired social behavior. These results demonstrate that Rnf146 is critical for social behavior and that dysregulation of Rnf146 underlies social deficits in VPA-exposed mice.
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Affiliation(s)
- Gaeun Park
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Wooyoung Eric Jang
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Seoyeon Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
- BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea
| | - Edson Luck Gonzales
- School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jungeun Ji
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
- BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea
| | - Seunghwan Choi
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - Yujin Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
- BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea
| | - Ji Hwan Park
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | | | - Geul Bang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, 28119, Republic of Korea
| | - Minkyung Kang
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Soobin Kim
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Se Jin Jeon
- School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jin Young Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, 28119, Republic of Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, 17104, Republic of Korea
- Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Chan Young Shin
- School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul, 05029, Republic of Korea.
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.
- BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea.
| | - Min-Sik Kim
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea.
- New Biology Research Center, DGIST, Daegu, 42988, Republic of Korea.
- Center for Cell Fate Reprogramming and Control, DGIST, Daegu, 42988, Republic of Korea.
| | - Yong-Seok Lee
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
- Wide River Institute of Immunology, Seoul National University, Hongcheon, 25159, Republic of Korea.
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Workman S, Wilson MJ. RNA sequencing and expression analysis reveal a role for Lhx9 in the haploinsufficient adult mouse ovary. Mol Reprod Dev 2023; 90:295-309. [PMID: 37084273 DOI: 10.1002/mrd.23686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 02/26/2023] [Accepted: 04/05/2023] [Indexed: 04/23/2023]
Abstract
Understanding the molecular pathways that underpin ovarian development and function is vital for improving the research approaches to investigating fertility. Despite a significant improvement in our knowledge of molecular activity in the ovary, many questions remain unanswered in the quest to understand factors influencing fertility and ovarian pathologies such as cancer. Here, we present an investigation into the expression and function of the developmental transcription factor LIM Homeobox 9 (LHX9) in the adult mouse ovary. We have characterized Lhx9 expression in several cell types of the mature ovary across follicle stages. To evaluate possible LHX9 function in the adult ovary, we investigated ovarian anatomy and transcription in an Lhx9+/- knockout mouse model displaying subfertility. Despite a lack of gross anatomical differences between genotypes, RNA-sequencing found that 90 differentially expressed genes between Lhx9+/ - and Lhx9+/+ mice. Gene ontology analyses revealed a reduced expression of genes with major roles in ovarian steroidogenesis and an increased expression of genes associated with ovarian cancer. Analysis of the ovarian epithelium revealed Lhx9+/ - mice have a disorganized epithelial phenotype, corresponding to a significant increase in epithelial marker gene expression. These results provide an analysis of Lhx9 in the adult mouse ovary, suggesting a role in fertility and ovarian epithelial cancer.
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Affiliation(s)
- Stephanie Workman
- Developmental Genomics Laboratory, Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Megan J Wilson
- Developmental Genomics Laboratory, Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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Singh N, Singh D, Bhide A, Sharma R, Bhowmick S, Patel V, Modi D. LHX2 in germ cells control tubular organization in the developing mouse testis. Exp Cell Res 2023; 425:113511. [PMID: 36796745 DOI: 10.1016/j.yexcr.2023.113511] [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: 08/01/2022] [Revised: 01/01/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023]
Abstract
In the gonads of mammalian XY embryos, the organization of cords is the hallmark of testis development. This organization is thought to be controlled by interactions of the Sertoli cells, endothelial and interstitial cells with little or no role of germ cells. Challenging this notion, herein we show that the germ cells play an active role in the organization of the testicular tubules. We observed that the LIM-homeobox gene, Lhx2 is expressed in the germ cells of the developing testis between E12.5-E15.5. In Lhx2 knockout-fetal testis there was altered expression of several genes not just in germ cells but also in the supporting (Sertoli) cells, endothelial cells, and interstitial cells. Further, loss of Lhx2 led to disrupted endothelial cell migration and expansion of interstitial cells in the XY gonads. The cords in the developing testis of Lhx2 knockout embryos are disorganized with a disrupted basement membrane. Together, our results show an important role of Lhx2 in testicular development and imply the involvement of germ cells in the tubular organization of the differentiating testis. The preprint version of this manuscript is available at https://doi.org/10.1101/2022.12.29.522214.
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Affiliation(s)
- Neha Singh
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Indian Council of Medical Research (ICMR), JM Street, Parel, Mumbai, 400012, India
| | - Domdatt Singh
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Indian Council of Medical Research (ICMR), JM Street, Parel, Mumbai, 400012, India
| | - Anshul Bhide
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Indian Council of Medical Research (ICMR), JM Street, Parel, Mumbai, 400012, India
| | - Richa Sharma
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Indian Council of Medical Research (ICMR), JM Street, Parel, Mumbai, 400012, India
| | - Shilpa Bhowmick
- Viral Immunopathogenesis Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Indian Council of Medical Research (ICMR), JM Street, Parel, Mumbai, 400012, India
| | - Vainav Patel
- Viral Immunopathogenesis Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Indian Council of Medical Research (ICMR), JM Street, Parel, Mumbai, 400012, India
| | - Deepak Modi
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Indian Council of Medical Research (ICMR), JM Street, Parel, Mumbai, 400012, India.
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11
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Govek KW, Chen S, Sgourdou P, Yao Y, Woodhouse S, Chen T, Fuccillo MV, Epstein DJ, Camara PG. Developmental trajectories of thalamic progenitors revealed by single-cell transcriptome profiling and Shh perturbation. Cell Rep 2022; 41:111768. [PMID: 36476860 PMCID: PMC9880597 DOI: 10.1016/j.celrep.2022.111768] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 10/06/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
The thalamus is the principal information hub of the vertebrate brain, with essential roles in sensory and motor information processing, attention, and memory. The complex array of thalamic nuclei develops from a restricted pool of neural progenitors. We apply longitudinal single-cell RNA sequencing and regional abrogation of Sonic hedgehog (Shh) to map the developmental trajectories of thalamic progenitors, intermediate progenitors, and post-mitotic neurons as they coalesce into distinct thalamic nuclei. These data reveal that the complex architecture of the thalamus is established early during embryonic brain development through the coordinated action of four cell differentiation lineages derived from Shh-dependent and -independent progenitors. We systematically characterize the gene expression programs that define these thalamic lineages across time and demonstrate how their disruption upon Shh depletion causes pronounced locomotor impairment resembling infantile Parkinson's disease. These results reveal key principles of thalamic development and provide mechanistic insights into neurodevelopmental disorders resulting from thalamic dysfunction.
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Affiliation(s)
- Kiya W. Govek
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104, USA,Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104, USA,These authors contributed equally
| | - Sixing Chen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104, USA,These authors contributed equally
| | - Paraskevi Sgourdou
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104, USA
| | - Yao Yao
- Department of Animal and Dairy Science, Regenerative Bioscience Center, University of Georgia, 425 River Road, Athens, GA 30602, USA
| | - Steven Woodhouse
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104, USA,Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104, USA
| | - Tingfang Chen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104, USA
| | - Marc V. Fuccillo
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Douglas J. Epstein
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104, USA,Correspondence: (D.J.E.), (P.G.C.)
| | - Pablo G. Camara
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104, USA,Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104, USA,Lead contact,Correspondence: (D.J.E.), (P.G.C.)
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12
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Wullimann MF. The Neuromeric/Prosomeric Model in Teleost Fish Neurobiology. BRAIN, BEHAVIOR AND EVOLUTION 2022; 97:336-360. [PMID: 35728561 PMCID: PMC9808694 DOI: 10.1159/000525607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 06/08/2022] [Indexed: 01/07/2023]
Abstract
The neuromeric/prosomeric model has been rejuvenated by Puelles and Rubenstein [Trends Neurosci. 1993;16(11):472-9]. Here, its application to the (teleostean) fish brain is detailed, beginning with a historical account. The second part addresses three main issues with particular interest for fish neuroanatomy and looks at the impact of the neuromeric model on their understanding. The first one is the occurrence of four early migrating forebrain areas (M1 through M4) in teleosts and their comparative interpretation. The second issue addresses the complex development and neuroanatomy of the teleostean alar and basal hypothalamus. The third topic is the vertebrate dopaminergic system, with the focus on some teleostean peculiarities. Most of the information will be coming from zebrafish studies, although the general ductus is a comparative one. Throughout the manuscript, comparative developmental and organizational aspects of the teleostean amygdala are discussed. One particular focus is cellular migration streams into the medial amygdala.
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Affiliation(s)
- Mario F. Wullimann
- Division of Neurobiology, Department Biologie II, Ludwig-Maximilians-Universität München (LMU Munich), Martinsried, Germany,Department Genes-Circuits-Behavior, Max-Planck-Institute for Biological Intelligence (i.F.), Martinsried, Germany,*Mario F. Wullimann,
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13
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Uzquiano A, Kedaigle AJ, Pigoni M, Paulsen B, Adiconis X, Kim K, Faits T, Nagaraja S, Antón-Bolaños N, Gerhardinger C, Tucewicz A, Murray E, Jin X, Buenrostro J, Chen F, Velasco S, Regev A, Levin JZ, Arlotta P. Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex. Cell 2022; 185:3770-3788.e27. [PMID: 36179669 PMCID: PMC9990683 DOI: 10.1016/j.cell.2022.09.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 03/25/2022] [Accepted: 09/01/2022] [Indexed: 01/26/2023]
Abstract
Realizing the full utility of brain organoids to study human development requires understanding whether organoids precisely replicate endogenous cellular and molecular events, particularly since acquisition of cell identity in organoids can be impaired by abnormal metabolic states. We present a comprehensive single-cell transcriptomic, epigenetic, and spatial atlas of human cortical organoid development, comprising over 610,000 cells, from generation of neural progenitors through production of differentiated neuronal and glial subtypes. We show that processes of cellular diversification correlate closely to endogenous ones, irrespective of metabolic state, empowering the use of this atlas to study human fate specification. We define longitudinal molecular trajectories of cortical cell types during organoid development, identify genes with predicted human-specific roles in lineage establishment, and uncover early transcriptional diversity of human callosal neurons. The findings validate this comprehensive atlas of human corticogenesis in vitro as a resource to prime investigation into the mechanisms of human cortical development.
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Affiliation(s)
- Ana Uzquiano
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amanda J Kedaigle
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Martina Pigoni
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bruna Paulsen
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xian Adiconis
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kwanho Kim
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tyler Faits
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Surya Nagaraja
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Noelia Antón-Bolaños
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chiara Gerhardinger
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ashley Tucewicz
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Evan Murray
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xin Jin
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Society of Fellows, Harvard University, Cambridge, MA 02138, USA
| | - Jason Buenrostro
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fei Chen
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Silvia Velasco
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paola Arlotta
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Long-Term Treatment with Bortezomib Induces Specific Methylation Changes in Differentiated Neuronal Cells. Cancers (Basel) 2022; 14:cancers14143402. [PMID: 35884461 PMCID: PMC9319119 DOI: 10.3390/cancers14143402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary We exposed LUHMES cells, differentiated into mature neurons, to bortezomib (BTZ) in two treatment cycles and analyzed the methylomes of these cells after each cycle, controlling the analysis for the methylation changes potentially induced by the long-term culture. Our results show that BTZ induces methylation changes that may affect cell morphogenesis, neurogenesis, and neurotransmission. These changes are specifically enriched within transcription factor binding sites of EBF, PAX, DLX, LHX, and HNF family members, which have been shown to regulate neurogenesis and neuronal differentiation. We further show that the observed methylation changes are not present in the SH-SY5Y cells that we used to study mechanisms of development of BTZ resistance. Altogether, our results show that BTZ treatment induces very specific changes in the methylomes of neuronal cells. Abstract Bortezomib (BTZ) is proteasome inhibitor, effectively used in the treatment of multiple myeloma, but frequently discontinued due to peripheral neuropathy, which develops in patients after consecutive treatment cycles. The molecular mechanisms affected by BTZ in neuronal cells, which result in neuropathy, remain unknown. However, BTZ is unlikely to lead to permanent morphological nerve damage, because neuropathy reverses after discontinuation of treatment, and nerve cells have very limited renewal capacity. We have previously shown that BTZ induces methylation changes in SH-SY5Y cells, which take part in the development of treatment resistance. Here, we hypothesized that BTZ affects the methylomes of mature neurons, and these changes are associated with BTZ neurotoxicity. Thus, we studied methylomes of neuronal cells, differentiated from the LUHMES cell line, after cycles of treatment with BTZ. Our results show that BTZ induces specific methylation changes in mature neurons, which are not present in SH-SY5Y cells after BTZ treatment. These changes appear to affect genes involved in morphogenesis, neurogenesis, and neurotransmission. Furthermore, identified methylation changes are significantly enriched within binding sites of transcription factors previously linked to neuron physiology, including EBF, PAX, DLX, LHX, and HNF family members. Altogether, our results indicate that methylation changes are likely to be involved in BTZ neurotoxicity.
