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Taylor SR, Kobayashi M, Vilella A, Tiwari D, Zolboot N, Du JX, Spencer KR, Hartzell A, Girgiss C, Abaci YT, Shao Y, De Sanctis C, Bellenchi GC, Darnell RB, Gross C, Zoli M, Berg DK, Lippi G. MicroRNA-218 instructs proper assembly of hippocampal networks. eLife 2023; 12:e82729. [PMID: 37862092 PMCID: PMC10637775 DOI: 10.7554/elife.82729] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/10/2023] [Indexed: 10/21/2023] Open
Abstract
The assembly of the mammalian brain is orchestrated by temporally coordinated waves of gene expression. Post-transcriptional regulation by microRNAs (miRNAs) is a key aspect of this program. Indeed, deletion of neuron-enriched miRNAs induces strong developmental phenotypes, and miRNA levels are altered in patients with neurodevelopmental disorders. However, the mechanisms used by miRNAs to instruct brain development remain largely unexplored. Here, we identified miR-218 as a critical regulator of hippocampal assembly. MiR-218 is highly expressed in the hippocampus and enriched in both excitatory principal neurons (PNs) and GABAergic inhibitory interneurons (INs). Early life inhibition of miR-218 results in an adult brain with a predisposition to seizures. Changes in gene expression in the absence of miR-218 suggest that network assembly is impaired. Indeed, we find that miR-218 inhibition results in the disruption of early depolarizing GABAergic signaling, structural defects in dendritic spines, and altered intrinsic membrane excitability. Conditional knockout of Mir218-2 in INs, but not PNs, is sufficient to recapitulate long-term instability. Finally, de-repressing Kif21b and Syt13, two miR-218 targets, phenocopies the effects on early synchronous network activity induced by miR-218 inhibition. Taken together, the data suggest that miR-218 orchestrates formative events in PNs and INs to produce stable networks.
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Affiliation(s)
- Seth R Taylor
- Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Mariko Kobayashi
- Laboratory of Molecular Neuro-oncology, Howard Hughes Medical Institute, Rockefeller UniversityNew YorkUnited States
| | - Antonietta Vilella
- Department of Biomedical, Metabolic and Neural Sciences; Center for Neuroscience and Neurotechnology (CfNN), University of Modena and Reggio EmiliaModenaItaly
| | - Durgesh Tiwari
- Division of Neurology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of MedicineCincinnatiUnited States
- Department of Pediatrics, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Norjin Zolboot
- Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Jessica X Du
- Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Kathryn R Spencer
- Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Andrea Hartzell
- Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Carol Girgiss
- Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Yusuf T Abaci
- Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Yufeng Shao
- Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | | | - Gian Carlo Bellenchi
- Institute of Genetics and Biophysics A Buzzati-TraversoNaplesItaly
- IRCCS Fondazione Santa LuciaRomeItaly
| | - Robert B Darnell
- Laboratory of Molecular Neuro-oncology, Howard Hughes Medical Institute, Rockefeller UniversityNew YorkUnited States
| | - Christina Gross
- Division of Neurology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of MedicineCincinnatiUnited States
- Department of Pediatrics, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Michele Zoli
- Department of Biomedical, Metabolic and Neural Sciences; Center for Neuroscience and Neurotechnology (CfNN), University of Modena and Reggio EmiliaModenaItaly
| | - Darwin K Berg
- Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Giordano Lippi
- Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
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Zolboot N, Xiao Y, Du JX, Ghanem MM, Choi SY, Junn MJ, Zampa F, Huang Z, MacRae IJ, Lippi G. MicroRNAs are necessary for the emergence of Purkinje cell identity. bioRxiv 2023:2023.09.28.560023. [PMID: 37808721 PMCID: PMC10557743 DOI: 10.1101/2023.09.28.560023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Brain computations are dictated by the unique morphology and connectivity of neuronal subtypes, features established by closely timed developmental events. MicroRNAs (miRNAs) are critical for brain development, but current technologies lack the spatiotemporal resolution to determine how miRNAs instruct the steps leading to subtype identity. Here, we developed new tools to tackle this major gap. Fast and reversible miRNA loss-of-function revealed that miRNAs are necessary for cerebellar