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Naveed M, Smedlund K, Zhou QG, Cai W, Hill JW. Astrocyte involvement in metabolic regulation and disease. Trends Endocrinol Metab 2024:S1043-2760(24)00220-0. [PMID: 39214743 DOI: 10.1016/j.tem.2024.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/30/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024]
Abstract
Astrocytes, the predominant glial cell type in the mammalian brain, influence a wide variety of brain parameters including neuronal energy metabolism. Exciting recent studies have shown that obesity and diabetes can impact on astrocyte function. We review evidence that dysregulation of astrocytic lipid metabolism and glucose sensing contributes to dysregulation of whole-body energy balance, thermoregulation, and insulin sensitivity. In addition, we consider the overlooked topic of the sex-specific roles of astrocytes and their response to hormonal fluctuations that provide insights into sex differences in metabolic regulation. Finally, we provide an update on potential ways to manipulate astrocyte function, including genetic targeting, optogenetic and chemogenetic techniques, transplantation, and tailored exosome-based therapies, which may lead to improved treatments for metabolic disease.
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Affiliation(s)
- Muhammad Naveed
- Department of Physiology and Pharmacology, School of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA
| | - Kathryn Smedlund
- Department of Physiology and Pharmacology, School of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA
| | - Qi-Gang Zhou
- Department of Clinical Pharmacology, School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Weikang Cai
- Department of Biomedical Sciences, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY, USA
| | - Jennifer W Hill
- Department of Physiology and Pharmacology, School of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA; Center for Diabetes and Endocrine Research, University of Toledo, Toledo, OH, USA.
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2
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Kocher AA, Dutrow EV, Uebbing S, Yim KM, Rosales Larios MF, Baumgartner M, Nottoli T, Noonan JP. CpG island turnover events predict evolutionary changes in enhancer activity. Genome Biol 2024; 25:156. [PMID: 38872220 PMCID: PMC11170920 DOI: 10.1186/s13059-024-03300-z] [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: 06/01/2023] [Accepted: 06/04/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Genetic changes that modify the function of transcriptional enhancers have been linked to the evolution of biological diversity across species. Multiple studies have focused on the role of nucleotide substitutions, transposition, and insertions and deletions in altering enhancer function. CpG islands (CGIs) have recently been shown to influence enhancer activity, and here we test how their turnover across species contributes to enhancer evolution. RESULTS We integrate maps of CGIs and enhancer activity-associated histone modifications obtained from multiple tissues in nine mammalian species and find that CGI content in enhancers is strongly associated with increased histone modification levels. CGIs show widespread turnover across species and species-specific CGIs are strongly enriched for enhancers exhibiting species-specific activity across all tissues and species. Genes associated with enhancers with species-specific CGIs show concordant biases in their expression, supporting that CGI turnover contributes to gene regulatory innovation. Our results also implicate CGI turnover in the evolution of Human Gain Enhancers (HGEs), which show increased activity in human embryonic development and may have contributed to the evolution of uniquely human traits. Using a humanized mouse model, we show that a highly conserved HGE with a large CGI absent from the mouse ortholog shows increased activity at the human CGI in the humanized mouse diencephalon. CONCLUSIONS Collectively, our results point to CGI turnover as a mechanism driving gene regulatory changes potentially underlying trait evolution in mammals.
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Affiliation(s)
- Acadia A Kocher
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Division of Molecular Genetics and Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Emily V Dutrow
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Zoetis, Inc, 333 Portage St, Kalamazoo, MI, 49007, USA
| | - Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Kristina M Yim
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | | | | | - Timothy Nottoli
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
- Yale Genome Editing Center, Yale School of Medicine, New Haven, CT, 06510, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA.
- Wu Tsai Institute, Yale University, New Haven, CT, 06510, USA.
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3
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Petersen C, Mucke L, Corces MR. CHOIR improves significance-based detection of cell types and states from single-cell data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576317. [PMID: 38328105 PMCID: PMC10849522 DOI: 10.1101/2024.01.18.576317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Clustering is a critical step in the analysis of single-cell data, as it enables the discovery and characterization of putative cell types and states. However, most popular clustering tools do not subject clustering results to statistical inference testing, leading to risks of overclustering or underclustering data and often resulting in ineffective identification of cell types with widely differing prevalence. To address these challenges, we present CHOIR (clustering hierarchy optimization by iterative random forests), which applies a framework of random forest classifiers and permutation tests across a hierarchical clustering tree to statistically determine which clusters represent distinct populations. We demonstrate the enhanced performance of CHOIR through extensive benchmarking against 14 existing clustering methods across 100 simulated and 4 real single-cell RNA-seq, ATAC-seq, spatial transcriptomic, and multi-omic datasets. CHOIR can be applied to any single-cell data type and provides a flexible, scalable, and robust solution to the important challenge of identifying biologically relevant cell groupings within heterogeneous single-cell data.
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Affiliation(s)
- Cathrine Petersen
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lennart Mucke
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - M. Ryan Corces
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
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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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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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6
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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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Kerstein PC, Agreda YS, Curran BM, Ma L, Wright KM. Gbx2 controls amacrine cell dendrite stratification through Robo1/2 receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551861. [PMID: 37577554 PMCID: PMC10418232 DOI: 10.1101/2023.08.03.551861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Within the neuronal classes of the retina, amacrine cells (ACs) exhibit the greatest neuronal diversity in morphology and function. We show that the selective expression of the transcription factor Gbx2 is required for cell fate specification and dendritic stratification of an individual AC subtype in the mouse retina. We identify Robo1 and Robo2 as downstream effectors that when deleted, phenocopy the dendritic misprojections seen in Gbx2 mutants. Slit1 and Slit2, the ligands of Robo receptors, are localized to the OFF layers of the inner plexiform layer where we observe the dendritic misprojections in both Gbx2 and Robo1/2 mutants. We show that Robo receptors also are required for the proper dendritic stratification of additional AC subtypes, such as Vglut3+ ACs. These results show both that Gbx2 functions as a terminal selector in a single AC subtype and identify Slit-Robo signaling as a developmental mechanism for ON-OFF pathway segregation in the retina.