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Ávila-González D, Portillo W, Barragán-Álvarez CP, Hernandez-Montes G, Flores-Garza E, Molina-Hernández A, Diaz-Martinez NE, Diaz NF. The human amniotic epithelium confers a bias to differentiate toward the neuroectoderm lineage in human embryonic stem cells. eLife 2022; 11:68035. [PMID: 35815953 PMCID: PMC9313526 DOI: 10.7554/elife.68035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/08/2022] [Indexed: 11/28/2022] Open
Abstract
Human embryonic stem cells (hESCs) derive from the epiblast and have pluripotent potential. To maintain the conventional conditions of the pluripotent potential in an undifferentiated state, inactivated mouse embryonic fibroblast (iMEF) is used as a feeder layer. However, it has been suggested that hESC under this conventional condition (hESC-iMEF) is an artifact that does not correspond to the in vitro counterpart of the human epiblast. Our previous studies demonstrated the use of an alternative feeder layer of human amniotic epithelial cells (hAECs) to derive and maintain hESC. We wondered if the hESC-hAEC culture could represent a different pluripotent stage than that of naïve or primed conventional conditions, simulating the stage in which the amniotic epithelium derives from the epiblast during peri-implantation. Like the conventional primed hESC-iMEF, hESC-hAEC has the same levels of expression as the ‘pluripotency core’ and does not express markers of naïve pluripotency. However, it presents a downregulation of HOX genes and genes associated with the endoderm and mesoderm, and it exhibits an increase in the expression of ectoderm lineage genes, specifically in the anterior neuroectoderm. Transcriptome analysis showed in hESC-hAEC an upregulated signature of genes coding for transcription factors involved in neural induction and forebrain development, and the ability to differentiate into a neural lineage was superior in comparison with conventional hESC-iMEF. We propose that the interaction of hESC with hAEC confers hESC a biased potential that resembles the anteriorized epiblast, which is predisposed to form the neural ectoderm.
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Affiliation(s)
- Daniela Ávila-González
- Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City, Mexico
| | - Wendy Portillo
- Behavioral and Cognitive Neurobiology, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Carla P Barragán-Álvarez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara, Mexico
| | | | - Eliezer Flores-Garza
- Departamento de Biología Molecular y Biotecnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Anayansi Molina-Hernández
- Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City, Mexico
| | | | - Nestor F Diaz
- Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City, Mexico
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16
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Brożko N, Baggio S, Lipiec MA, Jankowska M, Szewczyk ŁM, Gabriel MO, Chakraborty C, Ferran JL, Wiśniewska MB. Genoarchitecture of the Early Postmitotic Pretectum and the Role of Wnt Signaling in Shaping Pretectal Neurochemical Anatomy in Zebrafish. Front Neuroanat 2022; 16:838567. [PMID: 35356436 PMCID: PMC8959918 DOI: 10.3389/fnana.2022.838567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/26/2022] [Indexed: 01/10/2023] Open
Abstract
The pretectum has a distinct nuclear arrangement and complex neurochemical anatomy. While previous genoarchitectural studies have described rostrocaudal and dorsoventral progenitor domains and subdomains in different species, the relationship between these early partitions and its later derivatives in the mature anatomy is less understood. The signals and transcription factors that control the establishment of pretectal anatomy are practically unknown. We investigated the possibility that some aspects of the development of pretectal divisions are controlled by Wnt signaling, focusing on the transitional stage between neurogenesis and histogenesis in zebrafish. Using several molecular markers and following the prosomeric model, we identified derivatives from each rostrocaudal pretectal progenitor domain and described the localization of gad1b-positive GABAergic and vglut2.2-positive glutamatergic cell clusters. We also attempted to relate these clusters to pretectal nuclei in the mature brain. Then, we examined the influence of Wnt signaling on the size of neurochemically distinctive pretectal areas, using a chemical inhibitor of the Wnt pathway and the CRISPR/Cas9 approach to knock out genes that encode the Wnt pathway mediators, Lef1 and Tcf7l2. The downregulation of the Wnt pathway led to a decrease in two GABAergic clusters and an expansion of a glutamatergic subregion in the maturing pretectum. This revealed an instructive role of the Wnt signal in the development of the pretectum during neurogenesis. The molecular anatomy presented here improves our understanding of pretectal development during early postmitotic stages and support the hypothesis that Wnt signaling is involved in shaping the neurochemical organization of the pretectum.
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Affiliation(s)
- Nikola Brożko
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Suelen Baggio
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Marcin A. Lipiec
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Marta Jankowska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | | | | | | | - José L. Ferran
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia and Institute of Biomedical Research of Murcia -Ű IMIB, Virgen de la Arrixaca University Hospital, Murcia, Spain
| | - Marta B. Wiśniewska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- *Correspondence: Marta B. Wiśniewska,
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17
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Medina L, Abellán A, Desfilis E. Evolving Views on the Pallium. BRAIN, BEHAVIOR AND EVOLUTION 2021; 96:181-199. [PMID: 34657034 DOI: 10.1159/000519260] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/24/2021] [Indexed: 12/14/2022]
Abstract
The pallium is the largest part of the telencephalon in amniotes, and comparison of its subdivisions across species has been extremely difficult and controversial due to its high divergence. Comparative embryonic genoarchitecture studies have greatly contributed to propose models of pallial fundamental divisions, which can be compared across species and be used to extract general organizing principles as well as to ask more focused and insightful research questions. The use of these models is crucial to discern between conservation, convergence or divergence in the neural populations and networks found in the pallium. Here we provide a critical review of the models proposed using this approach, including tetrapartite, hexapartite and double-ring models, and compare them to other models. While recognizing the power of these models for understanding brain architecture, development and evolution, we also highlight limitations and comment on aspects that require attention for improvement. We also discuss on the use of transcriptomic data for understanding pallial evolution and advise for better contextualization of these data by discerning between gene regulatory networks involved in the generation of specific units and cell populations versus genes expressed later, many of which are activity dependent and their expression is more likely subjected to convergent evolution.
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Affiliation(s)
- Loreta Medina
- Department of Experimental Medicine, Faculty of Medicine, University of Lleida, Lleida's Institute for Biomedical Research - Dr. Pifarré Foundation (IRBLleida), Lleida, Spain
| | - Antonio Abellán
- Department of Experimental Medicine, Faculty of Medicine, University of Lleida, Lleida's Institute for Biomedical Research - Dr. Pifarré Foundation (IRBLleida), Lleida, Spain
| | - Ester Desfilis
- Department of Experimental Medicine, Faculty of Medicine, University of Lleida, Lleida's Institute for Biomedical Research - Dr. Pifarré Foundation (IRBLleida), Lleida, Spain
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18
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Gabriel E, Albanna W, Pasquini G, Ramani A, Josipovic N, Mariappan A, Schinzel F, Karch CM, Bao G, Gottardo M, Suren AA, Hescheler J, Nagel-Wolfrum K, Persico V, Rizzoli SO, Altmüller J, Riparbelli MG, Callaini G, Goureau O, Papantonis A, Busskamp V, Schneider T, Gopalakrishnan J. Human brain organoids assemble functionally integrated bilateral optic vesicles. Cell Stem Cell 2021; 28:1740-1757.e8. [PMID: 34407456 DOI: 10.1016/j.stem.2021.07.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/23/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023]
Abstract
During embryogenesis, optic vesicles develop from the diencephalon via a multistep process of organogenesis. Using induced pluripotent stem cell (iPSC)-derived human brain organoids, we attempted to simplify the complexities and demonstrate formation of forebrain-associated bilateral optic vesicles, cellular diversity, and functionality. Around day 30, brain organoids attempt to assemble optic vesicles, which develop progressively as visible structures within 60 days. These optic vesicle-containing brain organoids (OVB-organoids) constitute a developing optic vesicle's cellular components, including primitive corneal epithelial and lens-like cells, retinal pigment epithelia, retinal progenitor cells, axon-like projections, and electrically active neuronal networks. OVB-organoids also display synapsin-1, CTIP-positive myelinated cortical neurons, and microglia. Interestingly, various light intensities could trigger photosensitive activity of OVB-organoids, and light sensitivities could be reset after transient photobleaching. Thus, brain organoids have the intrinsic ability to self-organize forebrain-associated primitive sensory structures in a topographically restricted manner and can allow interorgan interaction studies within a single organoid.
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Affiliation(s)
- Elke Gabriel
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Walid Albanna
- Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany; Department of Neurosurgery, RWTH Aachen University, 52074 Aachen, Germany
| | - Giovanni Pasquini
- Department of Ophthalmology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Anand Ramani
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Natasa Josipovic
- Institute of Pathology, University Medicine Göttingen, Georg-August University Göttingen, 37075 Göttingen, Germany; Center for molecular medicine, Cologne, Universität zu Köln, 50931 Köln, Germany
| | - Aruljothi Mariappan
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Friedrich Schinzel
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Celeste M Karch
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO 63116, USA
| | - Guobin Bao
- Institute of Neurophysiology and Cellular Biophysics, University Medicine Göttingen, Georg-August-Universität Göttingen, 37073 Göttingen, Germany
| | - Marco Gottardo
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Ata Alp Suren
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Jürgen Hescheler
- Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Kerstin Nagel-Wolfrum
- Institute of Molecular Physiology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Veronica Persico
- Department of Life Sciences and Medical Biotechnology University of Siena, Siena 53100, Italy
| | - Silvio O Rizzoli
- Institute of Neurophysiology and Cellular Biophysics, University Medicine Göttingen, Georg-August-Universität Göttingen, 37073 Göttingen, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Universität zu Köln, Köln, Germany; Center for molecular medicine, Cologne, Universität zu Köln, 50931 Köln, Germany
| | | | - Giuliano Callaini
- Department of Life Sciences and Medical Biotechnology University of Siena, Siena 53100, Italy
| | - Olivier Goureau
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, 75012 Paris, France
| | - Argyris Papantonis
- Institute of Pathology, University Medicine Göttingen, Georg-August University Göttingen, 37075 Göttingen, Germany
| | - Volker Busskamp
- Department of Ophthalmology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Toni Schneider
- Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Jay Gopalakrishnan
- Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany.
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19
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Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, Casper T, Colantuoni C, Crabtree J, Creasy H, Crichton K, Crow M, Dee N, Dougherty EL, Doyle WI, Dudoit S, Fang R, Felix V, Fong O, Giglio M, Goldy J, Hawrylycz M, Herb BR, Hertzano R, Hou X, Hu Q, Kancherla J, Kroll M, Lathia K, Li YE, Lucero JD, Luo C, Mahurkar A, McMillen D, Nadaf NM, Nery JR, Nguyen TN, Niu SY, Ntranos V, Orvis J, Osteen JK, Pham T, Pinto-Duarte A, Poirion O, Preissl S, Purdom E, Rimorin C, Risso D, Rivkin AC, Smith K, Street K, Sulc J, Svensson V, Tieu M, Torkelson A, Tung H, Vaishnav ED, Vanderburg CR, van Velthoven C, Wang X, White OR, Huang ZJ, Kharchenko PV, Pachter L, Ngai J, Regev A, Tasic B, Welch JD, Gillis J, Macosko EZ, Ren B, Ecker JR, Zeng H, Mukamel EA. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature 2021; 598:103-110. [PMID: 34616066 PMCID: PMC8494649 DOI: 10.1038/s41586-021-03500-8] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 03/26/2021] [Indexed: 12/30/2022]
Abstract
Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain1-3. With the proliferation of multi-omics datasets, a major challenge is to validate and integrate results into a biological understanding of cell-type organization. Here we generated transcriptomes and epigenomes from more than 500,000 individual cells in the mouse primary motor cortex, a structure that has an evolutionarily conserved role in locomotion. We developed computational and statistical methods to integrate multimodal data and quantitatively validate cell-type reproducibility. The resulting reference atlas-containing over 56 neuronal cell types that are highly replicable across analysis methods, sequencing technologies and modalities-is a comprehensive molecular and genomic account of the diverse neuronal and non-neuronal cell types in the mouse primary motor cortex. The atlas includes a population of excitatory neurons that resemble pyramidal cells in layer 4 in other cortical regions4. We further discovered thousands of concordant marker genes and gene regulatory elements for these cell types. Our results highlight the complex molecular regulation of cell types in the brain and will directly enable the design of reagents to target specific cell types in the mouse primary motor cortex for functional analysis.