Purkinje cell (PC) differentiation, which previously appeared miRNA-independent, and resolved distinct miRNA critical windows in PC dendritogenesis and climbing fiber synaptogenesis, key determinants of PC identity. To identify underlying mechanisms, we generated a mouse model, which enables precise mapping of miRNAs and their targets in rare cell types. With PC-specific maps, we found that the PC-enriched miR-206 drives exuberant dendritogenesis and modulates synaptogenesis. Our results showcase vastly improved approaches for dissecting miRNA function and reveal that many critical miRNA mechanisms remain largely unexplored. Highlights Fast miRNA loss-of-function with T6B impairs postnatal Purkinje cell developmentReversible T6B reveals critical miRNA windows for dendritogenesis and synaptogenesisConditional Spy3-Ago2 mouse line enables miRNA-target network mapping in rare cellsPurkinje cell-enriched miR-206 regulates its unique dendritic and synaptic morphology.
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Zolboot N, Du JX, Zampa F, Lippi G. MicroRNAs Instruct and Maintain Cell Type Diversity in the Nervous System. Front Mol Neurosci 2021; 14:646072. [PMID: 33994943 PMCID: PMC8116551 DOI: 10.3389/fnmol.2021.646072] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/30/2021] [Indexed: 12/12/2022] Open
Abstract
Characterizing the diverse cell types that make up the nervous system is essential for understanding how the nervous system is structured and ultimately how it functions. The astonishing range of cellular diversity found in the nervous system emerges from a small pool of neural progenitor cells. These progenitors and their neuronal progeny proceed through sequential gene expression programs to produce different cell lineages and acquire distinct cell fates. These gene expression programs must be tightly regulated in order for the cells to achieve and maintain the proper differentiated state, remain functional throughout life, and avoid cell death. Disruption of developmental programs is associated with a wide range of abnormalities in brain structure and function, further indicating that elucidating their contribution to cellular diversity will be key to understanding brain health. A growing body of evidence suggests that tight regulation of developmental genes requires post-transcriptional regulation of the transcriptome by microRNAs (miRNAs). miRNAs are small non-coding RNAs that function by binding to mRNA targets containing complementary sequences and repressing their translation into protein, thereby providing a layer of precise spatial and temporal control over gene expression. Moreover, the expression profiles and targets of miRNAs show great specificity for distinct cell types, brain regions and developmental stages, suggesting that they are an important parameter of cell type identity. Here, we provide an overview of miRNAs that are critically involved in establishing neural cell identities, focusing on how miRNA-mediated regulation of gene expression modulates neural progenitor expansion, cell fate determination, cell migration, neuronal and glial subtype specification, and finally cell maintenance and survival.
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Affiliation(s)
- Norjin Zolboot
- The Scripps Research Institute, La Jolla, CA, United States
| | - Jessica X Du
- The Scripps Research Institute, La Jolla, CA, United States.,Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
| | - Federico Zampa
- The Scripps Research Institute, La Jolla, CA, United States
| | - Giordano Lippi
- The Scripps Research Institute, La Jolla, CA, United States
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Zampa F, Hartzell AL, Zolboot N, Lippi G. Non-coding RNAs: the gatekeepers of neural network activity. Curr Opin Neurobiol 2019; 57:54-61. [PMID: 30743177 DOI: 10.1016/j.conb.2019.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
Non-coding RNAs have emerged as potent regulators of numerous cellular processes. In neurons and circuits, these molecules serve especially critical functions that ensure neural activity is maintained within appropriate physiological parameters. Their targets include synaptic proteins, ion channels, neurotransmitter receptors, and components of essential signaling cascades. Here, we discuss how several species of non-coding RNAs (ncRNAs) regulate intrinsic excitability and synaptic transmission, both during development and in mature circuits. Furthermore, we present the relationships between aberrant ncRNA expression and psychiatric disorders. The research presented here demonstrates how ncRNAs can be useful tools for elucidating fundamental neurobiology mechanisms and identifying the key molecular players.
