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Pal A, Noble MA, Morales M, Pal R, Baumgartner M, Yang JW, Yim KM, Uebbing S, Noonan JP. Resolving the three-dimensional interactome of Human Accelerated Regions during human and chimpanzee neurodevelopment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600691. [PMID: 39091792 PMCID: PMC11291010 DOI: 10.1101/2024.06.25.600691] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Human Accelerated Regions (HARs) are highly conserved across species but exhibit a significant excess of human-specific sequence changes, suggesting they may have gained novel functions in human evolution. HARs include transcriptional enhancers with human-specific activity and have been implicated in the evolution of the human brain. However, our understanding of how HARs contributed to uniquely human features of the brain is hindered by a lack of insight into the genes and pathways that HARs regulate. It is unclear whether HARs acted by altering the expression of gene targets conserved between HARs and their chimpanzee orthologs or by gaining new gene targets in human, a mechanism termed enhancer hijacking. We generated a high-resolution map of chromatin interactions for 1,590 HARs and their orthologs in human and chimpanzee neural stem cells (NSCs) to comprehensively identify gene targets in both species. HARs and their chimpanzee orthologs targeted a conserved set of 2,963 genes enriched for neurodevelopmental processes including neurogenesis and synaptic transmission. Changes in HAR enhancer activity were correlated with changes in conserved gene target expression. Conserved targets were enriched among genes differentially expressed between human and chimpanzee NSCs or between human and non-human primate developing and adult brain. Species-specific HAR gene targets did not converge on known biological functions and were not significantly enriched among differentially expressed genes, suggesting that HARs did not alter gene expression via enhancer hijacking. HAR gene targets, including differentially expressed targets, also showed cell type-specific expression patterns in the developing human brain, including outer radial glia, which are hypothesized to contribute to human cortical expansion. Our findings support that HARs influenced human brain evolution by altering the expression of conserved gene targets and provide the means to functionally link HARs with novel human brain features.
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Rodríguez-Urgellés E, Casas-Torremocha D, Sancho-Balsells A, Ballasch I, García-García E, Miquel-Rio L, Manasanch A, Del Castillo I, Chen W, Pupak A, Brito V, Tornero D, Rodríguez MJ, Bortolozzi A, Sanchez-Vives MV, Giralt A, Alberch J. Thalamic Foxp2 regulates output connectivity and sensory-motor impairments in a model of Huntington's Disease. Cell Mol Life Sci 2023; 80:367. [PMID: 37987826 PMCID: PMC10663254 DOI: 10.1007/s00018-023-05015-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: 05/04/2023] [Revised: 08/25/2023] [Accepted: 10/07/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Huntington's Disease (HD) is a disorder that affects body movements. Altered glutamatergic innervation of the striatum is a major hallmark of the disease. Approximately 30% of those glutamatergic inputs come from thalamic nuclei. Foxp2 is a transcription factor involved in cell differentiation and reported low in patients with HD. However, the role of the Foxp2 in the thalamus in HD remains unexplored. METHODS We used two different mouse models of HD, the R6/1 and the HdhQ111 mice, to demonstrate a consistent thalamic Foxp2 reduction in the context of HD. We used in vivo electrophysiological recordings, microdialysis in behaving mice and rabies virus-based monosynaptic tracing to study thalamo-striatal and thalamo-cortical synaptic connectivity in R6/1 mice. Micro-structural synaptic plasticity was also evaluated in the striatum and cortex of R6/1 mice. We over-expressed Foxp2 in the thalamus of R6/1 mice or reduced Foxp2 in the thalamus of wild type mice to evaluate its role in sensory and motor skills deficiencies, as well as thalamo-striatal and thalamo-cortical connectivity in such mouse models. RESULTS Here, we demonstrate in a HD mouse model a clear and early thalamo-striatal aberrant connectivity associated with a reduction of thalamic Foxp2 levels. Recovering thalamic Foxp2 levels in the mouse rescued motor coordination and sensory skills concomitant with an amelioration of neuropathological features and with a repair of the structural and functional connectivity through a restoration of neurotransmitter release. In addition, reduction of thalamic Foxp2 levels in wild type mice induced HD-like phenotypes. CONCLUSIONS In conclusion, we show that a novel identified thalamic Foxp2 dysregulation alters basal ganglia circuits implicated in the pathophysiology of HD.