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Affiliation(s)
- Zizhen Yao
- grid.417881.3Allen Institute for Brain Science, Seattle, WA USA
| | - Hanqing Liu
- grid.250671.70000 0001 0662 7144Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA USA
| | - Fangming Xie
- grid.266100.30000 0001 2107 4242Department of Physics, University of California, San Diego, La Jolla, CA USA
| | - Stephan Fischer
- grid.225279.90000 0004 0387 3667Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | - Ricky S. Adkins
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - Andrew I. Aldridge
- grid.250671.70000 0001 0662 7144Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA USA
| | - Seth A. Ament
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - Anna Bartlett
- grid.250671.70000 0001 0662 7144Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA USA
| | - M. Margarita Behrens
- grid.250671.70000 0001 0662 7144Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA USA
| | - Koen Van den Berge
- grid.47840.3f0000 0001 2181 7878Department of Statistics, University of California, Berkeley, Berkeley, CA USA ,grid.5342.00000 0001 2069 7798Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Gent, Belgium
| | | | - Hector Roux de Bézieux
- grid.47840.3f0000 0001 2181 7878Division of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA USA
| | | | - A. Sina Booeshaghi
- grid.20861.3d0000000107068890California Institute of Technology, Pasadena, CA USA
| | - Héctor Corrada Bravo
- grid.164295.d0000 0001 0941 7177Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD USA
| | - Tamara Casper
- grid.417881.3Allen Institute for Brain Science, Seattle, WA USA
| | - Carlo Colantuoni
- grid.21107.350000 0001 2171 9311Johns Hopkins School of Medicine, Department of Neurology, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Johns Hopkins School of Medicine, Department of Neuroscience, Baltimore, MD USA ,grid.411024.20000 0001 2175 4264University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD USA
| | - Jonathan Crabtree
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - Heather Creasy
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | | | - Megan Crow
- grid.225279.90000 0004 0387 3667Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | - Nick Dee
- grid.417881.3Allen Institute for Brain Science, Seattle, WA USA
| | | | - Wayne I. Doyle
- grid.266100.30000 0001 2107 4242Department of Cognitive Science, University of California, San Diego, La Jolla, CA USA
| | - Sandrine Dudoit
- grid.47840.3f0000 0001 2181 7878Department of Statistics, University of California, Berkeley, Berkeley, CA USA
| | - Rongxin Fang
- grid.266100.30000 0001 2107 4242Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, San Diego, CA USA
| | - Victor Felix
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - Olivia Fong
- grid.417881.3Allen Institute for Brain Science, Seattle, WA USA
| | - Michelle Giglio
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - Jeff Goldy
- grid.417881.3Allen Institute for Brain Science, Seattle, WA USA
| | - Mike Hawrylycz
- grid.417881.3Allen Institute for Brain Science, Seattle, WA USA
| | - Brian R. Herb
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - Ronna Hertzano
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA ,grid.411024.20000 0001 2175 4264Department of Otorhinolaryngology, Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD USA
| | - Xiaomeng Hou
- grid.266100.30000 0001 2107 4242Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA USA
| | - Qiwen Hu
- grid.38142.3c000000041936754XDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA USA
| | - Jayaram Kancherla
- grid.164295.d0000 0001 0941 7177Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD USA
| | - Matthew Kroll
- grid.417881.3Allen Institute for Brain Science, Seattle, WA USA
| | - Kanan Lathia
- grid.417881.3Allen Institute for Brain Science, Seattle, WA USA
| | - Yang Eric Li
- grid.1052.60000000097371625Ludwig Institute for Cancer Research, La Jolla, CA USA
| | - Jacinta D. Lucero
- grid.250671.70000 0001 0662 7144Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA USA
| | - Chongyuan Luo
- grid.250671.70000 0001 0662 7144Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA USA ,grid.250671.70000 0001 0662 7144Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA USA
| | - Anup Mahurkar
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | | | - Naeem M. Nadaf
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Joseph R. Nery
- grid.250671.70000 0001 0662 7144Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA USA
| | | | - Sheng-Yong Niu
- grid.250671.70000 0001 0662 7144Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA USA
| | - Vasilis Ntranos
- grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Joshua Orvis
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - Julia K. Osteen
- grid.250671.70000 0001 0662 7144Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA USA
| | - Thanh Pham
- grid.417881.3Allen Institute for Brain Science, Seattle, WA USA
| | - Antonio Pinto-Duarte
- grid.250671.70000 0001 0662 7144Computational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA USA
| | - Olivier Poirion
- grid.266100.30000 0001 2107 4242Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA USA
| | - Sebastian Preissl
- grid.266100.30000 0001 2107 4242Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA USA
| | - Elizabeth Purdom
- grid.47840.3f0000 0001 2181 7878Department of Statistics, University of California, Berkeley, Berkeley, CA USA
| | | | - Davide Risso
- grid.5608.b0000 0004 1757 3470Department of Statistical Sciences, University of Padova, Padova, Italy
| | - Angeline C. Rivkin
- grid.250671.70000 0001 0662 7144Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA USA
| | - Kimberly Smith
- grid.417881.3Allen Institute for Brain Science, Seattle, WA USA
| | - Kelly Street
- grid.65499.370000 0001 2106 9910Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA USA
| | - Josef Sulc
- grid.417881.3Allen Institute for Brain Science, Seattle, WA USA
| | - Valentine Svensson
- grid.20861.3d0000000107068890California Institute of Technology, Pasadena, CA USA
| | - Michael Tieu
- grid.417881.3Allen Institute for Brain Science, Seattle, WA USA
| | - Amy Torkelson
- grid.417881.3Allen Institute for Brain Science, Seattle, WA USA
| | - Herman Tung
- grid.417881.3Allen Institute for Brain Science, Seattle, WA USA
| | | | | | | | - Xinxin Wang
- grid.266100.30000 0001 2107 4242Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA USA ,grid.4367.60000 0001 2355 7002Present Address: McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO USA
| | - Owen R. White
- grid.411024.20000 0001 2175 4264Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - Z. Josh Huang
- grid.225279.90000 0004 0387 3667Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | - Peter V. Kharchenko
- grid.38142.3c000000041936754XDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA USA
| | - Lior Pachter
- grid.20861.3d0000000107068890California Institute of Technology, Pasadena, CA USA
| | - John Ngai
- grid.47840.3f0000 0001 2181 7878Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA USA
| | - Aviv Regev
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, MA USA
| | - Bosiljka Tasic
- grid.417881.3Allen Institute for Brain Science, Seattle, WA USA
| | - Joshua D. Welch
- grid.214458.e0000000086837370Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI USA
| | - Jesse Gillis
- grid.225279.90000 0004 0387 3667Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | - Evan Z. Macosko
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Bing Ren
- grid.266100.30000 0001 2107 4242Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA USA ,grid.1052.60000000097371625Ludwig Institute for Cancer Research, La Jolla, CA USA
| | - Joseph R. Ecker
- grid.250671.70000 0001 0662 7144Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA USA ,grid.250671.70000 0001 0662 7144Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA.
| | - Eran A. Mukamel
- grid.266100.30000 0001 2107 4242Department of Cognitive Science, University of California, San Diego, La Jolla, CA USA
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20
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Luo X, Ge J, Chen T, Liu J, Liu Z, Bi C, Lan S. LHX9, a p53-binding protein, inhibits the progression of glioma by suppressing glycolysis. Aging (Albany NY) 2021; 13:22109-22119. [PMID: 34536269 PMCID: PMC8507291 DOI: 10.18632/aging.203436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/11/2021] [Indexed: 11/25/2022]
Abstract
PURPOSE LHX9 methylation has been reported in many tumors, but its functions and related mechanisms in glioma are still unknown and need to be verified. METHODS The protein level of LHX9 in glioma tissues was examined using western blotting and immunohistochemistry, and the functions of LHX9 in glioma cell lines were investigated using MTT and colony formation assays. In addition, the interaction between LHX9 and P53 was analyzed by immunoprecipitation, and the roles of LHX9 in cancer metabolism were explored by measuring metabolites. RESULTS In this study, we found that the LHX9 expression level was decreased in glioma specimens, and the upregulation of LHX9 expression inhibited the growth of glioma cells in liquid medium and on soft agar. Regarding the molecular mechanism, we found that LHX9 interacted with p53, and downregulation of LHX9 promoted the expression of the glycolysis-related enzyme PGK1 and increased the lactic acid content. By interfering with the expression of LHX9, the tumorigenicity of glioma cells was promoted, an outcome blocked by further interference with PGK1 expression. CONCLUSION In summary, the decreased expression of LHX9 in gliomas activates the expression of the glycolysis-related enzyme PGK1, thereby promoting the development of gliomas, suggesting that the LHX9-PGK1 signaling axis can be used as a target for the treatment of glioma.
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Affiliation(s)
- Xiangying Luo
- Department of Neurosurgery, XiangYa Hospital of Central South University, Changsha 410078, P.R. China
| | - Jianwei Ge
- Department of Neurosurgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200127, P.R. China
| | - Tao Chen
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, P.R. China
| | - Jinfang Liu
- Department of Neurosurgery, XiangYa Hospital of Central South University, Changsha 410078, P.R. China
| | - Ziyuan Liu
- Department of Neurosurgery, XiangYa Hospital of Central South University, Changsha 410078, P.R. China
| | - Changlong Bi
- Department of Neurosurgery, XiangYa Hospital of Central South University, Changsha 410078, P.R. China
| | - Song Lan
- Department of Neurosurgery, XiangYa Hospital of Central South University, Changsha 410078, P.R. China
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21
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Han S, Okawa S, Wilkinson GA, Ghazale H, Adnani L, Dixit R, Tavares L, Faisal I, Brooks MJ, Cortay V, Zinyk D, Sivitilli A, Li S, Malik F, Ilnytskyy Y, Angarica VE, Gao J, Chinchalongporn V, Oproescu AM, Vasan L, Touahri Y, David LA, Raharjo E, Kim JW, Wu W, Rahmani W, Chan JAW, Kovalchuk I, Attisano L, Kurrasch D, Dehay C, Swaroop A, Castro DS, Biernaskie J, Del Sol A, Schuurmans C. Proneural genes define ground-state rules to regulate neurogenic patterning and cortical folding. Neuron 2021; 109:2847-2863.e11. [PMID: 34407390 DOI: 10.1016/j.neuron.2021.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 05/19/2021] [Accepted: 07/08/2021] [Indexed: 02/06/2023]
Abstract
Asymmetric neuronal expansion is thought to drive evolutionary transitions between lissencephalic and gyrencephalic cerebral cortices. We report that Neurog2 and Ascl1 proneural genes together sustain neurogenic continuity and lissencephaly in rodent cortices. Using transgenic reporter mice and human cerebral organoids, we found that Neurog2 and Ascl1 expression defines a continuum of four lineage-biased neural progenitor cell (NPC) pools. Double+ NPCs, at the hierarchical apex, are least lineage restricted due to Neurog2-Ascl1 cross-repression and display unique features of multipotency (more open chromatin, complex gene regulatory network, G2 pausing). Strikingly, selectively eliminating double+ NPCs by crossing Neurog2-Ascl1 split-Cre mice with diphtheria toxin-dependent "deleter" strains locally disrupts Notch signaling, perturbs neurogenic symmetry, and triggers cortical folding. In support of our discovery that double+ NPCs are Notch-ligand-expressing "niche" cells that control neurogenic periodicity and cortical folding, NEUROG2, ASCL1, and HES1 transcript distribution is modular (adjacent high/low zones) in gyrencephalic macaque cortices, prefiguring future folds.
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Affiliation(s)
- Sisu Han
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Satoshi Okawa
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Integrated BioBank of Luxembourg, 3555, 3531 Dudelange, Luxembourg
| | - Grey Atteridge Wilkinson
- Department of Biochemistry and Molecular Biology, ACHRI, HBI, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Hussein Ghazale
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Lata Adnani
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry and Molecular Biology, ACHRI, HBI, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Rajiv Dixit
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ligia Tavares
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Imrul Faisal
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Matthew J Brooks
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892-1204, USA
| | - Veronique Cortay
- Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Dawn Zinyk
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada
| | - Adam Sivitilli
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Saiqun Li
- Department of Biochemistry and Molecular Biology, ACHRI, HBI, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Faizan Malik
- Department of Medical Genetics, ACHRI, HBI, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Yaroslav Ilnytskyy
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Vladimir Espinosa Angarica
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
| | - Jinghua Gao
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Vorapin Chinchalongporn
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ana-Maria Oproescu
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Lakshmy Vasan
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Yacine Touahri
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Luke Ajay David
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Eko Raharjo
- Department of Comparative Biology and Experimental Medicine, HBI, ACHRI, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jung-Woong Kim
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892-1204, USA
| | - Wei Wu
- Department of Pathology and Laboratory Medicine, Charbonneau Cancer Institute, HBI, University of Calgary, Calgary, AB T2N 4Z6, Canada
| | - Waleed Rahmani
- Department of Comparative Biology and Experimental Medicine, HBI, ACHRI, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jennifer Ai-Wen Chan
- Department of Pathology and Laboratory Medicine, Charbonneau Cancer Institute, HBI, University of Calgary, Calgary, AB T2N 4Z6, Canada
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Liliana Attisano
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Deborah Kurrasch
- Department of Medical Genetics, ACHRI, HBI, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Colette Dehay
- Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Anand Swaroop
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892-1204, USA
| | - Diogo S Castro
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Jeff Biernaskie
- Department of Comparative Biology and Experimental Medicine, HBI, ACHRI, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain
| | - Carol Schuurmans
- Sunnybrook Research Institute, 2075 Bayview Ave, Toronto, ON M4N 3M5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry and Molecular Biology, ACHRI, HBI, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada.
