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Book ; Online: Building the gateway to consciousness - about the development of the thalamus

Scholpp, Steffen / Shimogori, Tomomi

2015

Abstract: Since years, patterning and function of some brain parts such as the cortex in the forebrain and the optical tectum or cerebellum in the midbrain/hindbrain region are under strong investigation. Interestingly the diencephalon located in the caudal ... ...

Abstract	Since years, patterning and function of some brain parts such as the cortex in the forebrain and the optical tectum or cerebellum in the midbrain/hindbrain region are under strong investigation. Interestingly the diencephalon located in the caudal forebrain has been ignored for decades. Consequently, the existing knowledge from the development of this region to function in the mature brain is very fragmented. The central part of the diencephalon is the thalamus. This central relay station plays a crucial role in distributing incoming sensory information to appropriate regions of the cortex. The thalamus develops in the posterior part of the embryonic forebrain, where early cell fate decisions are controlled by local signaling centers. In this Research Topic we discuss recent achievements elucidating thalamic neurogenesis - from neural progenitor cells to highly specialized neurons with cortical target cells in great distance. In parallel, we highlight developmental aspects leading from the early thalamic anlage to the late the organization of the complex relay station of the brain
Keywords	Neurosciences. Biological psychiatry. Neuropsychiatry ; Science (General)
Size	1 electronic resource (107 p.)
Publisher	Frontiers Media SA
Document type	Book ; Online
Note	English ; Open Access
HBZ-ID	HT020091039
ISBN	9782889194704 ; 2889194701
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article: Molecular architecture of primate specific neural circuit formation.

Shimogori, Tomomi / Onishi, Kohei / Hoshino, Takafumi / Nakanishi, Moe

Research square

2024

Abstract: The mammalian cortex is a highly evolved brain region, but we still lack a comprehensive understanding of the molecular mechanisms underlying primate-specific neural circuits formation. In this study, we employed spatial transcriptomics to assess gene ... ...

Abstract	The mammalian cortex is a highly evolved brain region, but we still lack a comprehensive understanding of the molecular mechanisms underlying primate-specific neural circuits formation. In this study, we employed spatial transcriptomics to assess gene expression dynamics in the marmoset cortex during development, focusing on key regions and time points. Spatial transcriptomics identified genes that are sexually, spatially, and temporally differentially expressed in the developing marmoset cortex. Our detailed analysis of the visual cortex unveiled dynamic changes in gene expression across layers with distinct projections and functions. Notably, we discovered numerous axon guidance molecules with spatiotemporal expression patterns unique to the developing marmoset prefrontal cortex (PFC), which control PFC neuronal circuits. Among these molecules,
Language	English
Publishing date	2024-03-22
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-4082064/v1
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Article: [Molecular mechanisms for cortical area map formation and activity dependent dendrite formation].

Shimogori, Tomomi

Seikagaku. The Journal of Japanese Biochemical Society

2015 Volume 87, Issue 1, Page(s) 133–137

MeSH term(s)	Animals ; Brain/growth & development ; Brain Mapping ; Dendrites ; Gene Expression Regulation/physiology ; Humans ; Nerve Net/growth & development ; Organogenesis/physiology
Language	Japanese
Publishing date	2015-02
Publishing country	Japan
Document type	Journal Article ; Review
ZDB-ID	282319-6
ISSN	0037-1017
ISSN	0037-1017
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Article ; Online: The transcription factor NF-YA is crucial for neural progenitor maintenance during brain development.

Yamanaka, Tomoyuki / Kurosawa, Masaru / Yoshida, Aya / Shimogori, Tomomi / Hiyama, Akiko / Maity, Sankar N / Hattori, Nobutaka / Matsui, Hideaki / Nukina, Nobuyuki

The Journal of biological chemistry

2024 Volume 300, Issue 2, Page(s) 105629

Abstract: In contrast to stage-specific transcription factors, the role of ubiquitous transcription factors in neuronal development remains a matter of scrutiny. Here, we demonstrated that a ubiquitous factor NF-Y is essential for neural progenitor maintenance ... ...