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8
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Kocher AA, Dutrow EV, Uebbing S, Yim KM, Larios MFR, Baumgartner M, Nottoli T, Noonan JP. CpG island turnover events predict evolutionary changes in enhancer activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540063. [PMID: 37214934 PMCID: PMC10197647 DOI: 10.1101/2023.05.09.540063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Genetic changes that modify the function of transcriptional enhancers have been linked to the evolution of biological diversity across species. Multiple studies have focused on the role of nucleotide substitutions, transposition, and insertions and deletions in altering enhancer function. Here we show that turnover of CpG islands (CGIs), which contribute to enhancer activation, is broadly associated with changes in enhancer activity across mammals, including humans. We integrated maps of CGIs and enhancer activity-associated histone modifications obtained from multiple tissues in nine mammalian species and found that CGI content in enhancers was strongly associated with increased histone modification levels. CGIs showed widespread turnover across species and species-specific CGIs were strongly enriched for enhancers exhibiting species-specific activity across all tissues and species we examined. Genes associated with enhancers with species-specific CGIs showed concordant biases in their expression, supporting that CGI turnover contributes to gene regulatory innovation. Our results also implicate CGI turnover in the evolution of Human Gain Enhancers (HGEs), which show increased activity in human embryonic development and may have contributed to the evolution of uniquely human traits. Using a humanized mouse model, we show that a highly conserved HGE with a large CGI absent from the mouse ortholog shows increased activity at the human CGI in the humanized mouse diencephalon. Collectively, our results point to CGI turnover as a mechanism driving gene regulatory changes potentially underlying trait evolution in mammals.
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Affiliation(s)
- Acadia A. Kocher
- Department of Genetics, Yale School of Medicine, New Haven CT 06510, USA
| | - Emily V. Dutrow
- Department of Genetics, Yale School of Medicine, New Haven CT 06510, USA
- Present address: Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven CT 06510, USA
| | - Kristina M. Yim
- Department of Genetics, Yale School of Medicine, New Haven CT 06510, USA
| | | | | | - Timothy Nottoli
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA
- Yale Genome Editing Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - James P. Noonan
- Department of Genetics, Yale School of Medicine, New Haven CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Wu Tsai Institute, Yale University, New Haven, CT 06510, USA
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9
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Huerga-Gómez I, Martini FJ, López-Bendito G. Building thalamic neuronal networks during mouse development. Front Neural Circuits 2023; 17:1098913. [PMID: 36817644 PMCID: PMC9936079 DOI: 10.3389/fncir.2023.1098913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
The thalamic nuclear complex contains excitatory projection neurons and inhibitory local neurons, the two cell types driving the main circuits in sensory nuclei. While excitatory neurons are born from progenitors that reside in the proliferative zone of the developing thalamus, inhibitory local neurons are born outside the thalamus and they migrate there during development. In addition to these cell types, which occupy most of the thalamus, there are two small thalamic regions where inhibitory neurons target extra-thalamic regions rather than neighboring neurons, the intergeniculate leaflet and the parahabenular nucleus. Like excitatory thalamic neurons, these inhibitory neurons are derived from progenitors residing in the developing thalamus. The assembly of these circuits follows fine-tuned genetic programs and it is coordinated by extrinsic factors that help the cells find their location, associate with thalamic partners, and establish connections with their corresponding extra-thalamic inputs and outputs. In this review, we bring together what is currently known about the development of the excitatory and inhibitory components of the thalamocortical sensory system, in particular focusing on the visual pathway and thalamic interneurons in mice.
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Affiliation(s)
- Irene Huerga-Gómez
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d’Alacant, Spain
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10
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van de Haar LL, Riga D, Boer JE, Garritsen O, Adolfs Y, Sieburgh TE, van Dijk RE, Watanabe K, van Kronenburg NCH, Broekhoven MH, Posthuma D, Meye FJ, Basak O, Pasterkamp RJ. Molecular signatures and cellular diversity during mouse habenula development. Cell Rep 2022; 40:111029. [PMID: 35793630 DOI: 10.1016/j.celrep.2022.111029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/18/2022] [Accepted: 06/10/2022] [Indexed: 11/27/2022] Open
Abstract
The habenula plays a key role in various motivated and pathological behaviors and is composed of molecularly distinct neuron subtypes. Despite progress in identifying mature habenula neuron subtypes, how these subtypes develop and organize into functional brain circuits remains largely unknown. Here, we performed single-cell transcriptional profiling of mouse habenular neurons at critical developmental stages, instructed by detailed three-dimensional anatomical data. Our data reveal cellular and molecular trajectories during embryonic and postnatal development, leading to different habenular subtypes. Further, based on this analysis, our work establishes the distinctive functional properties and projection target of a subtype of Cartpt+ habenula neurons. Finally, we show how comparison of single-cell transcriptional profiles and GWAS data links specific developing habenular subtypes to psychiatric disease. Together, our study begins to dissect the mechanisms underlying habenula neuron subtype-specific development and creates a framework for further interrogation of habenular development in normal and disease states.
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Affiliation(s)
- Lieke L van de Haar
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Danai Riga
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Juliska E Boer
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Oxana Garritsen
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Youri Adolfs
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Thomas E Sieburgh
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Roland E van Dijk
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Kyoko Watanabe
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, 1081 Amsterdam, the Netherlands
| | - Nicky C H van Kronenburg
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Mark H Broekhoven
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, 1081 Amsterdam, the Netherlands
| | - Frank J Meye
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Onur Basak
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands.
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11
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Direct neuronal reprogramming: Fast forward from new concepts toward therapeutic approaches. Neuron 2021; 110:366-393. [PMID: 34921778 DOI: 10.1016/j.neuron.2021.11.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/25/2021] [Accepted: 11/19/2021] [Indexed: 12/21/2022]
Abstract
Differentiated cells have long been considered fixed in their identity. However, about 20 years ago, the first direct conversion of glial cells into neurons in vitro opened the field of "direct neuronal reprogramming." Since then, neuronal reprogramming has achieved the generation of fully functional, mature neurons with remarkable efficiency, even in diseased brain environments. Beyond their clinical implications, these discoveries provided basic insights into crucial mechanisms underlying conversion of specific cell types into neurons and maintenance of neuronal identity. Here we discuss such principles, including the importance of the starter cell for shaping the outcome of neuronal reprogramming. We further highlight technical concerns for in vivo reprogramming and propose a code of conduct to avoid artifacts and pitfalls. We end by pointing out next challenges for development of less invasive cell replacement therapies for humans.