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22
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Wang F, Zhao J, Zhang M, Yang J, Zeng G. Genome-wide analysis of the mouse LIM gene family reveals its roles in regulating pathological cardiac hypertrophy. FEBS Lett 2021; 595:2271-2289. [PMID: 34328660 DOI: 10.1002/1873-3468.14168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/27/2021] [Accepted: 07/17/2021] [Indexed: 11/08/2022]
Abstract
LIM-domain proteins have been shown to be associated with heart development and diseases. Systematic studies of LIM family members at the genome-wide level, which are crucial to further understand their functions in cardiac hypertrophy, are currently lacking. Here, 70 LIM genes were identified and characterised in mice. The expression patterns of LIM genes differ greatly during cardiac development and in the case of hypertrophy. Both Crip2 and Xirp2 are differentially expressed in cardiac hypertrophy and during heart failure. In addition, the hypertrophic state of cardiomyocytes is controlled by the relative expression levels of Crip2 and Xirp2. This study provides a foundation for further understanding of the special roles of LIM proteins in mammalian cardiac development and hypertrophy.
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Affiliation(s)
- Fangfang Wang
- Department of Cardiology, The Second Affiliated Hospital of Air Force Medical University, Xi'an, China
| | - Jieqiong Zhao
- Department of Cardiology, The Second Affiliated Hospital of Air Force Medical University, Xi'an, China
| | - Mingming Zhang
- Department of Cardiology, The Second Affiliated Hospital of Air Force Medical University, Xi'an, China
| | - Jingxiao Yang
- Department of Cardiology, The Second Affiliated Hospital of Air Force Medical University, Xi'an, China
| | - Guangwei Zeng
- Department of Cardiology, The Second Affiliated Hospital of Air Force Medical University, Xi'an, China
- Department of Cardiology, Xi'an International Medical Center Hospital, Northwest University, Xi'an, China
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23
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REGγ regulates hair cycle by activating Lgr5 positive hair follicle stem cells. J Dermatol Sci 2021; 102:101-108. [PMID: 33933312 DOI: 10.1016/j.jdermsci.2021.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 03/27/2021] [Accepted: 04/12/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND REGγ acts as a proteasome activating factor mediating proteasome degradation of substrate proteins in an ATP and ubiquitination independent manner and also as an important regulator of cell cycle, proliferation and apoptosis. Hair cycle involves dynamic, continuous morphological changes of three stages (anagen, catagen and telogen). OBJECTIVE The function of REGγ in hair cycling is still unclear. METHODS Here, we used REGγ knockout 293 T cells, inducible 293WT and 293N151Y cell, REGγ knockout mice to identify the novel molecular mechanism of REGγ in regulating hair follicle stem cells. RESULTS In the present study, we found that REGγ deletion markedly delayed the transition of hair follicles from telogen to anagen and hair regeneration in mice. We also observed significant decrease of hair follicle stem cell number, stem-like property and proliferation ability. Interestingly, the results from real-time PCR, FACS, Western Blot and immunofluorescent analysis showed that REGγ deletion could greatly downregulate Lgr5 expression in the hair follicles. Meanwhile, REGγ was demonstrated to directly interact with LHX2 and promotes its degradation. Importantly, REGγ specific deletion in Lgr5+ stem cells induced the marked delay of hair regeneration after depilation. CONCLUSION These data together indicate that REGγ was a new mediator of Lgr5 expression in hair follicle at least partly by promoting the degradation of its suppressive transcription factor LHX2. It seemed that REGγ regulated hair anagen entry and hair regrowth by activating Lgr5 positive hair follicle stem cells.
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24
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Cheng AH, Cheng HYM. Genesis of the Master Circadian Pacemaker in Mice. Front Neurosci 2021; 15:659974. [PMID: 33833665 PMCID: PMC8021851 DOI: 10.3389/fnins.2021.659974] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022] Open
Abstract
The suprachiasmatic nucleus (SCN) of the hypothalamus is the central circadian clock of mammals. It is responsible for communicating temporal information to peripheral oscillators via humoral and endocrine signaling, ultimately controlling overt rhythms such as sleep-wake cycles, body temperature, and locomotor activity. Given the heterogeneity and complexity of the SCN, its genesis is tightly regulated by countless intrinsic and extrinsic factors. Here, we provide a brief overview of the development of the SCN, with special emphasis on the murine system.
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Affiliation(s)
- Arthur H. Cheng
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Hai-Ying Mary Cheng
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
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25
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Liu SJ, Magill ST, Vasudevan HN, Hilz S, Villanueva-Meyer JE, Lastella S, Daggubati V, Spatz J, Choudhury A, Orr BA, Demaree B, Seo K, Ferris SP, Abate AR, Oberheim Bush NA, Bollen AW, McDermott MW, Costello JF, Raleigh DR. Multiplatform Molecular Profiling Reveals Epigenomic Intratumor Heterogeneity in Ependymoma. Cell Rep 2021; 30:1300-1309.e5. [PMID: 32023450 PMCID: PMC7313374 DOI: 10.1016/j.celrep.2020.01.018] [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: 10/31/2018] [Revised: 06/19/2019] [Accepted: 01/06/2020] [Indexed: 12/24/2022] Open
Abstract
Ependymomas exist within distinct genetic subgroups, but the molecular diversity within individual ependymomas is unknown. We perform multiplatform molecular profiling of 6 spatially distinct samples from an ependymoma with C11orf95-RELA fusion. DNA methylation and RNA sequencing distinguish clusters of samples according to neuronal development gene expression programs that could also be delineated by differences in magnetic resonance blood perfusion. Exome sequencing and phylogenetic analysis reveal epigenomic intratumor heterogeneity and suggest that chromosomal structural alterations may precede accumulation of single-nucleotide variants during ependymoma tumorigenesis. In sum, these findings shed light on the oncogenesis and intratumor heterogeneity of ependymoma. Tumor heterogeneity poses a barrier to cancer treatment. Liu etal. investigate radiographically distinct regions of an ependymoma tumor using transcriptomic, genetic, and epigenomic profiling and discover axes of gene expression programs that recapitulate normal brain development in addition to phylogenies that shed light on the tumorigenesis of ependymoma.
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Affiliation(s)
- S John Liu
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stephen T Magill
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Harish N Vasudevan
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stephanie Hilz
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Javier E Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sydney Lastella
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Vikas Daggubati
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jordan Spatz
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Abrar Choudhury
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Benjamin Demaree
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kyounghee Seo
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sean P Ferris
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nancy Ann Oberheim Bush
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Andrew W Bollen
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael W McDermott
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.
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26
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Guo R, Li F, Lu M, Ge K, Gan L, Sheng D. LIM Homeobox 9 knockdown by morpholino does not affect zebrafish retinal development. Biol Open 2021; 10:bio.056382. [PMID: 33579692 PMCID: PMC7969587 DOI: 10.1242/bio.056382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
LIM homeobox 9 (Lhx9) is a member of the LIM homeodomain transcription factor family, which expresses and functions in various vertebrate tissues, such as the gonads and pineal gland. Previous studies on lhx9 in zebrafish have mainly focused on the brain. However, little is known about the expression pattern of lhx9 during embryogenesis. Here, we detected lhx9 expression in zebrafish embryos using whole-mount in situ hybridization and found lhx9 expressed in heart, pectoral fin, and retina during their development in zebrafish. We then detailed the expression of lhx9 in retinal development. To further investigate the function of Lhx9 in retinogenesis, we performed morpholino (MO) knockdown experiments and found that upon lhx9 knockdown by MO, larvae presented normal eye development, retinal neural development, differentiation, proliferation, apoptosis, and responses to light stimulus. We not only elaborated the expression pattern of lhx9 in zebrafish embryogenesis, but we also demonstrated that lhx9 knockdown by morpholino does not affect the zebrafish retinal development, and our study provides data for further understanding of the role of Lhx9 in zebrafish retinal development. Summary:lhx9 is expressed in the development of the zebrafish heart, pectoral fin, and retina, but lhx9 knockdown by morpholino does not affect zebrafish retinal development.
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Affiliation(s)
- Rui Guo
- Key Laboratory of Organ Development and Regeneration of Zhejiang Province, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311100 Zhejiang, China.,College of Life Sciences, Zhejiang University, Hangzhou 310013 Zhejiang, China
| | - Fei Li
- Key Laboratory of Organ Development and Regeneration of Zhejiang Province, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311100 Zhejiang, China
| | - Minxia Lu
- Key Laboratory of Organ Development and Regeneration of Zhejiang Province, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311100 Zhejiang, China
| | - Kangkang Ge
- Hangzhou jingbai biotechnology Co, LTD., Hangzhou 310004 Zhejiang, China
| | - Lin Gan
- Key Laboratory of Organ Development and Regeneration of Zhejiang Province, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311100 Zhejiang, China .,College of Life Sciences, Zhejiang University, Hangzhou 310013 Zhejiang, China
| | - Donglai Sheng
- Key Laboratory of Organ Development and Regeneration of Zhejiang Province, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311100 Zhejiang, China
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27
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Humbert J, Salian S, Makrythanasis P, Lemire G, Rousseau J, Ehresmann S, Garcia T, Alasiri R, Bottani A, Hanquinet S, Beaver E, Heeley J, Smith ACM, Berger SI, Antonarakis SE, Yang XJ, Côté J, Campeau PM. De Novo KAT5 Variants Cause a Syndrome with Recognizable Facial Dysmorphisms, Cerebellar Atrophy, Sleep Disturbance, and Epilepsy. Am J Hum Genet 2020; 107:564-574. [PMID: 32822602 PMCID: PMC7477011 DOI: 10.1016/j.ajhg.2020.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/21/2020] [Indexed: 12/11/2022] Open
Abstract
KAT5 encodes an essential lysine acetyltransferase, previously called TIP60, which is involved in regulating gene expression, DNA repair, chromatin remodeling, apoptosis, and cell proliferation; but it remains unclear whether variants in this gene cause a genetic disease. Here, we study three individuals with heterozygous de novo missense variants in KAT5 that affect normally invariant residues, with one at the chromodomain (p.Arg53His) and two at or near the acetyl-CoA binding site (p.Cys369Ser and p.Ser413Ala). All three individuals have cerebral malformations, seizures, global developmental delay or intellectual disability, and severe sleep disturbance. Progressive cerebellar atrophy was also noted. Histone acetylation assays with purified variant KAT5 demonstrated that the variants decrease or abolish the ability of the resulting NuA4/TIP60 multi-subunit complexes to acetylate the histone H4 tail in chromatin. Transcriptomic analysis in affected individual fibroblasts showed deregulation of multiple genes that control development. Moreover, there was also upregulated expression of PER1 (a key gene involved in circadian control) in agreement with sleep anomalies in all of the individuals. In conclusion, dominant missense KAT5 variants cause histone acetylation deficiency with transcriptional dysregulation of multiples genes, thereby leading to a neurodevelopmental syndrome with sleep disturbance, cerebellar atrophy, and facial dysmorphisms, and suggesting a recognizable syndrome.