Abstract	In contrast to stage-specific transcription factors, the role of ubiquitous transcription factors in neuronal development remains a matter of scrutiny. Here, we demonstrated that a ubiquitous factor NF-Y is essential for neural progenitor maintenance during brain morphogenesis. Deletion of the NF-YA subunit in neural progenitors by using nestin-cre transgene in mice resulted in significant abnormalities in brain morphology, including a thinner cerebral cortex and loss of striatum during embryogenesis. Detailed analyses revealed a progressive decline in multiple neural progenitors in the cerebral cortex and ganglionic eminences, accompanied by induced apoptotic cell death and reduced cell proliferation. In neural progenitors, the NF-YA short isoform lacking exon 3 is dominant and co-expressed with cell cycle genes. ChIP-seq analysis from the cortex during early corticogenesis revealed preferential binding of NF-Y to the cell cycle genes, some of which were confirmed to be downregulated following NF-YA deletion. Notably, the NF-YA short isoform disappears and is replaced by its long isoform during neuronal differentiation. Forced expression of the NF-YA long isoform in neural progenitors resulted in a significant decline in neuronal count, possibly due to the suppression of cell proliferation. Collectively, we elucidated a critical role of the NF-YA short isoform in maintaining neural progenitors, possibly by regulating cell proliferation and apoptosis. Moreover, we identified an isoform switch in NF-YA within the neuronal lineage in vivo, which may explain the stage-specific role of NF-Y during neuronal development.
MeSH term(s)	Animals ; Mice ; CCAAT-Binding Factor/genetics ; CCAAT-Binding Factor/metabolism ; Cerebral Cortex/cytology ; Cerebral Cortex/growth & development ; Cerebral Cortex/metabolism ; Gene Expression Regulation ; Neurogenesis ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; Transcription Factors/metabolism
Chemical Substances	CCAAT-Binding Factor ; Protein Isoforms ; Transcription Factors ; Nfya protein, mouse
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2024.105629
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Article ; Online: Proteomics-Based Approach Identifies Altered ER Domain Properties by ALS-Linked VAPB Mutation.

Yamanaka, Tomoyuki / Nishiyama, Risa / Shimogori, Tomomi / Nukina, Nobuyuki

Scientific reports

2020 Volume 10, Issue 1, Page(s) 7610

Abstract: An ER transmembrane protein, vesicle-associated membrane protein-associated protein B (VAPB), binds to several organelle-resident membrane proteins to mediate ER-organelle tethering. Mutation in amyotrophic lateral sclerosis (ALS) induces protein ... ...

Abstract	An ER transmembrane protein, vesicle-associated membrane protein-associated protein B (VAPB), binds to several organelle-resident membrane proteins to mediate ER-organelle tethering. Mutation in amyotrophic lateral sclerosis (ALS) induces protein misfolding and aggregation, leading to ER disorganization. Gain or loss of function is suggested for VAPB mutation, however comprehensive study focusing on VAPB-ER domain has yet been performed. We here conducted proteomic characterization of the ER containing VAPB and its ALS-linked P56S mutant. For this purpose, we first optimized the proteomics of different ER domains immuno-isolated from cultured cells, and identified ER sheet- and tubule-specific proteomes. By using these as references, we found that VAPB-ER proteome had intermediate ER domain properties but its tubular property was specifically decreased by its mutation. Biochemical, immunofluorescence and proximity ligation assays suggested this was mediated by delocalization of VAPB from ER tubules. The VAPB-ER proteomics further suggested reduced incorporation of multiple proteins located in different organelles, which was confirmed by proximity ligation assay. Taken together, our proteomics-based approach indicates altered ER domain properties and impaired ER-organelle tethering by VAPB mutation.
MeSH term(s)	Amyotrophic Lateral Sclerosis/genetics ; Animals ; Cell Line ; Endoplasmic Reticulum/metabolism ; Mice ; Mutation ; Protein Domains ; Protein Interaction Mapping ; Proteomics ; Vesicular Transport Proteins/chemistry ; Vesicular Transport Proteins/genetics ; Vesicular Transport Proteins/metabolism
Chemical Substances	VAPB protein, mouse ; Vesicular Transport Proteins
Language	English
Publishing date	2020-05-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-64517-z
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Article ; Online: Anatomical Development of the Cerebellothalamic Tract in Embryonic Mice.

Dumas, Daniël B / Gornati, Simona V / Adolfs, Youri / Shimogori, Tomomi / Pasterkamp, R Jeroen / Hoebeek, Freek E

Cells

2022 Volume 11, Issue 23

Abstract: The main connection from cerebellum to cerebrum is formed by cerebellar nuclei axons that synapse in the thalamus. Apart from its role in coordinating sensorimotor integration in the adult brain, the cerebello-thalamic tract (CbT) has also been ... ...