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12
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Herrero-Navarro Á, Puche-Aroca L, Moreno-Juan V, Sempere-Ferràndez A, Espinosa A, Susín R, Torres-Masjoan L, Leyva-Díaz E, Karow M, Figueres-Oñate M, López-Mascaraque L, López-Atalaya JP, Berninger B, López-Bendito G. Astrocytes and neurons share region-specific transcriptional signatures that confer regional identity to neuronal reprogramming. SCIENCE ADVANCES 2021; 7:7/15/eabe8978. [PMID: 33827819 PMCID: PMC8026135 DOI: 10.1126/sciadv.abe8978] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/18/2021] [Indexed: 05/15/2023]
Abstract
Neural cell diversity is essential to endow distinct brain regions with specific functions. During development, progenitors within these regions are characterized by specific gene expression programs, contributing to the generation of diversity in postmitotic neurons and astrocytes. While the region-specific molecular diversity of neurons and astrocytes is increasingly understood, whether these cells share region-specific programs remains unknown. Here, we show that in the neocortex and thalamus, neurons and astrocytes express shared region-specific transcriptional and epigenetic signatures. These signatures not only distinguish cells across these two brain regions but are also detected across substructures within regions, such as distinct thalamic nuclei, where clonal analysis reveals the existence of common nucleus-specific progenitors for neurons and astrocytes. Consistent with their shared molecular signature, regional specificity is maintained following astrocyte-to-neuron reprogramming. A detailed understanding of these regional-specific signatures may thus inform strategies for future cell-based brain repair.
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Affiliation(s)
- Álvaro Herrero-Navarro
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain
| | - Lorenzo Puche-Aroca
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain
| | - Verónica Moreno-Juan
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain
| | - Alejandro Sempere-Ferràndez
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain
| | - Ana Espinosa
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain
| | - Rafael Susín
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain
| | - Laia Torres-Masjoan
- Institute of Psychiatry, Psychology, and Neuroscience, Centre for Developmental Neurobiology, and MRC Centre for Neurodevelopmental Disorders, King's College London, SE1 1UL London, UK
| | - Eduardo Leyva-Díaz
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain
| | - Marisa Karow
- Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg, 91054 Erlangen, Germany
- Physiological Genomics, Biomedical Center, Ludwig Maximilians University Munich, 82152 Planegg/Munich, Germany
| | | | | | - José P López-Atalaya
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain
| | - Benedikt Berninger
- Institute of Psychiatry, Psychology, and Neuroscience, Centre for Developmental Neurobiology, and MRC Centre for Neurodevelopmental Disorders, King's College London, SE1 1UL London, UK
- Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Guillermina López-Bendito
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d'Alacant, Spain.
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13
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Wang GT, Pan HY, Lang WH, Yu YD, Hsieh CH, Kuan YS. Three-dimensional multi-gene expression maps reveal cell fate changes associated with laterality reversal of zebrafish habenula. J Neurosci Res 2021; 99:1632-1645. [PMID: 33638209 DOI: 10.1002/jnr.24806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 11/09/2022]
Abstract
The conserved bilateral habenular nuclei (HA) in vertebrate diencephalon develop into compartmentalized structures containing neurons derived from different cell lineages. Despite extensive studies demonstrated that zebrafish larval HA display distinct left-right (L-R) asymmetry in gene expression and connectivity, the spatial gene expression domains were mainly obtained from two-dimensional (2D) snapshots of colorimetric RNA in situ hybridization staining which could not properly reflect different HA neuronal lineages constructed in three-dimension (3D). Combing the tyramide-based fluorescent mRNA in situ hybridization, confocal microscopy and customized imaging processing procedures, we have created spatial distribution maps of four genes for 4-day-old zebrafish and in sibling fish whose L-R asymmetry was spontaneously reversed. 3D volumetric analyses showed that ratios of cpd2, lov, ron, and nrp1a expression in L-R reversed HA were reversed according to the parapineal positions. However, the quantitative changes of gene expression in reversed larval brains do not mirror the gene expression level in the obverse larval brains. There were a total 87.78% increase in lov+ nrp1a+ and a total 12.45% decrease in lov+ ron+ double-positive neurons when the L-R asymmetry of HA was reversed. Thus, our volumetric analyses of the 3D maps indicate that changes of HA neuronal cell fates are associated with the reversal of HA laterality. These changes likely account for the behavior changes associated with HA laterality alterations.
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Affiliation(s)
- Guo-Tzau Wang
- National Center for High-Performance Computing, Hsinchu, Taiwan R.O.C
| | - He-Yen Pan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan R.O.C
| | - Wei-Han Lang
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan R.O.C
| | - Yuan-Ding Yu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan R.O.C
| | - Chang-Huain Hsieh
- National Center for High-Performance Computing, Hsinchu, Taiwan R.O.C
| | - Yung-Shu Kuan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan R.O.C.,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan R.O.C.,Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan R.O.C.,Neuroscience Program, Academia Sinica, Taipei, Taiwan R.O.C
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14
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Cao J, O'Day DR, Pliner HA, Kingsley PD, Deng M, Daza RM, Zager MA, Aldinger KA, Blecher-Gonen R, Zhang F, Spielmann M, Palis J, Doherty D, Steemers FJ, Glass IA, Trapnell C, Shendure J. A human cell atlas of fetal gene expression. Science 2020; 370:370/6518/eaba7721. [PMID: 33184181 DOI: 10.1126/science.aba7721] [Citation(s) in RCA: 346] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 09/10/2020] [Indexed: 12/14/2022]
Abstract
The gene expression program underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of gene expression and chromatin accessibility in fetal tissues. For gene expression, we applied three-level combinatorial indexing to >110 samples representing 15 organs, ultimately profiling ~4 million single cells. We leveraged the literature and other atlases to identify and annotate hundreds of cell types and subtypes, both within and across tissues. Our analyses focused on organ-specific specializations of broadly distributed cell types (such as blood, endothelial, and epithelial), sites of fetal erythropoiesis (which notably included the adrenal gland), and integration with mouse developmental atlases (such as conserved specification of blood cells). These data represent a rich resource for the exploration of in vivo human gene expression in diverse tissues and cell types.