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Affiliation(s)
- Federico Zampa
- Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Andrea L Hartzell
- Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Norjin Zolboot
- Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Giordano Lippi
- Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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Oshima T, Niwa Y, Kuwata K, Srivastava A, Hyoda T, Tsuchiya Y, Kumagai M, Tsuyuguchi M, Tamaru T, Sugiyama A, Ono N, Zolboot N, Aikawa Y, Oishi S, Nonami A, Arai F, Hagihara S, Yamaguchi J, Tama F, Kunisaki Y, Yagita K, Ikeda M, Kinoshita T, Kay SA, Itami K, Hirota T. Cell-based screen identifies a new potent and highly selective CK2 inhibitor for modulation of circadian rhythms and cancer cell growth. Sci Adv 2019; 5:eaau9060. [PMID: 30746467 PMCID: PMC6357737 DOI: 10.1126/sciadv.aau9060] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 12/11/2018] [Indexed: 05/08/2023]
Abstract
Compounds targeting the circadian clock have been identified as potential treatments for clock-related diseases, including cancer. Our cell-based phenotypic screen revealed uncharacterized clock-modulating compounds. Through affinity-based target deconvolution, we identified GO289, which strongly lengthened circadian period, as a potent and selective inhibitor of CK2. Phosphoproteomics identified multiple phosphorylation sites inhibited by GO289 on clock proteins, including PER2 S693. Furthermore, GO289 exhibited cell type-dependent inhibition of cancer cell growth that correlated with cellular clock function. The x-ray crystal structure of the CK2α-GO289 complex revealed critical interactions between GO289 and CK2-specific residues and no direct interaction of GO289 with the hinge region that is highly conserved among kinases. The discovery of GO289 provides a direct link between the circadian clock and cancer regulation and reveals unique design principles underlying kinase selectivity.
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Affiliation(s)
- Tsuyoshi Oshima
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan
| | - Yoshimi Niwa
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Ashutosh Srivastava
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Tomoko Hyoda
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yoshiki Tsuchiya
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Megumi Kumagai
- Department of Physiology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan
| | - Masato Tsuyuguchi
- Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan
| | - Teruya Tamaru
- Department of Physiology and Advanced Research Center for Medical Science, Toho University School of Medicine, Tokyo 143-8540, Japan
| | - Akiko Sugiyama
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Natsuko Ono
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Norjin Zolboot
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Yoshiki Aikawa
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Shunsuke Oishi
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Atsushi Nonami
- Center for Advanced Medical Innovation, Kyushu University, Fukuoka 812-8582, Japan
| | - Fumio Arai
- Department of Stem Cell Biology and Medicine/Cancer Stem Cell Research, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Shinya Hagihara
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan
- PRESTO, JST, Nagoya 464-8601, Japan
| | | | - Florence Tama
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan, and RIKEN Center for Computational Science, Kobe 650-0047, Japan
| | - Yuya Kunisaki
- Department of Stem Cell Biology and Medicine/Cancer Stem Cell Research, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Kazuhiro Yagita
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Masaaki Ikeda
- Department of Physiology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan
| | - Takayoshi Kinoshita
- Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan
| | - Steve A. Kay
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan
- ERATO Itami Molecular Nanocarbon Project, JST, Nagoya 464-8601, Japan
- Corresponding author. (T.H.); (K.I.)
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- PRESTO, JST, Nagoya 464-8601, Japan
- Corresponding author. (T.H.); (K.I.)
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