Abstract	The main connection from cerebellum to cerebrum is formed by cerebellar nuclei axons that synapse in the thalamus. Apart from its role in coordinating sensorimotor integration in the adult brain, the cerebello-thalamic tract (CbT) has also been implicated in developmental disorders, such as autism spectrum disorders. Although the development of the cerebellum, thalamus and cerebral cortex have been studied, there is no detailed description of the ontogeny of the mammalian CbT. Here we investigated the development of the CbT at embryonic stages using transgenic
Language	English
Publishing date	2022-11-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells11233800
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Article ; Online: Remodeling of the postsynaptic proteome in male mice and marmosets during synapse development.

Kaizuka, Takeshi / Suzuki, Takehiro / Kishi, Noriyuki / Tamada, Kota / Kilimann, Manfred W / Ueyama, Takehiko / Watanabe, Masahiko / Shimogori, Tomomi / Okano, Hideyuki / Dohmae, Naoshi / Takumi, Toru

Nature communications

2024 Volume 15, Issue 1, Page(s) 2496

Abstract: Postsynaptic proteins play crucial roles in synaptic function and plasticity. During brain development, alterations in synaptic number, shape, and stability occur, known as synapse maturation. However, the postsynaptic protein composition changes during ... ...

Abstract	Postsynaptic proteins play crucial roles in synaptic function and plasticity. During brain development, alterations in synaptic number, shape, and stability occur, known as synapse maturation. However, the postsynaptic protein composition changes during development are not fully understood. Here, we show the trajectory of the postsynaptic proteome in developing male mice and common marmosets. Proteomic analysis of mice at 2, 3, 6, and 12 weeks of age shows that proteins involved in synaptogenesis are differentially expressed during this period. Analysis of published transcriptome datasets shows that the changes in postsynaptic protein composition in the mouse brain after 2 weeks of age correlate with gene expression changes. Proteomic analysis of marmosets at 0, 2, 3, 6, and 24 months of age show that the changes in the marmoset brain can be categorized into two parts: the first 2 months and after that. The changes observed in the first 2 months are similar to those in the mouse brain between 2 and 12 weeks of age. The changes observed in marmoset after 2 months old include differential expression of synaptogenesis-related molecules, which hardly overlap with that in mice. Our results provide a comprehensive proteomic resource that underlies developmental synapse maturation in rodents and primates.
MeSH term(s)	Animals ; Mice ; Male ; Callithrix ; Proteome/metabolism ; Proteomics ; Synapses/metabolism ; Biological Phenomena
Chemical Substances	Proteome
Language	English
Publishing date	2024-03-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-46529-9
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Article ; Online: Spatially restricted long-term transgene expression in the developing skin used for studying the interaction of epidermal development and sensory innervation.

Chan, Carmen / Kamiguchi, Hiroyuki / Shimogori, Tomomi

Development, growth & differentiation

2019 Volume 61, Issue 4, Page(s) 276–282

Abstract: Skin development is tightly temporally coordinated with its sensory innervation, which consists of the peripheral branches of the dorsal root ganglion (DRG) axons. Various studies suggest that the skin produces a long-range attractant for the sensory ... ...

Abstract	Skin development is tightly temporally coordinated with its sensory innervation, which consists of the peripheral branches of the dorsal root ganglion (DRG) axons. Various studies suggest that the skin produces a long-range attractant for the sensory axons. However, the exact identity of the guidance cue(s) remains unclear. To reveal the detailed molecular mechanism that controls DRG axon guidance and targeting, manipulation of specific skin layers at specific time points are required. To test a variety of attractants that can be expressed in specific skin layers at specific timepoints, we combined in utero electroporation with the Tol2 transposon system to induce long-term transgene expression in the developing mouse skin, including in the highly proliferative epidermal stem cells (basal layer) and their descendants (spinous and granular layer cells). The plasmid solution was injected as close to the hindpaw plantar surface as possible. Immediately, electric pulses were passed through the embryo to transduce the plasmid DNA into hindpaw skin cells. Balancing outcome measurements including: embryo survival, transfection efficiency, and the efficiency of transgene integration into host cells, we found that IUE was best performed on E13.5, and using an electroporation voltage of 34V. After immunostaining embryonic and early postnatal skin tissue sections for keratinocyte and sensory axon markers, we observe the growth of axons into skin epidermal layers including areas expressing EGFP. Therefore, this method is useful for studying the interaction between axon growth and epidermal cell division/differentiation.
MeSH term(s)	Animals ; Axons/metabolism ; Epidermal Cells/cytology ; Epidermal Cells/metabolism ; Epidermis/embryology ; Epidermis/growth & development ; Epidermis/innervation ; Epidermis/metabolism ; Female ; Mice ; Mice, Inbred C57BL ; Neurons/cytology ; Neurons/metabolism ; Pregnancy ; Skin/embryology ; Skin/growth & development ; Skin/innervation ; Skin/metabolism ; Transgenes/genetics
Language	English
Publishing date	2019-04-09
Publishing country	Japan
Document type	Journal Article
ZDB-ID	280433-5
ISSN	1440-169X ; 0012-1592
ISSN (online)	1440-169X
ISSN	0012-1592
DOI	10.1111/dgd.12603
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Article ; Online: Generation and characterization of cerebellar granule neurons specific knockout mice of Golli-MBP.