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Affiliation(s)
- Ened Rodríguez-Urgellés
- Facultat de Medicina, Departament de Biomedicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | | | - Anna Sancho-Balsells
- Facultat de Medicina, Departament de Biomedicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Iván Ballasch
- Facultat de Medicina, Departament de Biomedicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Esther García-García
- Facultat de Medicina, Departament de Biomedicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Lluis Miquel-Rio
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036, Barcelona, Spain
- Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029, Madrid, Spain
| | - Arnau Manasanch
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Ignacio Del Castillo
- Facultat de Medicina, Departament de Biomedicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Wanqi Chen
- Facultat de Medicina, Departament de Biomedicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Anika Pupak
- Facultat de Medicina, Departament de Biomedicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Veronica Brito
- Facultat de Medicina, Departament de Biomedicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Daniel Tornero
- Facultat de Medicina, Departament de Biomedicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Faculty of Medicine and Health Science, Production and Validation Center of Advanced Therapies (Creatio), University of Barcelona, 08036, Barcelona, Spain
| | - Manuel J Rodríguez
- Facultat de Medicina, Departament de Biomedicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Analia Bortolozzi
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036, Barcelona, Spain
- Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029, Madrid, Spain
| | - Maria V Sanchez-Vives
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Albert Giralt
- Facultat de Medicina, Departament de Biomedicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain.
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain.
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
- Faculty of Medicine and Health Science, Production and Validation Center of Advanced Therapies (Creatio), University of Barcelona, 08036, Barcelona, Spain.
| | - Jordi Alberch
- Facultat de Medicina, Departament de Biomedicina, Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Spain.
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain.
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
- Faculty of Medicine and Health Science, Production and Validation Center of Advanced Therapies (Creatio), University of Barcelona, 08036, Barcelona, Spain.
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BMP signaling alters aquaporin-4 expression in the mouse cerebral cortex. Sci Rep 2021; 11:10540. [PMID: 34006980 PMCID: PMC8131757 DOI: 10.1038/s41598-021-89997-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/20/2021] [Indexed: 11/21/2022] Open
Abstract
Aquaporin-4 (AQP4) is a predominant water channel expressed in astrocytes in the mammalian brain. AQP4 is crucial for the regulation of homeostatic water movement across the blood–brain barrier (BBB). Although the molecular mechanisms regulating AQP4 levels in the cerebral cortex under pathological conditions have been intensively investigated, those under normal physiological conditions are not fully understood. Here we demonstrate that AQP4 is selectively expressed in astrocytes in the mouse cerebral cortex during development. BMP signaling was preferentially activated in AQP4-positive astrocytes. Furthermore, activation of BMP signaling by in utero electroporation markedly increased AQP4 levels in the cerebral cortex, and inhibition of BMP signaling strongly suppressed them. These results indicate that BMP signaling alters AQP4 levels in the mouse cerebral cortex during development.
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4
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Development of Auditory Cortex Circuits. J Assoc Res Otolaryngol 2021; 22:237-259. [PMID: 33909161 DOI: 10.1007/s10162-021-00794-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/03/2021] [Indexed: 02/03/2023] Open
Abstract
The ability to process and perceive sensory stimuli is an essential function for animals. Among the sensory modalities, audition is crucial for communication, pleasure, care for the young, and perceiving threats. The auditory cortex (ACtx) is a key sound processing region that combines ascending signals from the auditory periphery and inputs from other sensory and non-sensory regions. The development of ACtx is a protracted process starting prenatally and requires the complex interplay of molecular programs, spontaneous activity, and sensory experience. Here, we review the development of thalamic and cortical auditory circuits during pre- and early post-natal periods.
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Glial cell type-specific gene expression in the mouse cerebrum using the piggyBac system and in utero electroporation. Sci Rep 2021; 11:4864. [PMID: 33649472 PMCID: PMC7921133 DOI: 10.1038/s41598-021-84210-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Glial cells such as astrocytes and oligodendrocytes play crucial roles in the central nervous system. To investigate the molecular mechanisms underlying the development and the biological functions of glial cells, simple and rapid techniques for glial cell-specific genetic manipulation in the mouse cerebrum would be valuable. Here we uncovered that the Gfa2 promoter is suitable for selective gene expression in astrocytes when used with the piggyBac system and in utero electroporation. In contrast, the Blbp promoter, which has been used to induce astrocyte-specific gene expression in transgenic mice, did not result in astrocyte-specific gene expression. We also identified the Plp1 and Mbp promoters could be used with the piggyBac system and in utero electroporation to induce selective gene expression in oligodendrocytes. Furthermore, using our technique, neuron-astrocyte or neuron-oligodendrocyte interactions can be visualized by labeling neurons, astrocytes and oligodendrocytes differentially. Our study provides a fundamental basis for specific transgene expression in astrocytes and/or oligodendrocytes in the mouse cerebrum.