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Affiliation(s)
- Jonathan Humbert
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Axe Oncologie du Centre de Recherche du Centre Hospitalier Universitaire de Quebec-Université Laval, Quebec City, QC G1R 3S3, Canada
| | - Smrithi Salian
- Sainte-Justine Hospital Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Periklis Makrythanasis
- Biomedical Research Foundation of the Academy of Athens, Athens 115 27, Greece; Department of Genetic Medicine and Development, University of Geneva Medical School and Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Gabrielle Lemire
- Sainte-Justine Hospital Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Justine Rousseau
- Sainte-Justine Hospital Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Sophie Ehresmann
- Sainte-Justine Hospital Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Thomas Garcia
- Sainte-Justine Hospital Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Rami Alasiri
- Rosalind and Morris Goodman Cancer Research Centre, Department of Medicine, McGill University, Montreal, QC H3A 1A3, Canada
| | - Armand Bottani
- Service of Genetic Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Sylviane Hanquinet
- Unit of Pediatric Radiology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Erin Beaver
- Mercy Kids Genetics, St. Louis, MO 63141, USA
| | | | - Ann C M Smith
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20894, USA
| | - Seth I Berger
- Children's National Health System, Washington, DC 20010, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School and Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Xiang-Jiao Yang
- Rosalind and Morris Goodman Cancer Research Centre, Department of Medicine, McGill University, Montreal, QC H3A 1A3, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Axe Oncologie du Centre de Recherche du Centre Hospitalier Universitaire de Quebec-Université Laval, Quebec City, QC G1R 3S3, Canada
| | - Philippe M Campeau
- Sainte-Justine Hospital Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada.
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28
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Cui K, Wang Y, Zhu Y, Tao T, Yin F, Guo Y, Liu H, Li F, Wang P, Chen Y, Qin J. Neurodevelopmental impairment induced by prenatal valproic acid exposure shown with the human cortical organoid-on-a-chip model. MICROSYSTEMS & NANOENGINEERING 2020; 6:49. [PMID: 34567661 PMCID: PMC8433196 DOI: 10.1038/s41378-020-0165-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 05/05/2023]
Abstract
Prenatal exposure to environmental insults can increase the risk of developing neurodevelopmental disorders. Administration of the antiepileptic drug valproic acid (VPA) during pregnancy is tightly associated with a high risk of neurological disorders in offspring. However, the lack of an ideal human model hinders our comprehensive understanding of the impact of VPA exposure on fetal brain development, especially in early gestation. Herein, we present the first report indicating the effects of VPA on brain development at early stages using engineered cortical organoids from human induced pluripotent stem cells (hiPSCs). Cortical organoids were generated on micropillar arrays in a controlled manner, recapitulating the critical features of human brain development during early gestation. With VPA exposure, cortical organoids exhibited neurodevelopmental dysfunction characterized by increased neuron progenitors, inhibited neuronal differentiation and altered forebrain regionalization. Transcriptome analysis showed new markedly altered genes (e.g., KLHL1, LHX9, and MGARP) and a large number of differential expression genes (DEGs), some of which are related to autism. In particular, comparison of transcriptome data via GSEA and correlation analysis revealed the high similarity between VPA-exposed organoids with the postmortem ASD brain and autism patient-derived organoids, implying the high risk of autism with prenatal VPA exposure, even in early gestation. These new findings facilitate a better understanding of the cellular and molecular mechanisms underlying postnatal brain disorders (such as autism) with prenatal VPA exposure. This established cortical organoid-on-a-chip platform is valuable for probing neurodevelopmental disorders under environmental exposure and can be extended to applications in the study of diseases and drug testing.
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Affiliation(s)
- Kangli Cui
- Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yaqing Wang
- Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yujuan Zhu
- Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Tingting Tao
- Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Fangchao Yin
- Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yaqiong Guo
- Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Haitao Liu
- Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Fei Li
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Peng Wang
- Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023 China
| | - Yuejun Chen
- University of Chinese Academy of Sciences, Beijing, 100049 China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Jianhua Qin
- Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031 China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
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Lhx2/9 and Etv1 Transcription Factors have Complementary roles in Regulating the Expression of Guidance Genes slit1 and sema3a. Neuroscience 2020; 434:66-82. [PMID: 32200077 DOI: 10.1016/j.neuroscience.2020.03.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 01/02/2023]
Abstract
During neural network development, growing axons read a map of guidance cues expressed in the surrounding tissue that lead the axons toward their targets. In particular, Xenopus retinal ganglion axons use the cues Slit1 and Semaphorin 3a (Sema3a) at a key guidance decision point in the mid-diencephalon in order to continue on to their midbrain target, the optic tectum. The mechanisms that control the expression of these cues, however, are poorly understood. Extrinsic Fibroblast Growth Factor (Fgf) signals are known to help coordinate the development of the brain by regulating gene expression. Here, we propose Lhx2/9 and Etv1 as potential downstream effectors of Fgf signalling to regulate slit1 and sema3a expression in the Xenopus forebrain. We find that lhx2/9 and etv1 mRNAs are expressed complementary to and within slit1/sema3a expression domains, respectively. Our data indicate that Lhx2 functions as an indirect repressor in that lhx2 overexpression within the forebrain downregulates the mRNA expression of both guidance genes, and in vitro lhx2/9 overexpression decreases the activity of slit1 and sema3a promoters. The Lhx2-VP16 constitutive activator fusion reduces sema3a promoter function, and the Lhx2-En constitutive repressor fusion increases slit1 induction. In contrast, etv1 gain of function transactivates both guidance genes in vitro and in the forebrain. Based on these data, together with our previous work, we hypothesize that Fgf signalling promotes both slit1 and sema3a expression in the forebrain through Etv1, while using Lhx2/9 to limit the extent of expression, thereby establishing the proper boundaries of guidance cue expression.
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Guglielmi L, Bühler A, Moro E, Argenton F, Poggi L, Carl M. Temporal control of Wnt signaling is required for habenular neuron diversity and brain asymmetry. Development 2020; 147:147/6/dev182865. [PMID: 32179574 DOI: 10.1242/dev.182865] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 02/11/2020] [Indexed: 12/31/2022]
Abstract
Precise temporal coordination of signaling processes is pivotal for cellular differentiation during embryonic development. A vast number of secreted molecules are produced and released by cells and tissues, and travel in the extracellular space. Whether they induce a signaling pathway and instruct cell fate, however, depends on a complex network of regulatory mechanisms, which are often not well understood. The conserved bilateral left-right asymmetrically formed habenulae of the zebrafish are an excellent model for investigating how signaling control facilitates the generation of defined neuronal populations. Wnt signaling is required for habenular neuron type specification, asymmetry and axonal connectivity. The temporal regulation of this pathway and the players involved have, however, have remained unclear. We find that tightly regulated temporal restriction of Wnt signaling activity in habenular precursor cells is crucial for the diversity and asymmetry of habenular neuron populations. We suggest a feedback mechanism whereby the tumor suppressor Wnt inhibitory factor Wif1 controls the Wnt dynamics in the environment of habenular precursor cells. This mechanism might be common to other cell types, including tumor cells.
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Affiliation(s)
- Luca Guglielmi
- Heidelberg University, Medical Faculty Mannheim, Department of Cell and Molecular Biology, 68167 Mannheim, Germany.
| | - Anja Bühler
- University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), 38123 Trento, Italy.
| | - Enrico Moro
- University of Padova, Department of Molecular Medicine, 35121 Padova, Italy
| | | | - Lucia Poggi
- University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), 38123 Trento, Italy.
| | - Matthias Carl
- Heidelberg University, Medical Faculty Mannheim, Department of Cell and Molecular Biology, 68167 Mannheim, Germany. ,University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), 38123 Trento, Italy.
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31
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Andersen RE, Hong SJ, Lim JJ, Cui M, Harpur BA, Hwang E, Delgado RN, Ramos AD, Liu SJ, Blencowe BJ, Lim DA. The Long Noncoding RNA Pnky Is a Trans-acting Regulator of Cortical Development In Vivo. Dev Cell 2020; 49:632-642.e7. [PMID: 31112699 DOI: 10.1016/j.devcel.2019.04.032] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/15/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023]
Abstract
While it is now appreciated that certain long noncoding RNAs (lncRNAs) have important functions in cell biology, relatively few have been shown to regulate development in vivo, particularly with genetic strategies that establish cis versus trans mechanisms. Pnky is a nuclear-enriched lncRNA that is transcribed divergently from the neighboring proneural transcription factor Pou3f2. Here, we show that conditional deletion of Pnky from the developing cortex regulates the production of projection neurons from neural stem cells (NSCs) in a cell-autonomous manner, altering postnatal cortical lamination. Surprisingly, Pou3f2 expression is not disrupted by deletion of the entire Pnky gene. Moreover, expression of Pnky from a BAC transgene rescues the differential gene expression and increased neurogenesis of Pnky-knockout NSCs, as well as the developmental phenotypes of Pnky-deletion in vivo. Thus, despite being transcribed divergently from a key developmental transcription factor, the lncRNA Pnky regulates development in trans.
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Affiliation(s)
- Rebecca E Andersen
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sung Jun Hong
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Justin J Lim
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Miao Cui
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brock A Harpur
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Elizabeth Hwang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ryan N Delgado
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexander D Ramos
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Siyuan John Liu
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Benjamin J Blencowe
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121, USA.
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32
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Li SQ, Tu C, Wan L, Chen RQ, Duan ZX, Ren XL, Li ZH. FGF-induced LHX9 regulates the progression and metastasis of osteosarcoma via FRS2/TGF-β/β-catenin pathway. Cell Div 2019; 14:13. [PMID: 31788020 PMCID: PMC6876112 DOI: 10.1186/s13008-019-0056-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/09/2019] [Indexed: 01/21/2023] Open
Abstract
Background Fibroblast growth factor (FGF) and tumor growth factor-β (TGFβ) have emerged as pivotal regulators during the progression of osteosarcoma (OS). LHX9 is one crucial transcription factor controlled by FGF, however, its function in OS has not been investigated yet. Methods The expression of LHX9, FRS2, BMP4, TGF-beta R1, SMAD2, beta-catenin and metastasis-related proteins was measured by real-time quantitative PCR (RT-qPCR) and Western blot. CCK-8 assay and colony formation assay were employed to determine the proliferation of OS cells, while scratch wound healing assay and transwell assay were used to evaluate their migration and invasion, respectively. In vivo tumor growth and metastasis were determined by subcutaneous or intravenous injection of OS cells into nude mice. Results LHX9 expression was evidently up-regulated in OS tumor tissues and cell lines. Knockdown of LHX9 impaired the proliferation, migration, invasion and metastasis of OS cells. Mechanistically, LHX9 silencing led to the down-regulation of BMP-4, β-catenin and metastasis-related proteins, which was also observed in beta-catenin knockdown OS cells. By contrast, FRS2 knockdown conduced to the up-regulation of LHX9, BMP4, β-catenin and TGF-βR1, while TGF-beta inhibition repressed the expression of LHX9 and metastasis-related proteins. Additionally, let-7c modulates LHX9 and metastasis-related proteins by suppressing TGF-beta R1 expression on transcriptional level. Conclusions This study revealed LHX9 was essential for the proliferation, migration, invasion, and metastasis of OS cells via FGF and TGF-β/β-catenin signaling pathways.
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Affiliation(s)
- Shuang-Qing Li
- Orthopaedics, Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, No. 139 Renming Road, Changsha, 410010 Hunan People's Republic of China
| | - Chao Tu
- Orthopaedics, Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, No. 139 Renming Road, Changsha, 410010 Hunan People's Republic of China
| | - Lu Wan
- Orthopaedics, Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, No. 139 Renming Road, Changsha, 410010 Hunan People's Republic of China
| | - Rui-Qi Chen
- Orthopaedics, Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, No. 139 Renming Road, Changsha, 410010 Hunan People's Republic of China
| | - Zhi-Xi Duan
- Orthopaedics, Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, No. 139 Renming Road, Changsha, 410010 Hunan People's Republic of China
| | - Xiao-Lei Ren
- Orthopaedics, Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, No. 139 Renming Road, Changsha, 410010 Hunan People's Republic of China
| | - Zhi-Hong Li
- Orthopaedics, Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, No. 139 Renming Road, Changsha, 410010 Hunan People's Republic of China
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Chen T, Zhang B, Ziegenhals T, Prusty AB, Fröhler S, Grimm C, Hu Y, Schaefke B, Fang L, Zhang M, Kraemer N, Kaindl AM, Fischer U, Chen W. A missense mutation in SNRPE linked to non-syndromal microcephaly interferes with U snRNP assembly and pre-mRNA splicing. PLoS Genet 2019; 15:e1008460. [PMID: 31671093 PMCID: PMC6850558 DOI: 10.1371/journal.pgen.1008460] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 11/12/2019] [Accepted: 10/04/2019] [Indexed: 12/15/2022] Open
Abstract
Malfunction of pre-mRNA processing factors are linked to several human diseases including cancer and neurodegeneration. Here we report the identification of a de novo heterozygous missense mutation in the SNRPE gene (c.65T>C (p.Phe22Ser)) in a patient with non-syndromal primary (congenital) microcephaly and intellectual disability. SNRPE encodes SmE, a basal component of pre-mRNA processing U snRNPs. We show that the microcephaly-linked SmE variant is unable to interact with the SMN complex and as a consequence fails to assemble into U snRNPs. This results in widespread mRNA splicing alterations in fibroblast cells derived from this patient. Similar alterations were observed in HEK293 cells upon SmE depletion that could be rescued by the expression of wild type but not mutant SmE. Importantly, the depletion of SmE in zebrafish causes aberrant mRNA splicing alterations and reduced brain size, reminiscent of the patient microcephaly phenotype. We identify the EMX2 mRNA, which encodes a protein required for proper brain development, as a major mis-spliced down stream target. Together, our study links defects in the SNRPE gene to microcephaly and suggests that alterations of cellular splicing of specific mRNAs such as EMX2 results in the neurological phenotype of the disease. In higher eukaryotes, the protein coding genes are first transcribed as precursor mRNAs (pre-mRNAs) and further processed by the spliceosome to form the mature mRNA for translation. Malfunction of pre-mRNA processing factors are linked to several human diseases including cancer and neurodegeneration. Here we report the identification of a de novo heterozygous missense mutation in the SNRPE/SmE gene in a patient with non-syndromal primary (congenital) microcephaly and intellectual disability. The effect of identified de novo mutation on SNRPE/SmE was characterized in vitro. The zebrafish was used as in vivo model to further dissect the physiological consequence and pathomechanism. Finally, the EMX2 gene was identified as one of the major down stream target genes responsible for the phenotype. Our study links defects in the SNRPE/SmE gene to microcephaly and provides the new pathogenic mechanism for microcephaly.