Miyazaki, Haruko / Nishioka, Saki / Yamanaka, Tomoyuki / Abe, Manabu / Imamura, Yukio / Miyasaka, Tomohiro / Kakuda, Nobuto / Oohashi, Toshitaka / Shimogori, Tomomi / Yamakawa, Kazuhiro / Ikawa, Masahito / Nukina, Nobuyuki

Transgenic research

2024

Abstract: Golli-myelin basic proteins, encoded by the myelin basic protein gene, are widely expressed in neurons and oligodendrocytes in the central nervous system. Further, prior research has shown that Golli-myelin basic protein is necessary for myelination and ... ...

Abstract	Golli-myelin basic proteins, encoded by the myelin basic protein gene, are widely expressed in neurons and oligodendrocytes in the central nervous system. Further, prior research has shown that Golli-myelin basic protein is necessary for myelination and neuronal maturation during central nervous system development. In this study, we established Golli-myelin basic protein-floxed mice to elucidate the cell-type-specific effects of Golli-myelin basic protein knockout through the generation of conditional knockout mice (Golli-myelin basic proteins
Language	English
Publishing date	2024-04-29
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	31620-9
ISSN	1573-9368 ; 0962-8819
ISSN (online)	1573-9368
ISSN	0962-8819
DOI	10.1007/s11248-024-00382-0
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Article ; Online: Molecular cell identities in the mediodorsal thalamus of infant mice and marmoset.

Onishi, Kohei / Kikuchi, Satomi S / Abe, Takaya / Tokuhara, Tomoko / Shimogori, Tomomi

The Journal of comparative neurology

2021 Volume 530, Issue 7, Page(s) 963–977

Abstract: The mediodorsal thalamus (MD) is a higher-order nucleus located within the central thalamus in many mammalian species. Emerging evidence from MD lesions and tracer injections suggests that the MD is reciprocally connected to the prefrontal cortex (PFC) ... ...

Abstract	The mediodorsal thalamus (MD) is a higher-order nucleus located within the central thalamus in many mammalian species. Emerging evidence from MD lesions and tracer injections suggests that the MD is reciprocally connected to the prefrontal cortex (PFC) and plays an essential role in specific cognitive processes and tasks. MD subdivisions (medial, central, and lateral) are poorly segregated at the molecular level in rodents, leading to a lack of MD subdivision-specific Cre driver mice. Moreover, this lack of molecular identifiers hinders MD subdivision- and cell-type-specific circuit formation and function analysis. Therefore, using publicly available databases, we explored molecules separately expressed in MD subdivisions. In addition to MD subdivision markers, we identified several genes expressed in a subdivision-specific combination and classified them. Furthermore, after developing medial MD (MDm) or central MD (MDc) region-specific Cre mouse lines, we identified diverse region- and layer-specific PFC projection patterns. Comparison between classified MD marker genes in mice and common marmosets, a nonhuman primate model, revealed diverging gene expression patterns. These results highlight the species-specific organization of cell types and their projections in the MD thalamus.
MeSH term(s)	Animals ; Callithrix ; Humans ; Mammals ; Mice ; Neural Pathways ; Prefrontal Cortex ; Thalamus
Language	English
Publishing date	2021-07-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	3086-7
ISSN	1096-9861 ; 0021-9967 ; 0092-7317
ISSN (online)	1096-9861
ISSN	0021-9967 ; 0092-7317
DOI	10.1002/cne.25203
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