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6
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Co M, Anderson AG, Konopka G. FOXP transcription factors in vertebrate brain development, function, and disorders. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2020; 9:e375. [PMID: 31999079 PMCID: PMC8286808 DOI: 10.1002/wdev.375] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/17/2019] [Accepted: 01/08/2020] [Indexed: 12/22/2022]
Abstract
FOXP transcription factors are an evolutionarily ancient protein subfamily coordinating the development of several organ systems in the vertebrate body. Association of their genes with neurodevelopmental disorders has sparked particular interest in their expression patterns and functions in the brain. Here, FOXP1, FOXP2, and FOXP4 are expressed in distinct cell type-specific spatiotemporal patterns in multiple regions, including the cortex, hippocampus, amygdala, basal ganglia, thalamus, and cerebellum. These varied sites and timepoints of expression have complicated efforts to link FOXP1 and FOXP2 mutations to their respective developmental disorders, the former affecting global neural functions and the latter specifically affecting speech and language. However, the use of animal models, particularly those with brain region- and cell type-specific manipulations, has greatly advanced our understanding of how FOXP expression patterns could underlie disorder-related phenotypes. While many questions remain regarding FOXP expression and function in the brain, studies to date have illuminated the roles of these transcription factors in vertebrate brain development and have greatly informed our understanding of human development and disorders. This article is categorized under: Nervous System Development > Vertebrates: General Principles Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics Nervous System Development > Vertebrates: Regional Development.
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Affiliation(s)
- Marissa Co
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon
| | - Ashley G Anderson
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas
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7
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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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8
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FGF Signaling Directs the Cell Fate Switch from Neurons to Astrocytes in the Developing Mouse Cerebral Cortex. J Neurosci 2019; 39:6081-6094. [PMID: 31175212 DOI: 10.1523/jneurosci.2195-18.2019] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 05/09/2019] [Accepted: 05/17/2019] [Indexed: 11/21/2022] Open
Abstract
During mammalian neocortical development, neural precursor cells generate neurons first and astrocytes later. The cell fate switch from neurons to astrocytes is a key process generating proper numbers of neurons and astrocytes. Although the intracellular mechanisms regulating this cell fate switch have been well characterized, extracellular regulators are still largely unknown. Here, we uncovered that fibroblast growth factor (FGF) regulates the cell fate switch from neurons to astrocytes in the developing cerebral cortex using mice of both sexes. We found that the FGF signaling pathway is activated in radial glial cells of the ventricular zone at time points corresponding to the switch in cell fate. Our loss- and gain-of-function studies using in utero electroporation indicate that activation of FGF signaling is necessary and sufficient to change cell fates from neurons to astrocytes. We further found that the FGF-induced neuron-astrocyte cell fate switch is mediated by the MAPK pathway. These results indicate that FGF is a critical extracellular regulator of the cell fate switch from neurons to astrocytes in the mammalian cerebral cortex.SIGNIFICANCE STATEMENT Although the intracellular mechanisms regulating the neuron-astrocyte cell fate switch in the mammalian cerebral cortex during development have been well studied, their upstream extracellular regulators remain unknown. By using in utero electroporation, our study provides in vivo data showing that activation of FGF signaling is necessary and sufficient for changing cell fates from neurons to astrocytes. Manipulation of FGF signaling activity led to drastic changes in the numbers of neurons and astrocytes. These results indicate that FGF is a key extracellular regulator determining the numbers of neurons and astrocytes in the mammalian cerebral cortex, and is indispensable for the establishment of appropriate neural circuitry.