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Affiliation(s)
- Junyue Cao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Diana R O'Day
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Hannah A Pliner
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Paul D Kingsley
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Mei Deng
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Michael A Zager
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Center for Data Visualization, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kimberly A Aldinger
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Ronnie Blecher-Gonen
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Malte Spielmann
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - James Palis
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Dan Doherty
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Ian A Glass
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. .,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. .,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.,Howard Hughes Medical Institute, Seattle, WA, USA
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15
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Kerstein PC, Leffler J, Sivyer B, Taylor WR, Wright KM. Gbx2 Identifies Two Amacrine Cell Subtypes with Distinct Molecular, Morphological, and Physiological Properties. Cell Rep 2020; 33:108382. [PMID: 33207201 PMCID: PMC7713908 DOI: 10.1016/j.celrep.2020.108382] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/21/2020] [Accepted: 10/22/2020] [Indexed: 01/21/2023] Open
Abstract
Our understanding of nervous system function is limited by our ability to identify and manipulate neuronal subtypes within intact circuits. We show that the Gbx2CreERT2-IRES-EGFP mouse line labels two amacrine cell (AC) subtypes in the mouse retina that have distinct morphological, physiological, and molecular properties. Using a combination of RNA-seq, genetic labeling, and patch clamp recordings, we show that one subtype is GABAergic that receives excitatory input from On bipolar cells. The other population is a non-GABAergic, non-glycinergic (nGnG) AC subtype that lacks the expression of standard neurotransmitter markers. Gbx2+ nGnG ACs have smaller, asymmetric dendritic arbors that receive excitatory input from both On and Off bipolar cells. Gbx2+ nGnG ACs also exhibit spatially restricted tracer coupling to bipolar cells (BCs) through gap junctions. This study identifies a genetic tool for investigating the two distinct AC subtypes, and it provides a model for studying synaptic communication and visual circuit function. Investigations into neural circuit development and function are limited by the lack of genetic tools to label and perturb individual neuronal subtypes. Using the Gbx2CreERT2 mouse line, Kerstein et al. identify two amacrine cell subtypes in the mouse retina and explore their distinct molecular, morphological, and physiological characteristics.
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Affiliation(s)
- Patrick C Kerstein
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Joseph Leffler
- School of Optometry and Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Neuroscience Graduate Program, Oregon Health and Science University, Portland, OR 97239, USA
| | - Benjamin Sivyer
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, OR 97239, USA; Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR 97239, USA
| | - W Rowland Taylor
- School of Optometry and Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kevin M Wright
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA; Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, OR 97239, USA.
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16
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Lipiec MA, Bem J, Koziński K, Chakraborty C, Urban-Ciećko J, Zajkowski T, Dąbrowski M, Szewczyk ŁM, Toval A, Ferran JL, Nagalski A, Wiśniewska MB. TCF7L2 regulates postmitotic differentiation programmes and excitability patterns in the thalamus. Development 2020; 147:dev.190181. [PMID: 32675279 PMCID: PMC7473649 DOI: 10.1242/dev.190181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/08/2020] [Indexed: 12/14/2022]
Abstract
Neuronal phenotypes are controlled by terminal selector transcription factors in invertebrates, but only a few examples of such regulators have been provided in vertebrates. We hypothesised that TCF7L2 regulates different stages of postmitotic differentiation in the thalamus, and functions as a thalamic terminal selector. To investigate this hypothesis, we used complete and conditional knockouts of Tcf7l2 in mice. The connectivity and clustering of neurons were disrupted in the thalamo-habenular region in Tcf7l2-/- embryos. The expression of subregional thalamic and habenular transcription factors was lost and region-specific cell migration and axon guidance genes were downregulated. In mice with a postnatal Tcf7l2 knockout, the induction of genes that confer thalamic terminal electrophysiological features was impaired. Many of these genes proved to be direct targets of TCF7L2. The role of TCF7L2 in terminal selection was functionally confirmed by impaired firing modes in thalamic neurons in the mutant mice. These data corroborate the existence of master regulators in the vertebrate brain that control stage-specific genetic programmes and regional subroutines, maintain regional transcriptional network during embryonic development, and induce terminal selection postnatally.