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Affiliation(s)
- Tao Chen
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical System Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Bin Zhang
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, China
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Thomas Ziegenhals
- Department of Biochemistry, Theodor-Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Archana B. Prusty
- Department of Biochemistry, Theodor-Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Sebastian Fröhler
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical System Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Clemens Grimm
- Department of Biochemistry, Theodor-Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Yuhui Hu
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Bernhard Schaefke
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Liang Fang
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Min Zhang
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Nadine Kraemer
- Charité-Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Department of Pediatric Neurology, Berlin, Germany
| | - Angela M. Kaindl
- Charité-Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Department of Pediatric Neurology, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Center for Chronically Sick Children, Berlin, Germany
- * E-mail: (UF); (AK); (WC)
| | - Utz Fischer
- Department of Biochemistry, Theodor-Boveri-Institute, University of Würzburg, Würzburg, Germany
- * E-mail: (UF); (AK); (WC)
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), Shenzhen, China
- * E-mail: (UF); (AK); (WC)
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Williams RM, Candido-Ferreira I, Repapi E, Gavriouchkina D, Senanayake U, Ling ITC, Telenius J, Taylor S, Hughes J, Sauka-Spengler T. Reconstruction of the Global Neural Crest Gene Regulatory Network In Vivo. Dev Cell 2019; 51:255-276.e7. [PMID: 31639368 PMCID: PMC6838682 DOI: 10.1016/j.devcel.2019.10.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 05/31/2019] [Accepted: 10/01/2019] [Indexed: 02/07/2023]
Abstract
Precise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and dynamic molecular interactions. Here we present a genome-wide in vivo reconstruction of the GRN underlying development of the multipotent neural crest (NC) embryonic cell population. By coupling NC-specific epigenomic and transcriptional profiling at population and single-cell levels with genome/epigenome engineering in vivo, we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, novel trans-factors, and cis-signatures allowing reverse engineering of the NC-GRN at unprecedented resolution. Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits that define canonical and neural NC fates early during NC ontogeny. Our integrated approach, allowing dissection of cell-type-specific regulatory circuits in vivo, has broad implications for GRN discovery and investigation.
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Affiliation(s)
- Ruth M Williams
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Ivan Candido-Ferreira
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Emmanouela Repapi
- University of Oxford, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Daria Gavriouchkina
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Upeka Senanayake
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Irving T C Ling
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK; University of Oxford, Department of Paediatric Surgery, Children's Hospital Oxford, Oxford, UK
| | - Jelena Telenius
- University of Oxford, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK; University of Oxford, MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Stephen Taylor
- University of Oxford, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Jim Hughes
- University of Oxford, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK; University of Oxford, MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK.
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Guo Q, Li JYH. Defining developmental diversification of diencephalon neurons through single cell gene expression profiling. Development 2019; 146:dev174284. [PMID: 30872278 PMCID: PMC6602344 DOI: 10.1242/dev.174284] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/07/2019] [Indexed: 12/31/2022]
Abstract
The embryonic diencephalon forms integration centers and relay stations in the forebrain. Anecdotal expression studies suggest that the diencephalon contains multiple developmental compartments and subdivisions. Here, we utilized single cell RNA sequencing to profile transcriptomes of dissociated cells from the diencephalon of E12.5 mouse embryos. We identified the divergence of different progenitors, intermediate progenitors, and emerging neurons. By mapping the identified cell groups to their spatial origins, we characterized the molecular features of cell types and cell states arising from various diencephalic domains. Furthermore, we reconstructed the developmental trajectory of distinct cell lineages, and thereby identified the genetic cascades and gene regulatory networks underlying the progression of the cell cycle, neurogenesis and cellular diversification. The analysis provides new insights into the molecular mechanisms underlying the amplification of intermediate progenitor cells in the thalamus. The single cell-resolved trajectories not only confirm a close relationship between the rostral thalamus and prethalamus, but also uncover an unexpected close relationship between the caudal thalamus, epithalamus and rostral pretectum. Our data provide a useful resource for systematic studies of cell heterogeneity and differentiation kinetics within the diencephalon.
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Affiliation(s)
- Qiuxia Guo
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - James Y H Li
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 263 Farmington Avenue, Farmington, CT 06030-6403, USA
- Institute for Systems Genomics, University of Connecticut, 400 Farmington Avenue, Farmington, CT 06030-6403, USA
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Liang TS, Zheng YJ, Wang J, Zhao JY, Yang DK, Liu ZS. MicroRNA-506 inhibits tumor growth and metastasis in nasopharyngeal carcinoma through the inactivation of the Wnt/β-catenin signaling pathway by down-regulating LHX2. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:97. [PMID: 30791932 PMCID: PMC6385449 DOI: 10.1186/s13046-019-1023-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 01/06/2019] [Indexed: 12/22/2022]
Abstract
Background Epithelial-mesenchymal transition (EMT)-associated proteins play key roles in cancer progression and metastasis with the involvement of microRNAs (miRNAs). This study aims to assess the role of miR-506 working in tandem with LIM Homeobox 2 (LHX2) in EMT and metastasis through the Wnt/β-catenin signaling pathway in nasopharyngeal carcinoma (NPC). Methods Differentially expressed genes associated with NPC were screened using microarray analyses, from which LHX2 was identified. Next, the potential relationship between miR-506 and LHX2 was analyzed. In order to explore the effect of miR-506 or LHX2 on NPC cell proliferation, migration, invasion and apoptosis, serials of mimics, inhibitors or siRNA against LHX2 were transfected into NPC cells. Then, the expression patterns of LHX2, Wnt1, β-catenin, E-cadherin, Vimentin, TCF4 and Twist were determined to assess the influence of miR-506 or LHX2 on EMT as well as the relationship between the Wnt/β-catenin signaling pathway and TCF4. The tumorigenicity and lymph node metastasis (LNM) in xenograft tumors of nude mice were observed. Results The has-miR-506-3p was identified as the down-regulated gene in NPC based on the microarray data while LHX2 was negatively regulated by miR-506. Over-expression of miR-506 or silencing of LHK2 inhibited NPC cell proliferation, migration, invasion, tumorigenicity and LNM but promoted apoptosis indicated by decreased Wnt1, β-catenin, Vimentin, TCF4 and Twist expressions along with increased E-cadherin expressions. Conclusions miR-506 inhibits tumor growth and metastasis in NPC via inhibition of Wnt/β-catenin signaling by down-regulating LHX2, accompanied by decreased TCF4. Taken together, miR-506 targeted-inhibition LHX2 presents a promising therapeutic strategy for the treatment of NPC. Trial registration ChiCTR1800018889. Registered 15 October 2018. Electronic supplementary material The online version of this article (10.1186/s13046-019-1023-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tian-Song Liang
- Department of Radiotherapy, the First Affiliated Hospital of Zhengzhou University, Zhengdong Branch, Zhengzhou, 475000, Henan Province, People's Republic of China
| | - Ying-Juan Zheng
- Department of Radiotherapy, the First Affiliated Hospital of Zhengzhou University, Zhengdong Branch, Zhengzhou, 475000, Henan Province, People's Republic of China
| | - Juan Wang
- Department of Radiotherapy, the First Affiliated Hospital of Zhengzhou University, Zhengdong Branch, Zhengzhou, 475000, Henan Province, People's Republic of China
| | - Jing-Yi Zhao
- Department of Radiotherapy, the First Affiliated Hospital of Zhengzhou University, Zhengdong Branch, Zhengzhou, 475000, Henan Province, People's Republic of China
| | - Dao-Ke Yang
- Department of Radiotherapy, the First Affiliated Hospital of Zhengzhou University, Zhengdong Branch, Zhengzhou, 475000, Henan Province, People's Republic of China.
| | - Zhang-Suo Liu
- Department of Radiotherapy, the First Affiliated Hospital of Zhengzhou University, Zhengdong Branch, Zhengzhou, 475000, Henan Province, People's Republic of China.
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Newman EA, Wu D, Taketo MM, Zhang J, Blackshaw S. Canonical Wnt signaling regulates patterning, differentiation and nucleogenesis in mouse hypothalamus and prethalamus. Dev Biol 2018; 442:236-248. [PMID: 30063881 DOI: 10.1016/j.ydbio.2018.07.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/26/2018] [Accepted: 07/26/2018] [Indexed: 01/10/2023]
Abstract
The hypothalamus is a small, but anatomically and functionally complex region of the brain whose development is poorly understood. In this study, we have explored its development by studying the canonical Wnt signaling pathway, generating gain and loss of function mutations of beta-catenin (Ctnnb1) in both hypothalamic and prethalamic neuroepithelium. Deletion of Ctnnb1 resulted in an anteriorized and hypoplastic hypothalamus. Posterior structures were lost or reduced, and anterior structures were expanded. In contrast, overexpression of a constitutively active mutant form of Ctnnb1 resulted in severe hyperplasia of prethalamus and hypothalamus, and expanded expression of a subset of posterior and premamillary hypothalamic markers. Moderate defects in differentiation of Arx-positive GABAergic neural precursors were observed in both prethalamus and hypothalamus of Ctnnb1 loss of function mutants, while in gain of function mutants, their differentiation was completely suppressed, although markers of prethalamic progenitors were preserved. Multiple other region-specific markers, including several specific posterior hypothalamic structures, were also suppressed in Ctnnb1 gain of function mutations. Severe, region-specific defects in hypothalamic nucleogenesis were also observed in both gain and loss of function mutations of Ctnnb1. Finally, both gain and loss of function of Ctnnb1 also produced severe, non-cell autonomous disruptions of pituitary development. These findings demonstrate a central and multifaceted role for canonical Wnt signaling in regulating growth, patterning, differentiation and nucleogenesis in multiple diencephalic regions.
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Affiliation(s)
- Elizabeth A Newman
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dan Wu
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Makoto Mark Taketo
- Division of Experimental Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jiangyang Zhang
- Department of Radiology, NYU Langone School of Medicine, New York, NY, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Watson BA, Feenstra JM, Van Arsdale JM, Rai-Bhatti KS, Kim DJH, Coggins AS, Mattison GL, Yoo S, Steinman ED, Pira CU, Gongol BR, Oberg KC. LHX2 Mediates the FGF-to-SHH Regulatory Loop during Limb Development. J Dev Biol 2018; 6:E13. [PMID: 29914077 PMCID: PMC6027391 DOI: 10.3390/jdb6020013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/11/2018] [Accepted: 06/12/2018] [Indexed: 12/26/2022] Open
Abstract
During limb development, fibroblast growth factors (Fgfs) govern proximal⁻distal outgrowth and patterning. FGFs also synchronize developmental patterning between the proximal⁻distal and anterior⁻posterior axes by maintaining Sonic hedgehog (Shh) expression in cells of the zone of polarizing activity (ZPA) in the distal posterior mesoderm. Shh, in turn, maintains Fgfs in the apical ectodermal ridge (AER) that caps the distal tip of the limb bud. Crosstalk between Fgf and Shh signaling is critical for patterned limb development, but the mechanisms underlying this feedback loop are not well-characterized. Implantation of Fgf beads in the proximal posterior limb bud can maintain SHH expression in the former ZPA domain (evident 3 h after application), while prolonged exposure (24 h) can induce SHH outside of this domain. Although temporally and spatially disparate, comparative analysis of transcriptome data from these different populations accentuated genes involved in SHH regulation. Comparative analysis identified 25 candidates common to both treatments, with eight linked to SHH expression or function. Furthermore, we demonstrated that LHX2, a LIM Homeodomain transcription factor, is an intermediate in the FGF-mediated regulation of SHH. Our data suggest that LHX2 acts as a competency factor maintaining distal posterior SHH expression subjacent to the AER.