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9
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Kast RJ, Lanjewar AL, Smith CD, Levitt P. FOXP2 exhibits projection neuron class specific expression, but is not required for multiple aspects of cortical histogenesis. eLife 2019; 8:e42012. [PMID: 31099752 PMCID: PMC6561705 DOI: 10.7554/elife.42012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 05/14/2019] [Indexed: 12/15/2022] Open
Abstract
The expression patterns of the transcription factor FOXP2 in the developing mammalian forebrain have been described, and some studies have tested the role of this protein in the development and function of specific forebrain circuits by diverse methods and in multiple species. Clinically, mutations in FOXP2 are associated with severe developmental speech disturbances, and molecular studies indicate that impairment of Foxp2 may lead to dysregulation of genes involved in forebrain histogenesis. Here, anatomical and molecular phenotypes of the cortical neuron populations that express FOXP2 were characterized in mice. Additionally, Foxp2 was removed from the developing mouse cortex at different prenatal ages using two Cre-recombinase driver lines. Detailed molecular and circuit analyses were undertaken to identify potential disruptions of development. Surprisingly, the results demonstrate that Foxp2 function is not required for many functions that it has been proposed to regulate, and therefore plays a more limited role in cortical development than previously thought.
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Affiliation(s)
- Ryan J Kast
- Department of Pediatrics and Program in Developmental Neuroscience and NeurogeneticsThe Saban Research Institute, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Alexandra L Lanjewar
- Department of Pediatrics and Program in Developmental Neuroscience and NeurogeneticsThe Saban Research Institute, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Colton D Smith
- Department of Pediatrics and Program in Developmental Neuroscience and NeurogeneticsThe Saban Research Institute, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Pat Levitt
- Department of Pediatrics and Program in Developmental Neuroscience and NeurogeneticsThe Saban Research Institute, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
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10
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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 2018; 27:5054-5069. [PMID: 27655933 DOI: 10.1093/cercor/bhw290] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [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), 03550 Sant Joan d'Alacant, Spain
| | - Verónica Moreno-Juan
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550 Sant Joan d'Alacant, Spain
| | - Cecilia Mezzera
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550 Sant Joan d'Alacant, Spain.,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), 03550 Sant Joan d'Alacant, 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), 03550 Sant Joan d'Alacant, Spain
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11
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Furchtgott LA, Melton S, Menon V, Ramanathan S. Discovering sparse transcription factor codes for cell states and state transitions during development. eLife 2017; 6:e20488. [PMID: 28296636 PMCID: PMC5352226 DOI: 10.7554/elife.20488] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/31/2017] [Indexed: 12/16/2022] Open
Abstract
Computational analysis of gene expression to determine both the sequence of lineage choices made by multipotent cells and to identify the genes influencing these decisions is challenging. Here we discover a pattern in the expression levels of a sparse subset of genes among cell types in B- and T-cell developmental lineages that correlates with developmental topologies. We develop a statistical framework using this pattern to simultaneously infer lineage transitions and the genes that determine these relationships. We use this technique to reconstruct the early hematopoietic and intestinal developmental trees. We extend this framework to analyze single-cell RNA-seq data from early human cortical development, inferring a neocortical-hindbrain split in early progenitor cells and the key genes that could control this lineage decision. Our work allows us to simultaneously infer both the identity and lineage of cell types as well as a small set of key genes whose expression patterns reflect these relationships.
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Affiliation(s)
- Leon A Furchtgott
- FAS Center for Systems Biology, Harvard University, Cambridge, United States
- Biophysics Program, Harvard University, Cambridge, United States
| | - Samuel Melton
- FAS Center for Systems Biology, Harvard University, Cambridge, United States
- Harvard Stem Cell Institute, Harvard University, Cambridge, United States
| | - Vilas Menon
- Allen Institute for Brain Science, Seattle, United States
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Sharad Ramanathan
- FAS Center for Systems Biology, Harvard University, Cambridge, United States
- Harvard Stem Cell Institute, Harvard University, Cambridge, United States
- Allen Institute for Brain Science, Seattle, United States
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
- School of Engineering and Applied Sciences, Harvard University, Cambridge, United States
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Negwer M, Schubert D. Talking Convergence: Growing Evidence Links FOXP2 and Retinoic Acid in Shaping Speech-Related Motor Circuitry. Front Neurosci 2017; 11:19. [PMID: 28179876 PMCID: PMC5263127 DOI: 10.3389/fnins.2017.00019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 01/10/2017] [Indexed: 01/30/2023] Open
Affiliation(s)
- Moritz Negwer
- Max Planck Institute for PsycholinguisticsNijmegen, Netherlands
- Department of Cognitive Neuroscience, Radboud University Medical Center, Donders Institute for Brain, Cognition, and BehaviourNijmegen, Netherlands
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Radboud University Medical Center, Donders Institute for Brain, Cognition, and BehaviourNijmegen, Netherlands
- *Correspondence: Dirk Schubert
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