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Affiliation(s)
- Marcin Andrzej Lipiec
- Centre of New Technologies, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland.,Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Joanna Bem
- Centre of New Technologies, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Kamil Koziński
- Centre of New Technologies, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Chaitali Chakraborty
- Centre of New Technologies, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | | | - Tomasz Zajkowski
- Centre of New Technologies, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Michał Dąbrowski
- Nencki Institute of Experimental Biology, Pasteur 3, 02-093 Warsaw, Poland
| | | | - Angel Toval
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia and IMIB-Arrixaca Institute, Campus de la Salud, 30120 El Palmar, Murcia, Spain
| | - José Luis Ferran
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia and IMIB-Arrixaca Institute, Campus de la Salud, 30120 El Palmar, Murcia, Spain
| | - Andrzej Nagalski
- Centre of New Technologies, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
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17
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Wang Y, Hui J, Li R, Fu Q, Yang P, Xiao Y, Hui J. GBX2, as a tumor promoter in lung adenocarcinoma, enhances cells viability, invasion and migration by regulating the AKT/ERK signaling pathway. J Gene Med 2019; 22:e3147. [PMID: 31758726 DOI: 10.1002/jgm.3147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/07/2019] [Accepted: 11/20/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Increasing evidence shows that gastrulation brain homeobox 2 (GBX2) is involved in multiple cancers. However, whether GBX2 has an effect on the lung adenocarcinoma remains unclear. In the present study, we investigated the functions of GBX2 on lung adenocarcinoma and explored the underlying mechanism. METHODS Public data were obtained from the TCGA (https://cancergenome.nih.gov) and Oncomine (http://www.oncomine.org) databases. GBX2 expression and its prognostic value were analyzed by bioinformatics methods. Relative mRNA and protein expression levels of GBX2 in lung adenocarcinoma cell lines were evaluated via a quantitative reverse transcriptase polymerase chain reaction and western blotting. Lung adenocarcinoma cell lines LTEP-a-2 and A549, respectively, were selected for gain and loss function of GBX2 assays. Cell viability was detected by CCK8 and clone formation experiments. Cell invasion and migration were assessed by Transwell assays. The effect of GBX2 on the AKT/extracellular signal regulated kinase (ERK) pathway was tested by western blotting. RESULTS Compared to adjacent tissues, GBX2 expression was up-regulated in lung adenocarcinoma tissues. High expression of GBX2 led to a poor survival and could be seen as an independent predictor for lung adenocarcinoma patients. Furthermore, down-regulation of GBX2 notably restrained the viability, invasion and migration abilities of A549 cells, whereas up-regulation of GBX2 in LTEP-a-2 cells presented the opposite outcomes. Furthermore, western blot indicated that down-regulation of GBX2 decreases the protein levels of phosphorylated (p)-AKT and p-ERK in A549 cells, whereas up-regulation of GBX2 shows the opposite effects in LTEP-a-2 cells. CONCLUSIONS The results of present study indicate that GBX2 acts a cancer-promoting role to accelerate cell proliferation, invasion and migration partly by modulation of the AKT/ERK pathway in lung adenocarcinoma.
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Affiliation(s)
- Yuanchun Wang
- Department of Oncology, The Affiliated Hospital of Shaanxi University of Traditional Chinese Medicine, Xianyang, Shaanxi, China
| | - Jianping Hui
- Department of Gastroenterology, The Affiliated Hospital of Shaanxi University of Traditional Chinese Medicine, Xianyang, Shaanxi, China
| | - Renting Li
- Department of Oncology, The Affiliated Hospital of Shaanxi University of Traditional Chinese Medicine, Xianyang, Shaanxi, China
| | - Qiaoqiao Fu
- College of Acumox and Tuina, Shaanxi University of Traditional Chinese Medicine, Xi'an, Shaanxi, China
| | - Pu Yang
- College of Acumox and Tuina, Shaanxi University of Traditional Chinese Medicine, Xi'an, Shaanxi, China
| | - Yingchun Xiao
- College of Acumox and Tuina, Shaanxi University of Traditional Chinese Medicine, Xi'an, Shaanxi, China
| | - Jianrong Hui
- College of Acumox and Tuina, Shaanxi University of Traditional Chinese Medicine, Xi'an, Shaanxi, China
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18
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Self-organizing neuruloids model developmental aspects of Huntington's disease in the ectodermal compartment. Nat Biotechnol 2019; 37:1198-1208. [PMID: 31501559 DOI: 10.1038/s41587-019-0237-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 07/23/2019] [Indexed: 12/14/2022]
Abstract
Harnessing the potential of human embryonic stem cells to mimic normal and aberrant development with standardized models is a pressing challenge. Here we use micropattern technology to recapitulate early human neurulation in large numbers of nearly identical structures called neuruloids. Dual-SMAD inhibition followed by bone morphogenic protein 4 stimulation induced self-organization of neuruloids harboring neural progenitors, neural crest, sensory placode and epidermis. Single-cell transcriptomics unveiled the precise identities and timing of fate specification. Investigation of the molecular mechanism of neuruloid self-organization revealed a pulse of pSMAD1 at the edge that induced epidermis, whose juxtaposition to central neural fates specifies neural crest and placodes, modulated by fibroblast growth factor and Wnt. Neuruloids provide a unique opportunity to study the developmental aspects of human diseases. Using isogenic Huntington's disease human embryonic stem cells and deep neural network analysis, we show how specific phenotypic signatures arise in our model of early human development as a consequence of mutant huntingtin protein, outlining an approach for phenotypic drug screening.
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19
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Nakagawa Y. Development of the thalamus: From early patterning to regulation of cortical functions. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2019; 8:e345. [PMID: 31034163 DOI: 10.1002/wdev.345] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 02/06/2023]
Abstract
The thalamus is a brain structure of the vertebrate diencephalon that plays a central role in regulating diverse functions of the cerebral cortex. In traditional view of vertebrate neuroanatomy, the thalamus includes three regions, dorsal thalamus, ventral thalamus, and epithalamus. Recent molecular embryological studies have redefined the thalamus and the associated axial nomenclature of the diencephalon in the context of forebrain patterning. This new view has provided a useful conceptual framework for studies on molecular mechanisms of patterning, neurogenesis and fate specification in the thalamus as well as the guidance mechanisms for thalamocortical axons. Additionally, the availability of genetic tools in mice has led to important findings on how thalamic development is linked to the development of other brain regions, particularly the cerebral cortex. This article will give an overview of the organization of the embryonic thalamus and how progenitor cells in the thalamus generate neurons that are organized into discrete nuclei. I will then discuss how thalamic development is orchestrated with the development of the cerebral cortex and other brain regions. This article is categorized under: Nervous System Development > Vertebrates: Regional Development Nervous System Development > Vertebrates: General Principles.