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Affiliation(s)
- Billy A Watson
- Department of Pathology and Human Anatomy, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA.
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA.
| | - Jennifer M Feenstra
- Department of Pathology and Human Anatomy, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA.
| | - Jonathan M Van Arsdale
- Department of Pathology and Human Anatomy, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA.
| | - Karndeep S Rai-Bhatti
- Department of Pathology and Human Anatomy, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA.
| | - Diana J H Kim
- Department of Pathology and Human Anatomy, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA.
| | - Ashley S Coggins
- Department of Pathology and Human Anatomy, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA.
| | - Gennaya L Mattison
- Department of Pathology and Human Anatomy, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA.
| | - Stephen Yoo
- Department of Pathology and Human Anatomy, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA.
| | - Eric D Steinman
- Department of Pathology and Human Anatomy, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA.
| | - Charmaine U Pira
- Department of Pathology and Human Anatomy, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA.
| | - Brendan R Gongol
- Department of Cardiopulmonary Sciences, School of Allied Health Professions, Loma Linda University, Loma Linda, CA 92354, USA.
| | - Kerby C Oberg
- Department of Pathology and Human Anatomy, School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA.
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39
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Jesuthasan S. The thalamo-habenula projection revisited. Semin Cell Dev Biol 2018; 78:116-119. [DOI: 10.1016/j.semcdb.2017.08.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/07/2017] [Accepted: 08/07/2017] [Indexed: 11/29/2022]
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40
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Szemes M, Greenhough A, Melegh Z, Malik S, Yuksel A, Catchpoole D, Gallacher K, Kollareddy M, Park JH, Malik K. Wnt Signalling Drives Context-Dependent Differentiation or Proliferation in Neuroblastoma. Neoplasia 2018; 20:335-350. [PMID: 29505958 PMCID: PMC5909736 DOI: 10.1016/j.neo.2018.01.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/17/2018] [Accepted: 01/21/2018] [Indexed: 01/09/2023]
Abstract
Neuroblastoma is one of the commonest and deadliest solid tumours of childhood, and is thought to result from disrupted differentiation of the developing sympathoadrenergic lineage of the neural crest. Neuroblastoma exhibits intra- and intertumoural heterogeneity, with high risk tumours characterised by poor differentiation, which can be attributable to MYCN-mediated repression of genes involved in neuronal differentiation. MYCN is known to co-operate with oncogenic signalling pathways such as Alk, Akt and MEK/ERK signalling, and, together with c-MYC has been shown to be activated by Wnt signalling in various tissues. However, our previous work demonstrated that Wnt3a/Rspo2 treatment of some neuroblastoma cell lines can, paradoxically, decrease c-MYC and MYCN proteins. This prompted us to define the neuroblastoma-specific Wnt3a/Rspo2-driven transcriptome using RNA sequencing, and characterise the accompanying changes in cell biology. Here we report the identification of ninety Wnt target genes, and show that Wnt signalling is upstream of numerous transcription factors and signalling pathways in neuroblastoma. Using live-cell imaging, we show that Wnt signalling can drive differentiation of SK-N-BE(2)-C and SH-SY5Y cell-lines, but, conversely, proliferation of SK-N-AS cells. We show that cell-lines that differentiate show induction of pro-differentiation BMP4 and EPAS1 proteins, which is not apparent in the SK-N-AS cells. In contrast, SK-N-AS cells show increased CCND1, phosphorylated RB and E2F1 in response to Wnt3a/Rspo2, consistent with their proliferative response, and these proteins are not increased in differentiating lines. By meta-analysis of the expression of our 90 genes in primary tumour gene expression databases, we demonstrate discrete expression patterns of our Wnt genes in patient cohorts with different prognosis. Furthermore our analysis reveals interconnectivity within subsets of our Wnt genes, with one subset comprised of novel putative drivers of neuronal differentiation repressed by MYCN. Assessment of β-catenin immunohistochemistry shows high levels of β-catenin in tumours with better differentiation, further supporting a role for canonical Wnt signalling in neuroblastoma differentiation.
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Key Words
- alk, anaplastic lymphoma kinase
- atra, all-trans-retinoic acid
- bmp4, bone morphogenetic protein 4
- ccnd1, cyclin d1
- egf, epidermal growth factor
- epas1, endothelial pas domain protein 1
- erk, extracellular signal-regulated kinases
- emt, epithelial-mesenchymal transition
- kegg, kyoto encyclopedia of genes and genomes
- mapk, mitogen-activated protein kinase
- mek, mitogen-activated protein kinase kinase
- pbs, phosphate-buffered saline
- qrt-pcr, quantitative reverse-transcriptase polymerase chain reaction
- rb, retinoblastoma
- rnaseq, rna sequencing
- rspo2, r-spondin-2
- sds-page, sodium-dodecyl sulphate-polyacrylamide gel electrophoresis
- tcf/lef, t-cell factor/lymphoid enhancer binding factor
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Affiliation(s)
- Marianna Szemes
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Alexander Greenhough
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Zsombor Melegh
- Department of Cellular Pathology, Southmead Hospital, Bristol, UK
| | - Sally Malik
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Aysen Yuksel
- The Kids Research Institute, The Children's Hospital at Westmead, Westmead, Westmead NSW, 2145, Australia
| | - Daniel Catchpoole
- The Kids Research Institute, The Children's Hospital at Westmead, Westmead, Westmead NSW, 2145, Australia
| | - Kelli Gallacher
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Madhu Kollareddy
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Ji Hyun Park
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Karim Malik
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
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Hu F, Zhu Q, Sun B, Cui C, Li C, Zhang L. Smad ubiquitylation regulatory factor 1 promotes LIM‐homeobox gene 9 degradation and represses testosterone production in Leydig cells. FASEB J 2018; 32:4627-4640. [DOI: 10.1096/fj.201701480r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Fan Hu
- Department of Geriatric EndocrinologyChinese People's Liberation Army General HospitalNational Clinical Research Center for Geriatric DiseasesBeijingChina
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center of Protein SciencesBeijing Institute of LifeomicsBeijingChina
| | - Qiong Zhu
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center of Protein SciencesBeijing Institute of LifeomicsBeijingChina
| | - Banruo Sun
- Department of Geriatric EndocrinologyChinese People's Liberation Army General HospitalNational Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Chunping Cui
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center of Protein SciencesBeijing Institute of LifeomicsBeijingChina
| | - Chunlin Li
- Department of Geriatric EndocrinologyChinese People's Liberation Army General HospitalNational Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Lingqiang Zhang
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center of Protein SciencesBeijing Institute of LifeomicsBeijingChina
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42
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Evidence of sex-bias in gene expression in the brain transcriptome of two populations of rainbow trout (Oncorhynchus mykiss) with divergent life histories. PLoS One 2018; 13:e0193009. [PMID: 29447294 PMCID: PMC5814004 DOI: 10.1371/journal.pone.0193009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/03/2018] [Indexed: 11/19/2022] Open
Abstract
Sex-bias in gene expression is a mechanism that can generate phenotypic variance between the sexes, however, relatively little is known about how patterns of sex-bias vary during development, and how variable sex-bias is between different populations. To that end, we measured sex-bias in gene expression in the brain transcriptome of rainbow trout (Oncorhynchus mykiss) during the first two years of development. Our sampling included from the fry stage through to when O. mykiss either migrate to the ocean or remain resident and undergo sexual maturation. Samples came from two F1 lines: One from migratory steelhead trout and one from resident rainbow trout. All samples were reared in a common garden environment and RNA sequencing (RNA-seq) was used to estimate patterns of gene expression. A total of 1,716 (4.6% of total) genes showed evidence of sex-bias in gene expression in at least one time point. The majority (96.7%) of sex-biased genes were differentially expressed during the second year of development, indicating that patterns of sex-bias in expression are tied to key developmental events, such as migration and sexual maturation. Mapping of differentially expressed genes to the O. mykiss genome revealed that the X chromosome is enriched for female upregulated genes, and this may indicate a lack of dosage compensation in rainbow trout. There were many more sex-biased genes in the migratory line than the resident line suggesting differences in patterns of gene expression in the brain between populations subjected to different forces of selection. Overall, our results suggest that there is considerable variation in the extent and identity of genes exhibiting sex-bias during the first two years of life. These differentially expressed genes may be connected to developmental differences between the sexes, and/or between adopting a resident or migratory life history.
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43
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Sasaki K, Othman MB, Demura M, Watanabe M, Isoda H. Modulation of Neurogenesis through the Promotion of Energy Production Activity Is behind the Antidepressant-Like Effect of Colonial Green Alga, Botryococcus braunii. Front Physiol 2017; 8:900. [PMID: 29176952 PMCID: PMC5686089 DOI: 10.3389/fphys.2017.00900] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 10/24/2017] [Indexed: 12/31/2022] Open
Abstract
Algae have been recognized as important resources providing functional components due to their capacity to exert beneficial effects on health. Therefore, there is increasing interest in investigating the biological activity of algae. In this study, we evaluated the antidepressant-like effect of the administration of 100 mg/kg/day of the ethanol extract of colonial green alga Botryococcus braunii (EEB) for 14 consecutive days in the forced swimming test (FST)-induced depression in imprinting control region (ICR) mice. Imipramine, a commercial antidepressant drug, was used as a positive control. In addition, we investigated the molecular mechanisms underlying the effect of EEB by measuring ATP production and by assessing any change in gene expression at the end of the treatment using real-time polymerase chain reaction (PCR) and microarray assays. We showed that the immobility time in the water-administered control (FST stress) group gradually increased from day 1 to day 14. However, treatment with EEB caused a significant decrease of immobility time in the FST compared with that in the FST stress group. Microarray and real-time PCR results revealed that EEB treatment induced variation in the expression of several genes associated with neurogenesis, energy metabolism, and dopamine synthesis. Interestingly, we revealed that only EEB treatment enhanced the promotion of energy production, while treatment with imipramine was ineffective. Our study provides the first evidence that B. braunii enhances energy production, which may contribute to the modulation of neurogenesis and to the enhancement of dopaminergic function, in turn potentially underlying the antistress- and antidepressant-like effects that we observed.
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Affiliation(s)
- Kazunori Sasaki
- Interdisciplinary Research Center for Catalytic Chemistry, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan
| | - Mahmoud B Othman
- Alliance for Research on North Africa, University of Tsukuba, Tsukuba, Japan
| | - Mikihide Demura
- Algal Biomass and Energy System R&D Center, University of Tsukuba, Tsukuba, Japan
| | - Makoto Watanabe
- Algal Biomass and Energy System R&D Center, University of Tsukuba, Tsukuba, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Hiroko Isoda
- Alliance for Research on North Africa, University of Tsukuba, Tsukuba, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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Rajan TS, Scionti D, Diomede F, Piattelli A, Bramanti P, Mazzon E, Trubiani O. Prolonged Expansion Induces Spontaneous Neural Progenitor Differentiation from Human Gingiva-Derived Mesenchymal Stem Cells. Cell Reprogram 2017; 19:389-401. [PMID: 29058474 DOI: 10.1089/cell.2017.0012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Neural crest-derived mesenchymal stem cells (MSCs) obtained from dental tissues received considerable interest in regenerative medicine, particularly in nerve regeneration owing to their embryonic origin and ease of harvest. Proliferation efficacy and differentiation capacity into diverse cell lineages propose dental MSCs as an in vitro tool for disease modeling. In this study, we investigated the spontaneous differentiation efficiency of dental MSCs obtained from human gingiva tissue (hGMSCs) into neural progenitor cells after extended passaging. At passage 41, the morphology of hGMSCs changed from typical fibroblast-like shape into sphere-shaped cells with extending processes. Next-generation transcriptomics sequencing showed increased expression of neural progenitor markers such as NES, MEIS2, and MEST. In addition, de novo expression of neural precursor genes, such as NRN1, PHOX2B, VANGL2, and NTRK3, was noticed in passage 41. Immunocytochemistry results showed suppression of neurogenesis repressors TP53 and p21, whereas Western blot results revealed the expression of neurotrophic factors BDNF and NT3 at passage 41. Our results showed the spontaneous efficacy of hGMSCs to differentiate into neural precursor cells over prolonged passages and that these cells may assist in producing novel in vitro disease models that are associated with neural development.