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Affiliation(s)
- Yasushi Nakagawa
- Department of Neuroscience, University of Minnesota Medical School, Minneapolis, Minnesota
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20
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Alzu’bi A, Homman-Ludiye J, Bourne JA, Clowry GJ. Thalamocortical Afferents Innervate the Cortical Subplate much Earlier in Development in Primate than in Rodent. Cereb Cortex 2019; 29:1706-1718. [PMID: 30668846 PMCID: PMC6418397 DOI: 10.1093/cercor/bhy327] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/16/2018] [Accepted: 11/29/2018] [Indexed: 12/21/2022] Open
Abstract
The current model, based on rodent data, proposes that thalamocortical afferents (TCA) innervate the subplate towards the end of cortical neurogenesis. This implies that the laminar identity of cortical neurons is specified by intrinsic instructions rather than information of thalamic origin. In order to determine whether this mechanism is conserved in the primates, we examined the growth of thalamocortical (TCA) and corticofugal afferents in early human and monkey fetal development. In the human, TCA, identified by secretagogin, calbindin, and ROBO1 immunoreactivity, were observed in the internal capsule of the ventral telencephalon as early as 7-7.5 PCW, crossing the pallial/subpallial boundary (PSB) by 8 PCW before the calretinin immunoreactive corticofugal fibers do. Furthermore, TCA were observed to be passing through the intermediate zone and innervating the presubplate of the dorsolateral cortex, and already by 10-12 PCW TCAs were occupying much of the cortex. Observations at equivalent stages in the marmoset confirmed that this pattern is conserved across primates. Therefore, our results demonstrate that in primates, TCAs innervate the cortical presubplate at earlier stages than previously demonstrated by acetylcholinesterase histochemistry, suggesting that pioneer thalamic afferents may contribute to early cortical circuitry that can participate in defining cortical neuron phenotypes.
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Affiliation(s)
- Ayman Alzu’bi
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid, Jordan
| | - Jihane Homman-Ludiye
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - James A Bourne
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Gavin J Clowry
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
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21
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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: 18] [Impact Index Per Article: 3.6] [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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22
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Fang Y, Yuan Y, Zhang LL, Lu JW, Feng JF, Hu SN. Downregulated GBX2 gene suppresses proliferation, invasion and angiogenesis of breast cancer cells through inhibiting the Wnt/β-catenin signaling pathway. Cancer Biomark 2019; 23:405-418. [PMID: 30223390 DOI: 10.3233/cbm-181466] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Gastrulation brain homeobox 2 (GBX2), a gene involved in mid/hindbrain region, has been revealed as one of the oncogene associated with certain cancers, as an example being prostate cancer. However, despite years of worldwide research, the underlying mechanism of GBX2 as well as its significance in breast cancer still remains unclear. Therefore, the present study evaluates the abilities of GBX gene silencing providing for the proliferation, invasion and angiogenesis of breast cancer cells by way of the Wnt/β-catenin signaling pathway. METHODS We employed a microarray analysis to screen out differentially expressed genes relative to breast cancer. Moreover, we retrieved GBX2 expression in breast cancer to find out the relationship between GBX2 expression and prognosis in breast cancer. We performed RT-qPCR to screen out cell lines with high GBX2 expression. Subsequently, both RT-qPCR and western blot analysis were employed so as to measure the combination of the mRNA and protein expressions of GBX2, β-catenin, vascular endothelial growth factor (VEGF), matrix metalloproteinase (MMP)-2, and MMP-9. The effect that GBX2 gene silencing and the Wnt/β-catenin signaling pathway had on cell proliferation, invasion, angiogenesis, and tumorigenic ability were evaluated. RESULTS GBX2 gene was also identified having played a role in breast cancer development due to its association with the Wnt/β-catenin signaling pathway. GBX2 gene silencing was found to be an inhibitor for the mRNA and protein expressions regulating β-catenin, VEGF, MMP-2, and MMP-9. Cell proliferation, invasion, angiogenesis, as well as tumorigenic ability in breast cancer were investigated and found to have been suppressed by the GBX2 gene silencing or inactivation of the Wnt/β-catenin signaling pathway. CONCLUSION The study has made an attempt to provide evidence to the idea that GBX2 gene silencing has an inhibition effect on the proliferation, invasion and angiogenesis of the breast cancer cells by inhibiting the activation of the Wnt/β-catenin signaling pathway.
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Developmental Requirement of Homeoprotein Otx2 for Specific Habenulo-Interpeduncular Subcircuits. J Neurosci 2018; 39:1005-1019. [PMID: 30593496 DOI: 10.1523/jneurosci.1818-18.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/06/2018] [Accepted: 12/16/2018] [Indexed: 01/11/2023] Open
Abstract
The habenulo-interpeduncular system (HIPS) is now recognized as a critical circuit modulating aversion, reward, and social behavior. There is evidence that dysfunction of this circuit leads to psychiatric disorders. Because psychiatric diseases may originate in developmental abnormalities, it is crucial to investigate the developmental mechanisms controlling the formation of the HIPS. Thus far, this issue has been the focus of limited studies. Here, we explored the developmental processes underlying the formation of the medial habenula (MHb) and its unique output, the interpeduncular nucleus (IPN), in mice independently of their gender. We report that the Otx2 homeobox gene is essential for the proper development of both structures. We show that MHb and IPN neurons require Otx2 at different developmental stages and, in both cases, Otx2 deletion leads to disruption of HIPS subcircuits. Finally, we show that Otx2+ neurons tend to be preferentially interconnected. This study reveals that synaptically connected components of the HIPS, despite radically different developmental strategies, share high sensitivity to Otx2 expression.SIGNIFICANCE STATEMENT Brain reward circuits are highly complex and still poorly understood. In particular, it is important to understand how these circuits form as many psychiatric diseases may arise from their abnormal development. This work shows that Otx2, a critical evolutionary conserved gene implicated in brain development and a predisposing factor for psychiatric diseases, is required for the formation of the habenulo-interpeduncular system (HIPS), an important component of the reward circuit. Otx2 deletion affects multiple processes such as proliferation and migration of HIPS neurons. Furthermore, neurons expressing Otx2 are preferentially interconnected. Therefore, Otx2 expression may represent a code that specifies the connectivity of functional subunits of the HIPS. Importantly, the Otx2 conditional knock-out animals used in this study might represent a new genetic model of psychiatric diseases.
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Sevane N, Martínez R, Bruford MW. Genome-wide differential DNA methylation in tropically adapted Creole cattle and their Iberian ancestors. Anim Genet 2018; 50:15-26. [DOI: 10.1111/age.12731] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2018] [Indexed: 12/15/2022]
Affiliation(s)
- N. Sevane
- School of Biosciences; Cardiff University; Cathays Park Cardiff CF10 3AX UK
| | - R. Martínez
- Corporación Colombiana De Investigación Agropecuaria (Corpoica); Centro de Investigaciones Tibaitatá; km 14 via Bogotá 250047 Mosquera Colombia
| | - M. W. Bruford
- School of Biosciences; Cardiff University; Cathays Park Cardiff CF10 3AX UK
- Sustainable Places Research Institute; Cardiff University; Cardiff CF10 3BA UK
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Wang Z, Nakayama Y, Tsuda S, Yamasu K. The role of gastrulation brain homeobox 2 (gbx2) in the development of the ventral telencephalon in zebrafish embryos. Differentiation 2017; 99:28-40. [PMID: 29289755 DOI: 10.1016/j.diff.2017.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 02/03/2023]
Abstract
During vertebrate brain development, the gastrulation brain homeobox 2 gene (gbx2) is expressed in the forebrain, but its precise roles are still unknown. In this study, we addressed this issue in zebrafish (Danio rerio) first by carefully examining gbx2 expression in the developing forebrain. We showed that gbx2 was expressed in the telencephalon during late somitogenesis, from 18h post-fertilization (hpf) to 24 hpf, and in the thalamic primordium after 26 hpf. In contrast, another gbx gene, gbx1, was expressed in the anterior-most ventral telencephalon after 36 hpf. Thus, the expression patterns of these two gbx genes did not overlap, arguing against their redundant function in the forebrain. Two-color fluorescence in situ hybridization (FISH) showed close relationships between the telencephalic expression of gbx2 and other forebrain-forming genes, suggesting that their interactions contribute to the regionalization of the telencephalon. FISH further revealed that gbx2 is expressed in the ventricular region of the telencephalon. By using transgenic fish in which gbx2 can be induced by heat shock, we found that gbx2 induction at 16 hpf repressed the expression of emx3, dlx2a, and six3b in the ventral telencephalon. Among secreted factor genes, bmp2b and wnt1 were repressed in the vicinity of the gbx2 domain in the telencephalon. The expression of forebrain-forming genes was examined in mutant embryos lacking gbx2, showing emx3 and dlx2a to be upregulated in the subpallium at 24 hpf. Taken together, these findings indicate that gbx2 contributes to the development of the subpallium through its repressive activities against other telencephalon-forming genes. We further showed that inhibiting FGF signaling and activating Wnt signaling repressed gbx2 and affected the regionalization of the telencephalon, supporting a functional link between gbx2, intracellular signaling, and telencephalon development.
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Affiliation(s)
- Zhe Wang
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Yukiko Nakayama
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Sachiko Tsuda
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan; Saitama University Brain Science Institute, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan; Research and Development Bureau, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Kyo Yamasu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan; Saitama University Brain Science Institute, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan.
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Diao Y, Chen Y, Zhang P, Cui L, Zhang J. Molecular guidance cues in the development of visual pathway. Protein Cell 2017; 9:909-929. [PMID: 29181831 PMCID: PMC6208478 DOI: 10.1007/s13238-017-0490-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/30/2017] [Indexed: 01/23/2023] Open
Abstract
70%–80% of our sensory input comes from vision. Light hit the retina at the back of our eyes and the visual information is relayed into the dorsal lateral geniculate nuclei (dLGN) and primary visual cortex (V1) thereafter, constituting the image-forming visual circuit. Molecular cues are one of the key factors to guide the wiring and refinement of the image-forming visual circuit during pre- and post-embryonic stages. Distinct molecular cues are involved in different developmental stages and nucleus, suggesting diverse guidance mechanisms. In this review, we summarize molecular guidance cues throughout the image-forming visual circuit, including chiasm determination, eye-specific segregation and refinement in the dLGN, and at last the reciprocal connections between the dLGN and V1.
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Affiliation(s)
- Yupu Diao
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Yuqing Chen
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Peijun Zhang
- Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Liyuan Cui
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Jiayi Zhang
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, 200032, China.
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Roberson S, Halpern ME. Development and connectivity of the habenular nuclei. Semin Cell Dev Biol 2017; 78:107-115. [PMID: 29107475 PMCID: PMC5920772 DOI: 10.1016/j.semcdb.2017.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 10/09/2017] [Indexed: 10/17/2022]
Abstract
Accumulating evidence has reinforced that the habenular region of the vertebrate dorsal forebrain is an essential integrating center, and a region strongly implicated in neurological disorders and addiction. Despite the important and diverse neuromodulatory roles the habenular nuclei play, their development has been understudied. The emphasis of this review is on the dorsal habenular nuclei of zebrafish, homologous to the medial nuclei of mammals, as recent work has revealed new information about the signaling pathways that regulate their formation. Additionally, the zebrafish dorsal habenulae have become a valuable model for probing how left-right differences are established in a vertebrate brain. Sonic hedgehog, fibroblast growth factors and Wingless-INT proteins are all involved in the generation of progenitor cells and ultimately, along with Notch signaling, influence habenular neurogenesis and left-right asymmetry. Intriguingly, a genetic network has emerged that leads to the differentiation of dorsal habenular neurons and, through localized chemokine signaling, directs the posterior outgrowth of their newly emerging axons towards their postsynaptic target, the midbrain interpeduncular nucleus.