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Affiliation(s)
| | - Domenico Scionti
- 1 Department of Experimental Neurology, IRCCS Centro Neurolesi "Bonino-Pulejo," Messina , Italy
| | - Francesca Diomede
- 2 Stem Cells and Regenerative Medicine Laboratory, Department of Medical, Oral and Biotechnological Sciences, University "G. d'Annunzio," Chieti-Pescara, Chieti, Italy
| | - Adriano Piattelli
- 2 Stem Cells and Regenerative Medicine Laboratory, Department of Medical, Oral and Biotechnological Sciences, University "G. d'Annunzio," Chieti-Pescara, Chieti, Italy
| | - Placido Bramanti
- 1 Department of Experimental Neurology, IRCCS Centro Neurolesi "Bonino-Pulejo," Messina , Italy
| | - Emanuela Mazzon
- 1 Department of Experimental Neurology, IRCCS Centro Neurolesi "Bonino-Pulejo," Messina , Italy
| | - Oriana Trubiani
- 2 Stem Cells and Regenerative Medicine Laboratory, Department of Medical, Oral and Biotechnological Sciences, University "G. d'Annunzio," Chieti-Pescara, Chieti, Italy
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45
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Acharya CR, Owzar K, Allen AS. Mapping eQTL by leveraging multiple tissues and DNA methylation. BMC Bioinformatics 2017; 18:455. [PMID: 29047346 PMCID: PMC5648503 DOI: 10.1186/s12859-017-1856-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 10/02/2017] [Indexed: 12/24/2022] Open
Abstract
Background DNA methylation is an important tissue-specific epigenetic event that influences transcriptional regulation of gene expression. Differentially methylated CpG sites may act as mediators between genetic variation and gene expression, and this relationship can be exploited while mapping multi-tissue expression quantitative trait loci (eQTL). Current multi-tissue eQTL mapping techniques are limited to only exploiting gene expression patterns across multiple tissues either in a joint tissue or tissue-by-tissue frameworks. We present a new statistical approach that enables us to model the effect of germ-line variation on tissue-specific gene expression in the presence of effects due to DNA methylation. Results Our method efficiently models genetic and epigenetic variation to identify genomic regions of interest containing combinations of mRNA transcripts, CpG sites, and SNPs by jointly testing for genotypic effect and higher order interaction effects between genotype, methylation and tissues. We demonstrate using Monte Carlo simulations that our approach, in the presence of both genetic and DNA methylation effects, gives an improved performance (in terms of statistical power) to detect eQTLs over the current eQTL mapping approaches. When applied to an array-based dataset from 150 neuropathologically normal adult human brains, our method identifies eQTLs that were undetected using standard tissue-by-tissue or joint tissue eQTL mapping techniques. As an example, our method identifies eQTLs by leveraging methylated CpG sites in a LIM homeobox member gene (LHX9), which may have a role in the neural development. Conclusions Our score test-based approach does not need parameter estimation under the alternative hypothesis. As a result, our model parameters are estimated only once for each mRNA - CpG pair. Our model specifically studies the effects of non-coding regions of DNA (in this case, CpG sites) on mapping eQTLs. However, we can easily model micro-RNAs instead of CpG sites to study the effects of post-transcriptional events in mapping eQTL. Our model’s flexible framework also allows us to investigate other genomic events such as alternative gene splicing by extending our model to include gene isoform-specific data. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1856-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chaitanya R Acharya
- Program in Computational Biology and Bioinformatics, Duke University, 2424 Erwin Road, Suite 1104, Durham, 27710, NC, USA.,Department of Biostatistics and Bioinformatics, Duke University, 2424 Erwin Road, Suite 1104, Durham, 27710, NC, USA
| | - Kouros Owzar
- Department of Biostatistics and Bioinformatics, Duke University, 2424 Erwin Road, Suite 1104, Durham, 27710, NC, USA
| | - Andrew S Allen
- Program in Computational Biology and Bioinformatics, Duke University, 2424 Erwin Road, Suite 1104, Durham, 27710, NC, USA. .,Department of Biostatistics and Bioinformatics, Duke University, 2424 Erwin Road, Suite 1104, Durham, 27710, NC, USA.
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46
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Xie Y, Dorsky RI. Development of the hypothalamus: conservation, modification and innovation. Development 2017; 144:1588-1599. [PMID: 28465334 DOI: 10.1242/dev.139055] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The hypothalamus, which regulates fundamental aspects of physiological homeostasis and behavior, is a brain region that exhibits highly conserved anatomy across vertebrate species. Its development involves conserved basic mechanisms of induction and patterning, combined with a more plastic process of neuronal fate specification, to produce brain circuits that mediate physiology and behavior according to the needs of each species. Here, we review the factors involved in the induction, patterning and neuronal differentiation of the hypothalamus, highlighting recent evidence that illustrates how changes in Wnt/β-catenin signaling during development may lead to species-specific form and function of this important brain structure.
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Affiliation(s)
- Yuanyuan Xie
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Richard I Dorsky
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84112, USA
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47
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Ebisu H, Iwai-Takekoshi L, Fujita-Jimbo E, Momoi T, Kawasaki H. Foxp2 Regulates Identities and Projection Patterns of Thalamic Nuclei During Development. Cereb Cortex 2017; 27:3648-3659. [PMID: 27384060 DOI: 10.1093/cercor/bhw187] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The molecular mechanisms underlying the formation of the thalamus during development have been investigated intensively. Although transcription factors distinguishing the thalamic primordium from adjacent brain structures have been uncovered, those involved in patterning inside the thalamus are largely unclear. Here, we show that Foxp2, a member of the forkhead transcription factor family, regulates thalamic patterning during development. We found a graded expression pattern of Foxp2 in the thalamic primordium of the mouse embryo. The expression levels of Foxp2 were high in the posterior region and low in the anterior region of the thalamic primordium. In Foxp2 (R552H) knockin mice, which have a missense loss-of-function mutation in the forkhead domain of Foxp2, thalamic nuclei of the posterior region of the thalamus were shrunken, while those of the intermediate region were expanded. Consistently, Foxp2 (R552H) knockin mice showed changes in thalamocortical projection patterns. Our results uncovered important roles of Foxp2 in thalamic patterning and thalamocortical projections during development.
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Affiliation(s)
- Haruka Ebisu
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
- Brain/Liver Interface Medicine Research Center, Kanazawa University, Ishikawa 920-8640, Japan
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- Department of Molecular and Systems Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Lena Iwai-Takekoshi
- Department of Molecular and Systems Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Eriko Fujita-Jimbo
- Department of Pediatrics, Jichi Medical University, Tochigi 329-0498, Japan
| | - Takashi Momoi
- Department of Pathophysiology, Tokyo Medical University, Tokyo 160-8402, Japan
| | - Hiroshi Kawasaki
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Ishikawa 920-8640, Japan
- Brain/Liver Interface Medicine Research Center, Kanazawa University, Ishikawa 920-8640, Japan
- Department of Molecular and Systems Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
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48
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Balasubramanian R, Bui A, Dong X, Gan L. Lhx9 Is Required for the Development of Retinal Nitric Oxide-Synthesizing Amacrine Cell Subtype. Mol Neurobiol 2017; 55:2922-2933. [PMID: 28456934 DOI: 10.1007/s12035-017-0554-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/12/2017] [Indexed: 11/29/2022]
Abstract
Amacrine cells are the most diverse group of retinal neurons. Various subtypes of amacrine interneurons mediate a vast majority of image forming and non-image forming visual functions. The transcriptional regulation governing the development of individual amacrine cell subtypes is not well understood. One such amacrine cell subtype comprises neuronal nitric oxide synthase (nNOS/bNOS/NOS1)-expressing amacrine cells (NOACs) that regulate the release of nitric oxide (NO), a neurotransmitter with physiological and clinical implications in the retina. We have identified the LIM-homeodomain transcription factor LHX9 to be necessary for the genesis of NOACs. During retinal development, NOACs express Lhx9, and Lhx9-null retinas lack NOACs. Lhx9-null retinas also display aberrations in dendritic stratification at the inner plexiform layer. Our cell lineage-tracing studies show that Lhx9-expressing cells give rise to both the GAD65 and GAD67 expressing sub-populations of GABAergic amacrine cells. As development proceeds, Lhx9 is downregulated in the GAD65 sub-population of GABAergic cells and is largely restricted to the GAD67 sub-population of amacrine cells that NOACs are a part of. Taken together, we have uncovered Lhx9 as a new molecular marker that defines a subset of amacrine cells and show that it is necessary for the development of the NOAC subtype of amacrine cells.
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Affiliation(s)
- Revathi Balasubramanian
- Department of Ophthalmology and Flaum Eye Institute, University of Rochester, Rochester, NY, 14642, USA.,Department of Neurobiology and Anatomy, University of Rochester, Rochester, NY, 14642, USA.,Department of Ophthalmology, Columbia University, New York, NY, 10032, USA
| | - Andrew Bui
- Department of Ophthalmology and Flaum Eye Institute, University of Rochester, Rochester, NY, 14642, USA
| | - Xuhui Dong
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Lin Gan
- Department of Ophthalmology and Flaum Eye Institute, University of Rochester, Rochester, NY, 14642, USA. .,Department of Neurobiology and Anatomy, University of Rochester, Rochester, NY, 14642, USA.
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49
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Gezelius H, López-Bendito G. Thalamic neuronal specification and early circuit formation. Dev Neurobiol 2016; 77:830-843. [PMID: 27739248 DOI: 10.1002/dneu.22460] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/16/2016] [Accepted: 10/10/2016] [Indexed: 12/12/2022]
Abstract
The thalamus is a central structure of the brain, primarily recognized for the relay of incoming sensory and motor information to the cerebral cortex but also key in high order intracortical communication. It consists of glutamatergic projection neurons organized in several distinct nuclei, each having a stereotype connectivity pattern and functional roles. In the adult, these nuclei can be appreciated by architectural boundaries, although their developmental origin and specification is only recently beginning to be revealed. Here, we summarize the current knowledge on the specification of the distinct thalamic neurons and nuclei, starting from early embryonic patterning until the postnatal days when active sensory experience is initiated and the overall system connectivity is already established. We also include an overview of the guidance processes important for establishing thalamocortical connections, with emphasis on the early topographical specification. The extensively studied thalamocortical axon branching in the cortex is briefly mentioned; however, the maturation and plasticity of this connection are beyond the scope of this review. In separate chapters, additional mechanisms and/or features that influence the specification and development of thalamic neurons and their circuits are also discussed. Finally, an outlook of future directions is given. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 77: 830-843, 2017.
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Affiliation(s)
- Henrik Gezelius
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Avenida Ramón y Cajal, s/n, Sant Joan d'Alacant, Spain
| | - Guillermina López-Bendito
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Avenida Ramón y Cajal, s/n, Sant Joan d'Alacant, Spain
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Sena E, Feistel K, Durand BC. An Evolutionarily Conserved Network Mediates Development of the zona limitans intrathalamica, a Sonic Hedgehog-Secreting Caudal Forebrain Signaling Center. J Dev Biol 2016; 4:jdb4040031. [PMID: 29615594 PMCID: PMC5831802 DOI: 10.3390/jdb4040031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 09/29/2016] [Accepted: 10/13/2016] [Indexed: 12/16/2022] Open
Abstract
Recent studies revealed new insights into the development of a unique caudal forebrain-signaling center: the zona limitans intrathalamica (zli). The zli is the last brain signaling center to form and the first forebrain compartment to be established. It is the only part of the dorsal neural tube expressing the morphogen Sonic Hedgehog (Shh) whose activity participates in the survival, growth and patterning of neuronal progenitor subpopulations within the thalamic complex. Here, we review the gene regulatory network of transcription factors and cis-regulatory elements that underlies formation of a shh-expressing delimitated domain in the anterior brain. We discuss evidence that this network predates the origin of chordates. We highlight the contribution of Shh, Wnt and Notch signaling to zli development and discuss implications for the fact that the morphogen Shh relies on primary cilia for signal transduction. The network that underlies zli development also contributes to thalamus induction, and to its patterning once the zli has been set up. We present an overview of the brain malformations possibly associated with developmental defects in this gene regulatory network (GRN).
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Affiliation(s)
- Elena Sena
- Institut Curie, Université Paris Sud, INSERM U1021, CNRS UMR3347, Centre Universitaire, Bâtiment 110, F-91405 Orsay Cedex, France.
| | - Kerstin Feistel
- Institute of Zoology, University of Hohenheim, Garbenstr. 30, 70593 Stuttgart, Germany.
| | - Béatrice C Durand
- Institut Curie, Université Paris Sud, INSERM U1021, CNRS UMR3347, Centre Universitaire, Bâtiment 110, F-91405 Orsay Cedex, France.
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