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Affiliation(s)
- Sara Roberson
- Carnegie Institution for Science, Department of Embryology, 3520 San Martin Drive Baltimore, MD 21218, USA; Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Marnie E Halpern
- Carnegie Institution for Science, Department of Embryology, 3520 San Martin Drive Baltimore, MD 21218, USA; Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
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Gezelius H, Moreno-Juan V, Mezzera C, Thakurela S, Rodríguez-Malmierca LM, Pistolic J, Benes V, Tiwari VK, López-Bendito G. Genetic Labeling of Nuclei-Specific Thalamocortical Neurons Reveals Putative Sensory-Modality Specific Genes. Cereb Cortex 2017; 27:5054-5069. [PMID: 27655933 PMCID: PMC7610997 DOI: 10.1093/cercor/bhw290] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/22/2016] [Indexed: 11/14/2022] Open
Abstract
The thalamus is a central brain structure with topographically ordered long-range axonal projections that convey sensory information to the cortex via distinct nuclei. Although there is an increasing knowledge about genes important for thalamocortical (TC) development, the identification of genetic landmarks of the distinct thalamic nuclei during the embryonic development has not been addressed systematically. Indeed, a more comprehensive understanding of how the axons from the individual nuclei find their way and connect to their corresponding cortical area is called for. Here, we used a genetic dual labeling strategy in mice to purify distinct principal sensory thalamic neurons. Subsequent genome-wide transcriptome profiling revealed genes specifically expressed in each nucleus during embryonic development. Analysis of regulatory regions of the identified genes revealed key transcription factors and networks that likely underlie the specification of individual sensory-modality TC connections. Finally, the importance of correct axon targeting for the specific sensory-modality population transcriptome was evidenced in a Sema6A mutant, in which visual TC axons are derailed at embryonic life. In sum, our data determined the developmental transcriptional profile of the TC neurons that will eventually support sensory processing.
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Affiliation(s)
- Henrik Gezelius
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d’Alacant, 03550, Spain
| | - Verónica Moreno-Juan
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d’Alacant, 03550, Spain
| | - Cecilia Mezzera
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d’Alacant, 03550, Spain
- Present address: Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, 1400-038 Lisbon, Portugal
| | - Sudhir Thakurela
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128 Mainz, Germany
| | - Luis Miguel Rodríguez-Malmierca
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d’Alacant, 03550, Spain
| | | | - Vladimir Benes
- EMBL, GeneCore, Meyerhofstr. 1, D-69117 Heidelberg, Germany
| | - Vijay K. Tiwari
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128 Mainz, Germany
| | - Guillermina López-Bendito
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), Sant Joan d’Alacant, 03550, Spain
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Boutet A. The evolution of asymmetric photosensitive structures in metazoans and the Nodal connection. Mech Dev 2017; 147:49-60. [PMID: 28986126 DOI: 10.1016/j.mod.2017.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 07/26/2017] [Accepted: 09/25/2017] [Indexed: 01/12/2023]
Abstract
Asymmetries are observed in a great number of taxa in metazoans. More particularly, functional lateralization and neuroanatomical asymmetries within the central nervous system have been a matter of intense research for at least two hundred years. While asymmetries of some paired structures/organs (e.g. eyes, ears, kidneys, legs, arms) constitute random deviations from a pure bilateral symmetry, brain asymmetries such as those observed in the cortex and epithalamus are directional. This means that molecular and anatomical features located on one side of a given structure are observed in most individuals. For instance, in humans, the neuronal tract connecting the language areas is enlarged in the left hemisphere. When asymmetries are fixed, their molecular mechanisms can be studied using mutants displaying different phenotypes: left or right isomerism of the structure, reversed asymmetry or random asymmetry. Our understanding of asymmetry in the nervous system has been widely enriched thanks to the characterization of mutants affecting epithalamus asymmetry. Furthermore, two decades ago, pioneering studies revealed that a specific morphogen, Nodal, active only on one side of the embryo during development is an important molecule in asymmetry patterning. In this review, I have gathered important data bringing insight into the origin and evolution of epithalamus asymmetry and the role of Nodal in metazoans. After a short introduction on brain asymmetries (chapter I), I secondly focus on the molecular and anatomical characteristics of the epithalamus in vertebrates and explore some functional aspects such as its photosensitive ability related to the pineal complex (chapter II). Third, I discuss homology relationship of the parapineal organ among vertebrates (chapter III). Fourth, I discuss the possible origin of the epithalamus, presenting cells displaying photosensitive properties and/or asymmetry in the anterior part of the body in non-vertebrates (chapter IV). Finally, I report Nodal signaling expression data and functional experiments performed in different metazoan groups (chapter V).
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Affiliation(s)
- Agnès Boutet
- Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 8227, Laboratoire de Biologie Intégrative des Modèles Marins, Station Biologique, F-29688 Roscoff, France.
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30
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Comprehensive analysis of target genes in zebrafish embryos reveals gbx2 involvement in neurogenesis. Dev Biol 2017; 430:237-248. [DOI: 10.1016/j.ydbio.2017.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 11/21/2022]
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The molecular mechanisms controlling morphogenesis and wiring of the habenula. Pharmacol Biochem Behav 2017; 162:29-37. [PMID: 28843424 DOI: 10.1016/j.pbb.2017.08.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 07/07/2017] [Accepted: 08/21/2017] [Indexed: 11/22/2022]
Abstract
The habenula is an evolutionarily conserved brain region comprising bilaterally paired nuclei that plays a key role in processing reward information and mediating aversive responses to negative stimuli. An important aspect underlying habenula function is relaying information between forebrain and mid- and hindbrain areas. This is mediated by its complex organization into multiple subdomains and corresponding complexity in circuit organization. Additionally, in many species habenular nuclei display left-right differences at the anatomical and functional level. In order to ensure proper functional organization of habenular circuitry, sophisticated molecular programs control the morphogenesis and wiring of the habenula during development. Knowledge of how these mechanisms shape the habenula is crucial for obtaining a complete understanding of this brain region and can provide invaluable tools to study habenula evolution and function. In this review we will discuss how these molecular mechanisms pattern the early embryonic nervous system and control the formation of the habenula, how they shape its asymmetric organization, and how these mechanisms ensure proper wiring of the habenular circuit. Finally, we will address unexplored aspects of habenula development and how these may direct future research.
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Lee M, Yoon J, Song H, Lee B, Lam DT, Yoon J, Baek K, Clevers H, Jeong Y. Tcf7l2 plays crucial roles in forebrain development through regulation of thalamic and habenular neuron identity and connectivity. Dev Biol 2017; 424:62-76. [DOI: 10.1016/j.ydbio.2017.02.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/16/2017] [Accepted: 02/16/2017] [Indexed: 11/28/2022]
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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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